AF

momapy.sbgn.af

SBGN Activity Flow (AF) subpackage facade.

Layout-model mapping catalogue

This section lists, for each model-element category in SBGN-AF, the shape of the corresponding key in LayoutModelMapping. See LayoutModelMapping for the general concepts (singleton keys, frozenset keys, representatives).

Singleton keys (one layout element represents the model element):

Model element	Layout element used as the key
Compartment	CompartmentLayout
BiologicalActivity	BiologicalActivityLayout
Phenotype	PhenotypeLayout
UnitOfInformation and subclasses (e.g. MacromoleculeUnitOfInformation, NucleicAcidFeatureUnitOfInformation, SimpleChemicalUnitOfInformation, ComplexUnitOfInformation, UnspecifiedEntityUnitOfInformation, PerturbationUnitOfInformation)	The corresponding *UnitOfInformationLayout (e.g. MacromoleculeUnitOfInformationLayout, PerturbationUnitOfInformationLayout)
Submap	SubmapLayout
LogicalOperatorInput	LogicArcLayout
TagReference, TerminalReference	EquivalenceArcLayout

Frozenset keys (a cluster of layout elements jointly represents the model element; the representative is the layout that stands for the cluster on its own and must be passed as representative= when calling add_mapping):

Model element	Members of the frozenset key	Representative
LogicalOperator and subclasses (e.g. AndOperator, OrOperator, NotOperator, DelayOperator)	The operator *Layout (e.g. AndOperatorLayout, DelayOperatorLayout) + every LogicArcLayout input + every target layout those logic arcs point to	The operator *Layout
Influence and subclasses (e.g. UnknownInfluence, PositiveInfluence, NegativeInfluence, NecessaryStimulation)	The influence arc layout (e.g. UnknownInfluenceLayout, PositiveInfluenceLayout, NecessaryStimulationLayout) + all layouts in the source cluster (resolved via the source's own frozenset key if it has one, else the source layout itself) + all layouts in the target cluster (resolved the same way)	The influence arc layout
Tag or Terminal carrying TagReference or TerminalReference arcs	The TagLayout or TerminalLayout + every EquivalenceArcLayout reference arc + every referenced activity layout	The TagLayout or TerminalLayout

Standalone Tag and Terminal instances (with no reference arcs) use a singleton key: TagLayout or TerminalLayout.

Modules:

Name	Description
layout	Layout classes for SBGN Activity Flow (AF) maps.
map	Map classes for SBGN Activity Flow (AF) maps.
model	Model classes for SBGN Activity Flow (AF) maps.

Classes:

Name	Description
Activity	Abstract base class for activities.
AndOperator	AND operator.
AndOperatorLayout	AND operator layout.
BiologicalActivity	Biological activity.
BiologicalActivityLayout	Biological activity layout.
Compartment	Compartment.
CompartmentLayout	Compartment layout.
ComplexUnitOfInformation	Complex unit of information.
ComplexUnitOfInformationLayout	Complex unit of information layout.
DelayOperator	Delay operator.
DelayOperatorLayout	Delay operator layout.
EquivalenceArcLayout	Equivalence arc layout.
Influence	Abstract base class for influences.
LogicArcLayout	Logic arc layout.
LogicalOperator	Abstract base class for logical operators.
LogicalOperatorInput	Logical operator input.
MacromoleculeUnitOfInformation	Macromolecule unit of information.
MacromoleculeUnitOfInformationLayout	Macromolecule unit of information layout.
NecessaryStimulation	Necessary stimulation.
NecessaryStimulationLayout	Necessary stimulation layout.
NegativeInfluence	Negative influence.
NegativeInfluenceLayout	Negative influence layout.
NotOperator	NOT operator.
NotOperatorLayout	NOT operator layout.
NucleicAcidFeatureUnitOfInformation	Nucleic acid feature unit of information.
NucleicAcidFeatureUnitOfInformationLayout	Nucleic acid feature unit of information layout.
OrOperator	OR operator.
OrOperatorLayout	OR operator layout.
PerturbationUnitOfInformation	Perturbation unit of information.
PerturbationUnitOfInformationLayout	Perturbation unit of information layout.
Phenotype	Phenotype.
PhenotypeLayout	Phenotype layout.
PositiveInfluence	Positive influence.
PositiveInfluenceLayout	Positive influence layout.
SBGNAFLayout	SBGN AF layout.
SBGNAFMap	Class for SBGN-AF maps.
SBGNAFModel	SBGN AF model.
SimpleChemicalUnitOfInformation	Simple chemical unit of information.
SimpleChemicalUnitOfInformationLayout	Simple chemical unit of information layout.
Submap	Submap.
SubmapLayout	Submap layout.
Tag	Tag.
TagLayout	Tag layout.
TagReference	Tag reference.
Terminal	Terminal.
TerminalLayout	Terminal layout.
TerminalReference	Terminal reference.
UnitOfInformation	Abstract base class for units of information.
UnitOfInformationLayout	Unit of information layout.
UnknownInfluence	Unknown influence.
UnknownInfluenceLayout	Unknown influence layout.
UnspecifiedEntityUnitOfInformation	Unspecified entity unit of information.
UnspecifiedEntityUnitOfInformationLayout	Unspecified entity unit of information layout.

Activity dataclass

Activity(*, id_: str = make_uuid4_as_str(), label: str | None = None, compartment: Compartment | None = None)

Bases: SBGNModelElement

Abstract base class for activities.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'affcf585-ab9d-4578-a1a5-f8838e3135d7'
label	str | None	The label of the activity.	None
compartment	Compartment | None	The compartment containing this activity.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

AndOperator dataclass

AndOperator(*, id_: str = make_uuid4_as_str(), inputs: frozenset[LogicalOperatorInput] = frozenset())

Bases: LogicalOperator

AND operator.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'70608251-0384-49d5-a6e4-2015dbd5c475'
inputs	frozenset[LogicalOperatorInput]	Input connections to the logical operator.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

AndOperatorLayout dataclass

AndOperatorLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 30.0, text: str = 'AND', font_family: str = DEFAULT_FONT_FAMILY, font_fill: Color | NoneValueType = black, font_stroke: Color | NoneValueType = NoneValue, font_style: FontStyle = NORMAL, font_weight: FontWeight | float = NORMAL, orientation: Orientation = HORIZONTAL, left_to_right: bool = True, left_connector_length: float = 10.0, right_connector_length: float = 10.0, left_connector_stroke: NoneValueType | Color | None = None, left_connector_stroke_width: float | None = None, left_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, left_connector_stroke_dashoffset: float | None = None, left_connector_fill: NoneValueType | Color | None = None, left_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, left_connector_filter: NoneValueType | Filter | None = None, right_connector_stroke: NoneValueType | Color | None = None, right_connector_stroke_width: float | None = None, right_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, right_connector_stroke_dashoffset: float | None = None, right_connector_fill: NoneValueType | Color | None = None, right_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, right_connector_filter: NoneValueType | Filter | None = None)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

AND operator layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'a772eaa9-a46b-4be6-80ab-b7997f26c2cb'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	30.0
text	str	The text displayed inside the node.	'AND'
font_family	str	Font family for the text.	'DejaVu Sans'
font_fill	Color | NoneValueType	Fill color for the text.	Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType	Stroke color for the text outline.	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
font_style	FontStyle	Font style (normal, italic, etc.).	<FontStyle.NORMAL: 0>
font_weight	FontWeight | float	Font weight (normal, bold, etc.).	<FontWeight.NORMAL: 0>
orientation	Orientation	Orientation of connectors (HORIZONTAL or VERTICAL).	<Orientation.HORIZONTAL: 1>
left_to_right	bool	Whether connectors flow left to right.	True
left_connector_length	float	Length of the left connector.	10.0
right_connector_length	float	Length of the right connector.	10.0
left_connector_stroke	NoneValueType | Color | None	Stroke color for the left connector line.	None
left_connector_stroke_width	float | None	Stroke width for the left connector line.	None
left_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the left connector line.	None
left_connector_stroke_dashoffset	float | None	Dash offset for the left connector line.	None
left_connector_fill	NoneValueType | Color | None	Fill color for the left connector.	None
left_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the left connector.	None
left_connector_filter	NoneValueType | Filter | None	Filter applied to the left connector.	None
right_connector_stroke	NoneValueType | Color | None	Stroke color for the right connector line.	None
right_connector_stroke_width	float | None	Stroke width for the right connector line.	None
right_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the right connector line.	None
right_connector_stroke_dashoffset	float | None	Dash offset for the right connector line.	None
right_connector_fill	NoneValueType | Color | None	Fill color for the right connector.	None
right_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the right connector.	None
right_connector_filter	NoneValueType | Filter | None	Filter applied to the right connector.	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Get the east (right) anchor point.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
left_connector_base	Get the base point of the left connector.
left_connector_tip	Get the tip point of the left connector.
north	Get the north (top) anchor point.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
right_connector_base	Get the base point of the right connector.
right_connector_tip	Get the tip point of the right connector.
size	Return the size of the node.
south	Get the south (bottom) anchor point.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Get the west (left) anchor point.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Get the east (right) anchor point.

Returns:

Type	Description
Point	Point on the east side of the element.

Source code in src/momapy/sbgn/elements.py

def east(self) -> Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x + self.width / 2, self.y)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

left_connector_base

left_connector_base() -> Point

Get the base point of the left connector.

Returns:

Type	Description
Point	Point where the left connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def left_connector_base(self) -> Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2)
    else:
        return Point(self.x - self.width / 2, self.y)

left_connector_tip

left_connector_tip() -> Point

Get the tip point of the left connector.

Returns:

Type	Description
Point	Point at the end of the left connector line.

Source code in src/momapy/sbgn/elements.py

def left_connector_tip(self) -> Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

north

north() -> Point

Get the north (top) anchor point.

Returns:

Type	Description
Point	Point on the north side of the element.

Source code in src/momapy/sbgn/elements.py

def north(self) -> Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x, self.y - self.height / 2)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

right_connector_base

right_connector_base() -> Point

Get the base point of the right connector.

Returns:

Type	Description
Point	Point where the right connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def right_connector_base(self) -> Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2)
    else:
        return Point(self.x + self.width / 2, self.y)

right_connector_tip

right_connector_tip() -> Point

Get the tip point of the right connector.

Returns:

Type	Description
Point	Point at the end of the right connector line.

Source code in src/momapy/sbgn/elements.py

def right_connector_tip(self) -> Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Get the south (bottom) anchor point.

Returns:

Type	Description
Point	Point on the south side of the element.

Source code in src/momapy/sbgn/elements.py

def south(self) -> Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x, self.y + self.height / 2)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Get the west (left) anchor point.

Returns:

Type	Description
Point	Point on the west side of the element.

Source code in src/momapy/sbgn/elements.py

def west(self) -> Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x - self.width / 2, self.y)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

BiologicalActivity dataclass

BiologicalActivity(*, id_: str = make_uuid4_as_str(), label: str | None = None, compartment: Compartment | None = None, units_of_information: frozenset[UnitOfInformation] = frozenset())

Bases: Activity

Biological activity.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6f5511ab-659e-4d87-b5ff-c2fe52a86aa9'
label	str | None	The label of the activity.	None
compartment	Compartment | None	The compartment containing this activity.	None
units_of_information	frozenset[UnitOfInformation]	Units of information for the activity.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

BiologicalActivityLayout dataclass

BiologicalActivityLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 60.0)

Bases: _SimpleMixin, SBGNNode

Biological activity layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'851fe1bf-0af6-47bf-a347-55d5391cc243'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	60.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

Compartment dataclass

Compartment(*, id_: str = make_uuid4_as_str(), label: str | None = None, units_of_information: frozenset[UnitOfInformation] = frozenset())

Bases: SBGNModelElement

Compartment.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'17098f40-ea41-4882-b09b-2acb9bd990d7'
label	str | None	The label of the compartment.	None
units_of_information	frozenset[UnitOfInformation]	The units of information of the compartment.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

CompartmentLayout dataclass

CompartmentLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 80.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float = 3.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 80.0, rounded_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Compartment layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'5d5294d1-9a67-4fb6-b5f6-0918f22fa61f'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	80.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float	The stroke width of the node	3.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	80.0
rounded_corners	float	The radius of the rounded corners.	5.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

ComplexUnitOfInformation dataclass

ComplexUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Complex unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'165f0bad-01c0-4b50-bec1-0bd0fe20eac6'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

ComplexUnitOfInformationLayout dataclass

ComplexUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0, cut_corners: float = 3.0)

Bases: _SimpleMixin, SBGNNode

Complex unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'23d8ea7c-a46a-4be1-9449-13533196d47c'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0
cut_corners	float	The size of the cut corners.	3.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

DelayOperator dataclass

DelayOperator(*, id_: str = make_uuid4_as_str(), inputs: frozenset[LogicalOperatorInput] = frozenset())

Bases: LogicalOperator

Delay operator.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c4611012-9ad7-4822-b57e-75dffda9a232'
inputs	frozenset[LogicalOperatorInput]	Input connections to the logical operator.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

DelayOperatorLayout dataclass

DelayOperatorLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 30.0, text: str = 'τ', font_family: str = DEFAULT_FONT_FAMILY, font_fill: Color | NoneValueType = black, font_stroke: Color | NoneValueType = NoneValue, font_style: FontStyle = NORMAL, font_weight: FontWeight | float = NORMAL, orientation: Orientation = HORIZONTAL, left_to_right: bool = True, left_connector_length: float = 10.0, right_connector_length: float = 10.0, left_connector_stroke: NoneValueType | Color | None = None, left_connector_stroke_width: float | None = None, left_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, left_connector_stroke_dashoffset: float | None = None, left_connector_fill: NoneValueType | Color | None = None, left_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, left_connector_filter: NoneValueType | Filter | None = None, right_connector_stroke: NoneValueType | Color | None = None, right_connector_stroke_width: float | None = None, right_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, right_connector_stroke_dashoffset: float | None = None, right_connector_fill: NoneValueType | Color | None = None, right_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, right_connector_filter: NoneValueType | Filter | None = None)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

Delay operator layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c8ccad63-098c-41e3-96d7-e85a87d7195d'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	30.0
text	str	The text displayed inside the node.	'τ'
font_family	str	Font family for the text.	'DejaVu Sans'
font_fill	Color | NoneValueType	Fill color for the text.	Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType	Stroke color for the text outline.	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
font_style	FontStyle	Font style (normal, italic, etc.).	<FontStyle.NORMAL: 0>
font_weight	FontWeight | float	Font weight (normal, bold, etc.).	<FontWeight.NORMAL: 0>
orientation	Orientation	Orientation of connectors (HORIZONTAL or VERTICAL).	<Orientation.HORIZONTAL: 1>
left_to_right	bool	Whether connectors flow left to right.	True
left_connector_length	float	Length of the left connector.	10.0
right_connector_length	float	Length of the right connector.	10.0
left_connector_stroke	NoneValueType | Color | None	Stroke color for the left connector line.	None
left_connector_stroke_width	float | None	Stroke width for the left connector line.	None
left_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the left connector line.	None
left_connector_stroke_dashoffset	float | None	Dash offset for the left connector line.	None
left_connector_fill	NoneValueType | Color | None	Fill color for the left connector.	None
left_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the left connector.	None
left_connector_filter	NoneValueType | Filter | None	Filter applied to the left connector.	None
right_connector_stroke	NoneValueType | Color | None	Stroke color for the right connector line.	None
right_connector_stroke_width	float | None	Stroke width for the right connector line.	None
right_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the right connector line.	None
right_connector_stroke_dashoffset	float | None	Dash offset for the right connector line.	None
right_connector_fill	NoneValueType | Color | None	Fill color for the right connector.	None
right_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the right connector.	None
right_connector_filter	NoneValueType | Filter | None	Filter applied to the right connector.	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Get the east (right) anchor point.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
left_connector_base	Get the base point of the left connector.
left_connector_tip	Get the tip point of the left connector.
north	Get the north (top) anchor point.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
right_connector_base	Get the base point of the right connector.
right_connector_tip	Get the tip point of the right connector.
size	Return the size of the node.
south	Get the south (bottom) anchor point.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Get the west (left) anchor point.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Get the east (right) anchor point.

Returns:

Type	Description
Point	Point on the east side of the element.

Source code in src/momapy/sbgn/elements.py

def east(self) -> Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x + self.width / 2, self.y)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

left_connector_base

left_connector_base() -> Point

Get the base point of the left connector.

Returns:

Type	Description
Point	Point where the left connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def left_connector_base(self) -> Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2)
    else:
        return Point(self.x - self.width / 2, self.y)

left_connector_tip

left_connector_tip() -> Point

Get the tip point of the left connector.

Returns:

Type	Description
Point	Point at the end of the left connector line.

Source code in src/momapy/sbgn/elements.py

def left_connector_tip(self) -> Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

north

north() -> Point

Get the north (top) anchor point.

Returns:

Type	Description
Point	Point on the north side of the element.

Source code in src/momapy/sbgn/elements.py

def north(self) -> Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x, self.y - self.height / 2)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

right_connector_base

right_connector_base() -> Point

Get the base point of the right connector.

Returns:

Type	Description
Point	Point where the right connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def right_connector_base(self) -> Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2)
    else:
        return Point(self.x + self.width / 2, self.y)

right_connector_tip

right_connector_tip() -> Point

Get the tip point of the right connector.

Returns:

Type	Description
Point	Point at the end of the right connector line.

Source code in src/momapy/sbgn/elements.py

def right_connector_tip(self) -> Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Get the south (bottom) anchor point.

Returns:

Type	Description
Point	Point on the south side of the element.

Source code in src/momapy/sbgn/elements.py

def south(self) -> Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x, self.y + self.height / 2)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Get the west (left) anchor point.

Returns:

Type	Description
Point	Point on the west side of the element.

Source code in src/momapy/sbgn/elements.py

def west(self) -> Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x - self.width / 2, self.y)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

EquivalenceArcLayout dataclass

EquivalenceArcLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None)

Bases: SBGNSingleHeadedArc

Equivalence arc layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3685e9f1-c551-4104-bfa3-0bdb082dec32'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

Influence dataclass

Influence(*, id_: str = make_uuid4_as_str(), source: BiologicalActivity | LogicalOperator, target: Activity)

Bases: SBGNModelElement

Abstract base class for influences.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ae492ebb-e29c-4d14-b414-d1aa9389d173'
source	BiologicalActivity | LogicalOperator	The source activity or logical operator.	required
target	Activity	The target activity being influenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

LogicArcLayout dataclass

LogicArcLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None)

Bases: SBGNSingleHeadedArc

Logic arc layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'76c2c073-4d72-45ab-b71a-aa56673c9700'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

LogicalOperator dataclass

LogicalOperator(*, id_: str = make_uuid4_as_str(), inputs: frozenset[LogicalOperatorInput] = frozenset())

Bases: SBGNModelElement

Abstract base class for logical operators.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'a2e1b477-ce51-414d-8882-4e560bd7e3fd'
inputs	frozenset[LogicalOperatorInput]	Input connections to the logical operator.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

LogicalOperatorInput dataclass

LogicalOperatorInput(*, id_: str = make_uuid4_as_str(), referred_element: Union[BiologicalActivity, ForwardRef(LogicalOperator, module=__name__)])

Bases: SBGNRole

Logical operator input.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'7d7a37b2-f267-4c63-bdb4-d887e502ce4c'
referred_element	BiologicalActivity | ForwardRef	The biological activity or logical operator providing the input.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

MacromoleculeUnitOfInformation dataclass

MacromoleculeUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Macromolecule unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'68bd62b2-c4d6-4a22-81cd-68a8c105be19'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

MacromoleculeUnitOfInformationLayout dataclass

MacromoleculeUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0, rounded_corners: float = 3.0)

Bases: _SimpleMixin, SBGNNode

Macromolecule unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'b6d75e0b-9e1e-4716-9a04-3637c6ba4c50'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0
rounded_corners	float	The radius of the rounded corners.	3.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

NecessaryStimulation dataclass

NecessaryStimulation(*, id_: str = make_uuid4_as_str(), source: BiologicalActivity | LogicalOperator, target: Activity)

Bases: Influence

Necessary stimulation.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c6b9f318-1dc1-452e-8a73-209110b92681'
source	BiologicalActivity | LogicalOperator	The source activity or logical operator.	required
target	Activity	The target activity being influenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

NecessaryStimulationLayout dataclass

NecessaryStimulationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_bar_height: float = 12.0, arrowhead_sep: float = 3.0, arrowhead_triangle_height: float = 10.0, arrowhead_triangle_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Necessary stimulation layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c35c1fe5-925e-40c5-a146-d72e2cf557af'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None
arrowhead_bar_height	float	The height of the arrowhead bar.	12.0
arrowhead_sep	float	The separation between the bar and the triangle.	3.0
arrowhead_triangle_height	float	The height of the arrowhead triangle.	10.0
arrowhead_triangle_width	float	The width of the arrowhead triangle.	10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

NegativeInfluence dataclass

NegativeInfluence(*, id_: str = make_uuid4_as_str(), source: BiologicalActivity | LogicalOperator, target: Activity)

Bases: Influence

Negative influence.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'374870f4-0b5c-46c4-80cf-7c56e26304cd'
source	BiologicalActivity | LogicalOperator	The source activity or logical operator.	required
target	Activity	The target activity being influenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

NegativeInfluenceLayout dataclass

NegativeInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_height: float = 10.0)

Bases: SBGNSingleHeadedArc

Negative influence layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'483709c0-0033-47fe-88fc-130a6c5fd721'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None
arrowhead_height	float	The height of the arrowhead.	10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

NotOperator dataclass

NotOperator(*, id_: str = make_uuid4_as_str(), inputs: frozenset[LogicalOperatorInput] = frozenset())

Bases: LogicalOperator

NOT operator.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'd3721e51-055f-4ba1-8bc6-c674d1582a45'
inputs	frozenset[LogicalOperatorInput]	Input connections to the logical operator.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

NotOperatorLayout dataclass

NotOperatorLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 30.0, text: str = 'NOT', font_family: str = DEFAULT_FONT_FAMILY, font_fill: Color | NoneValueType = black, font_stroke: Color | NoneValueType = NoneValue, font_style: FontStyle = NORMAL, font_weight: FontWeight | float = NORMAL, orientation: Orientation = HORIZONTAL, left_to_right: bool = True, left_connector_length: float = 10.0, right_connector_length: float = 10.0, left_connector_stroke: NoneValueType | Color | None = None, left_connector_stroke_width: float | None = None, left_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, left_connector_stroke_dashoffset: float | None = None, left_connector_fill: NoneValueType | Color | None = None, left_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, left_connector_filter: NoneValueType | Filter | None = None, right_connector_stroke: NoneValueType | Color | None = None, right_connector_stroke_width: float | None = None, right_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, right_connector_stroke_dashoffset: float | None = None, right_connector_fill: NoneValueType | Color | None = None, right_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, right_connector_filter: NoneValueType | Filter | None = None)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

NOT operator layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'84f8c672-bc66-492a-be20-82cb4b639438'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	30.0
text	str	The text displayed inside the node.	'NOT'
font_family	str	Font family for the text.	'DejaVu Sans'
font_fill	Color | NoneValueType	Fill color for the text.	Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType	Stroke color for the text outline.	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
font_style	FontStyle	Font style (normal, italic, etc.).	<FontStyle.NORMAL: 0>
font_weight	FontWeight | float	Font weight (normal, bold, etc.).	<FontWeight.NORMAL: 0>
orientation	Orientation	Orientation of connectors (HORIZONTAL or VERTICAL).	<Orientation.HORIZONTAL: 1>
left_to_right	bool	Whether connectors flow left to right.	True
left_connector_length	float	Length of the left connector.	10.0
right_connector_length	float	Length of the right connector.	10.0
left_connector_stroke	NoneValueType | Color | None	Stroke color for the left connector line.	None
left_connector_stroke_width	float | None	Stroke width for the left connector line.	None
left_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the left connector line.	None
left_connector_stroke_dashoffset	float | None	Dash offset for the left connector line.	None
left_connector_fill	NoneValueType | Color | None	Fill color for the left connector.	None
left_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the left connector.	None
left_connector_filter	NoneValueType | Filter | None	Filter applied to the left connector.	None
right_connector_stroke	NoneValueType | Color | None	Stroke color for the right connector line.	None
right_connector_stroke_width	float | None	Stroke width for the right connector line.	None
right_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the right connector line.	None
right_connector_stroke_dashoffset	float | None	Dash offset for the right connector line.	None
right_connector_fill	NoneValueType | Color | None	Fill color for the right connector.	None
right_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the right connector.	None
right_connector_filter	NoneValueType | Filter | None	Filter applied to the right connector.	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Get the east (right) anchor point.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
left_connector_base	Get the base point of the left connector.
left_connector_tip	Get the tip point of the left connector.
north	Get the north (top) anchor point.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
right_connector_base	Get the base point of the right connector.
right_connector_tip	Get the tip point of the right connector.
size	Return the size of the node.
south	Get the south (bottom) anchor point.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Get the west (left) anchor point.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Get the east (right) anchor point.

Returns:

Type	Description
Point	Point on the east side of the element.

Source code in src/momapy/sbgn/elements.py

def east(self) -> Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x + self.width / 2, self.y)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

left_connector_base

left_connector_base() -> Point

Get the base point of the left connector.

Returns:

Type	Description
Point	Point where the left connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def left_connector_base(self) -> Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2)
    else:
        return Point(self.x - self.width / 2, self.y)

left_connector_tip

left_connector_tip() -> Point

Get the tip point of the left connector.

Returns:

Type	Description
Point	Point at the end of the left connector line.

Source code in src/momapy/sbgn/elements.py

def left_connector_tip(self) -> Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

north

north() -> Point

Get the north (top) anchor point.

Returns:

Type	Description
Point	Point on the north side of the element.

Source code in src/momapy/sbgn/elements.py

def north(self) -> Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x, self.y - self.height / 2)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

right_connector_base

right_connector_base() -> Point

Get the base point of the right connector.

Returns:

Type	Description
Point	Point where the right connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def right_connector_base(self) -> Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2)
    else:
        return Point(self.x + self.width / 2, self.y)

right_connector_tip

right_connector_tip() -> Point

Get the tip point of the right connector.

Returns:

Type	Description
Point	Point at the end of the right connector line.

Source code in src/momapy/sbgn/elements.py

def right_connector_tip(self) -> Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Get the south (bottom) anchor point.

Returns:

Type	Description
Point	Point on the south side of the element.

Source code in src/momapy/sbgn/elements.py

def south(self) -> Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x, self.y + self.height / 2)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Get the west (left) anchor point.

Returns:

Type	Description
Point	Point on the west side of the element.

Source code in src/momapy/sbgn/elements.py

def west(self) -> Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x - self.width / 2, self.y)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

NucleicAcidFeatureUnitOfInformation dataclass

NucleicAcidFeatureUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Nucleic acid feature unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'46eca30a-7eda-4d93-bcd9-3d5219766078'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

NucleicAcidFeatureUnitOfInformationLayout dataclass

NucleicAcidFeatureUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0, rounded_corners: float = 3.0)

Bases: _SimpleMixin, SBGNNode

Nucleic acid feature unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'aad3a223-3fc0-43cb-b6c3-a3fc9eb594d3'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0
rounded_corners	float	The radius of the rounded corners.	3.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

OrOperator dataclass

OrOperator(*, id_: str = make_uuid4_as_str(), inputs: frozenset[LogicalOperatorInput] = frozenset())

Bases: LogicalOperator

OR operator.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6f6f95c4-c360-4b59-a42f-47be48e9e675'
inputs	frozenset[LogicalOperatorInput]	Input connections to the logical operator.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

OrOperatorLayout dataclass

OrOperatorLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 30.0, text: str = 'OR', font_family: str = DEFAULT_FONT_FAMILY, font_fill: Color | NoneValueType = black, font_stroke: Color | NoneValueType = NoneValue, font_style: FontStyle = NORMAL, font_weight: FontWeight | float = NORMAL, orientation: Orientation = HORIZONTAL, left_to_right: bool = True, left_connector_length: float = 10.0, right_connector_length: float = 10.0, left_connector_stroke: NoneValueType | Color | None = None, left_connector_stroke_width: float | None = None, left_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, left_connector_stroke_dashoffset: float | None = None, left_connector_fill: NoneValueType | Color | None = None, left_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, left_connector_filter: NoneValueType | Filter | None = None, right_connector_stroke: NoneValueType | Color | None = None, right_connector_stroke_width: float | None = None, right_connector_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, right_connector_stroke_dashoffset: float | None = None, right_connector_fill: NoneValueType | Color | None = None, right_connector_transform: NoneValueType | tuple[Transformation, ...] | None = None, right_connector_filter: NoneValueType | Filter | None = None)

Bases: _ConnectorsMixin, _SimpleMixin, _TextMixin, SBGNNode

OR operator layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3f658771-2905-4199-ab73-2f4afcde4271'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	30.0
text	str	The text displayed inside the node.	'OR'
font_family	str	Font family for the text.	'DejaVu Sans'
font_fill	Color | NoneValueType	Fill color for the text.	Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType	Stroke color for the text outline.	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
font_style	FontStyle	Font style (normal, italic, etc.).	<FontStyle.NORMAL: 0>
font_weight	FontWeight | float	Font weight (normal, bold, etc.).	<FontWeight.NORMAL: 0>
orientation	Orientation	Orientation of connectors (HORIZONTAL or VERTICAL).	<Orientation.HORIZONTAL: 1>
left_to_right	bool	Whether connectors flow left to right.	True
left_connector_length	float	Length of the left connector.	10.0
right_connector_length	float	Length of the right connector.	10.0
left_connector_stroke	NoneValueType | Color | None	Stroke color for the left connector line.	None
left_connector_stroke_width	float | None	Stroke width for the left connector line.	None
left_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the left connector line.	None
left_connector_stroke_dashoffset	float | None	Dash offset for the left connector line.	None
left_connector_fill	NoneValueType | Color | None	Fill color for the left connector.	None
left_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the left connector.	None
left_connector_filter	NoneValueType | Filter | None	Filter applied to the left connector.	None
right_connector_stroke	NoneValueType | Color | None	Stroke color for the right connector line.	None
right_connector_stroke_width	float | None	Stroke width for the right connector line.	None
right_connector_stroke_dasharray	NoneValueType | tuple[float, ...] | None	Dash pattern for the right connector line.	None
right_connector_stroke_dashoffset	float | None	Dash offset for the right connector line.	None
right_connector_fill	NoneValueType | Color | None	Fill color for the right connector.	None
right_connector_transform	NoneValueType | tuple[Transformation, ...] | None	Transformations applied to the right connector.	None
right_connector_filter	NoneValueType | Filter | None	Filter applied to the right connector.	None

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Get the east (right) anchor point.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
left_connector_base	Get the base point of the left connector.
left_connector_tip	Get the tip point of the left connector.
north	Get the north (top) anchor point.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
right_connector_base	Get the base point of the right connector.
right_connector_tip	Get the tip point of the right connector.
size	Return the size of the node.
south	Get the south (bottom) anchor point.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Get the west (left) anchor point.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Get the east (right) anchor point.

Returns:

Type	Description
Point	Point on the east side of the element.

Source code in src/momapy/sbgn/elements.py

def east(self) -> Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x + self.width / 2, self.y)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

left_connector_base

left_connector_base() -> Point

Get the base point of the left connector.

Returns:

Type	Description
Point	Point where the left connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def left_connector_base(self) -> Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2)
    else:
        return Point(self.x - self.width / 2, self.y)

left_connector_tip

left_connector_tip() -> Point

Get the tip point of the left connector.

Returns:

Type	Description
Point	Point at the end of the left connector line.

Source code in src/momapy/sbgn/elements.py

def left_connector_tip(self) -> Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

north

north() -> Point

Get the north (top) anchor point.

Returns:

Type	Description
Point	Point on the north side of the element.

Source code in src/momapy/sbgn/elements.py

def north(self) -> Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y - self.height / 2 - self.left_connector_length)
    else:
        return Point(self.x, self.y - self.height / 2)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

right_connector_base

right_connector_base() -> Point

Get the base point of the right connector.

Returns:

Type	Description
Point	Point where the right connector attaches to the shape.

Source code in src/momapy/sbgn/elements.py

def right_connector_base(self) -> Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2)
    else:
        return Point(self.x + self.width / 2, self.y)

right_connector_tip

right_connector_tip() -> Point

Get the tip point of the right connector.

Returns:

Type	Description
Point	Point at the end of the right connector line.

Source code in src/momapy/sbgn/elements.py

def right_connector_tip(self) -> Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x + self.width / 2 + self.right_connector_length, self.y)

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Get the south (bottom) anchor point.

Returns:

Type	Description
Point	Point on the south side of the element.

Source code in src/momapy/sbgn/elements.py

def south(self) -> Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x, self.y + self.height / 2 + self.right_connector_length)
    else:
        return Point(self.x, self.y + self.height / 2)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Get the west (left) anchor point.

Returns:

Type	Description
Point	Point on the west side of the element.

Source code in src/momapy/sbgn/elements.py

def west(self) -> Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.orientation == Orientation.VERTICAL:
        return Point(self.x - self.width / 2, self.y)
    else:
        return Point(self.x - self.width / 2 - self.left_connector_length, self.y)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

PerturbationUnitOfInformation dataclass

PerturbationUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Perturbation unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'90b96ead-9e57-4da1-8b2f-3a920c649af4'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

PerturbationUnitOfInformationLayout dataclass

PerturbationUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Perturbation unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6e57884b-a5e8-427b-8ff8-719613744eb8'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0
angle	float	The angle of the notched sides.	70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = dataclasses.field(default=70.0, metadata={'description': 'The angle of the notched sides.'})

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

Phenotype dataclass

Phenotype(*, id_: str = make_uuid4_as_str(), label: str | None = None, compartment: Compartment | None = None)

Bases: Activity

Phenotype.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'39e26014-6f8d-4c3d-a694-3fc0418a2dc8'
label	str | None	The label of the activity.	None
compartment	Compartment | None	The compartment containing this activity.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

PhenotypeLayout dataclass

PhenotypeLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 60.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Phenotype layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8fa81939-f74f-4137-92e0-f7d1cf3681bf'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	30.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	60.0
angle	float	The angle of the slanted sides.	70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = dataclasses.field(default=70.0, metadata={'description': 'The angle of the slanted sides.'})

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

PositiveInfluence dataclass

PositiveInfluence(*, id_: str = make_uuid4_as_str(), source: BiologicalActivity | LogicalOperator, target: Activity)

Bases: Influence

Positive influence.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'e77292d3-cd5f-42f3-a1ea-8e62e6f830ef'
source	BiologicalActivity | LogicalOperator	The source activity or logical operator.	required
target	Activity	The target activity being influenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

PositiveInfluenceLayout dataclass

PositiveInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Positive influence layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'22e82c6f-3cdc-497c-9331-7b43dcad948f'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None
arrowhead_height	float	The height of the arrowhead.	10.0
arrowhead_width	float	The width of the arrowhead.	10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

SBGNAFLayout dataclass

SBGNAFLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float)

Bases: SBGNLayout

SBGN AF layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'0e97eaf8-6999-4d44-8ccf-67f9081defe5'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	required
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	NoneValueType | float | None	The stroke width of the node	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	required

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
is_sublayout	Return True if the layout is a sublayout of another given layout, False otherwise.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

is_sublayout

is_sublayout(other: Layout, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout is a sublayout of another given layout, False otherwise.

Source code in src/momapy/core/layout.py

def is_sublayout(
    self, other: "Layout", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout is a sublayout of another given layout, `False` otherwise."""

    def _is_sublist(
        list1: list[LayoutElement],
        list2: list[LayoutElement],
        unordered: bool = False,
    ) -> bool:
        if not unordered:
            i = 0
            for elem1 in list1:
                elem2 = list2[i]
                while elem2 != elem1 and i < len(list2) - 1:
                    i += 1
                    elem2 = list2[i]
                if not elem2 == elem1:
                    return False
                i += 1
        else:
            dlist1 = collections.defaultdict(int)
            dlist2 = collections.defaultdict(int)
            for elem1 in list1:
                dlist1[elem1] += 1
            for elem2 in list2:
                dlist2[elem2] += 1
            for elem in dlist1:
                if dlist1[elem] > dlist2[elem]:
                    return False
        return True

    if self.childless() != other.childless():
        return False
    if flattened:
        return _is_sublist(
            self.flattened()[1:],
            other.flattened()[1:],
            unordered=unordered,
        )
    return _is_sublist(self.children(), other.children(), unordered=unordered)

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

SBGNAFMap dataclass

SBGNAFMap(*, id_: str = make_uuid4_as_str(), model: SBGNAFModel | None = None, layout: SBGNAFLayout | None = None, layout_model_mapping: LayoutModelMapping | None = None)

Bases: SBGNMap

Class for SBGN-AF maps.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'317dd984-5c2b-460f-aa48-4839535f9345'
model	SBGNAFModel | None	The model of the map	None
layout	SBGNAFLayout | None	The layout of the map	None
layout_model_mapping	LayoutModelMapping | None	The layout model mapping of the map	None

Methods:

Name	Description
get_mapping	Return the model element or layout elements mapped to map_element.
is_submap	Return True if the Map is a submap of another given map, False otherwise.

get_mapping

get_mapping(map_element: MapElement) -> ModelElement | list[LayoutElement | frozenset[LayoutElement]] | None

Return the model element or layout elements mapped to map_element.

The lookup is bidirectional: a layout key (a singleton or frozenset) resolves to its model element, and a model element resolves to the list of layout keys mapped to it. Forwards to layout_model_mapping.get_mapping.

Returns None when the map has no layout_model_mapping (for example a layout-less map such as one read from SBML).

Source code in src/momapy/core/map.py

def get_mapping(
    self,
    map_element: "MapElement",
) -> "ModelElement | list[LayoutElement | frozenset[LayoutElement]] | None":
    """Return the model element or layout elements mapped to `map_element`.

    The lookup is bidirectional: a layout key (a singleton or frozenset)
    resolves to its model element, and a model element resolves to the
    list of layout keys mapped to it. Forwards to
    `layout_model_mapping.get_mapping`.

    Returns `None` when the map has no `layout_model_mapping` (for
    example a layout-less map such as one read from SBML).
    """
    if self.layout_model_mapping is None:
        return None
    return self.layout_model_mapping.get_mapping(map_element)

is_submap

is_submap(other: Map) -> bool

Return True if the Map is a submap of another given map, False otherwise.

A complete map is never a submap of an incomplete one: if either self or other has a None model, layout, or layout-model mapping, this returns False.

Source code in src/momapy/core/map.py

def is_submap(self, other: "Map") -> bool:
    """Return `True` if the `Map` is a submap of another given map, `False` otherwise.

    A complete map is never a submap of an incomplete one: if either `self`
    or `other` has a `None` model, layout, or layout-model mapping, this
    returns `False`.
    """
    if (
        self.model is None
        or self.layout is None
        or self.layout_model_mapping is None
        or other.model is None
        or other.layout is None
        or other.layout_model_mapping is None
    ):
        return False
    return (
        self.model.is_submodel(other.model)
        and self.layout.is_sublayout(other.layout)
        and self.layout_model_mapping.is_submapping(other.layout_model_mapping)
    )

SBGNAFModel dataclass

SBGNAFModel(*, id_: str = make_uuid4_as_str(), activities: frozenset[Activity] = frozenset(), compartments: frozenset[Compartment] = frozenset(), influences: frozenset[Influence] = frozenset(), logical_operators: frozenset[LogicalOperator] = frozenset(), submaps: frozenset[Submap] = frozenset(), tags: frozenset[Tag] = frozenset())

Bases: SBGNModel

SBGN AF model.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c4d25e9d-45c7-48cd-8868-d172e5546f4f'
activities	frozenset[Activity]	The activities of the SBGN-AF model.	<dynamic>
compartments	frozenset[Compartment]	The compartments of the SBGN-AF model.	<dynamic>
influences	frozenset[Influence]	The influences of the SBGN-AF model.	<dynamic>
logical_operators	frozenset[LogicalOperator]	The logical operators of the SBGN-AF model.	<dynamic>
submaps	frozenset[Submap]	The submaps of the SBGN-AF model.	<dynamic>
tags	frozenset[Tag]	The tags of the SBGN-AF model.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from this Model.
is_submodel	Check if this model is a submodel of another model.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from this Model.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers of the Model, deduplicating by object identity. The Model itself is not a ModelElement and is not included.

This mirrors ModelElement.descendants and contrasts with LayoutElement.descendants, which walks the explicit children() tree (visual containment) rather than reference reachability.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order.

Source code in src/momapy/core/model.py

def descendants(self) -> list[ModelElement]:
    """Return every `ModelElement` reachable from this `Model`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers of the `Model`, deduplicating by
    object identity. The `Model` itself is not a `ModelElement` and is
    not included.

    This mirrors
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and contrasts with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which walks the explicit `children()` tree (visual *containment*)
    rather than reference reachability.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order.
    """
    seen: set[int] = set()
    result: list[ModelElement] = []
    for field in dataclasses.fields(type(self)):
        _walk_model_graph(getattr(self, field.name), seen, result)
    return result

is_submodel

is_submodel(other: SBGNAFModel) -> bool

Check if this model is a submodel of another model.

Parameters:

Name	Type	Description	Default
other	SBGNAFModel	Another SBGN-AF model to compare against.	required

Returns:

Type	Description
bool	True if this model is a submodel of other, False otherwise.

Source code in src/momapy/sbgn/af/model.py

def is_submodel(self, other: "SBGNAFModel") -> bool:
    """Check if this model is a submodel of another model.

    Args:
        other: Another SBGN-AF model to compare against.

    Returns:
        True if this model is a submodel of `other`, False otherwise.
    """
    return (
        self.activities.issubset(other.activities)
        and self.compartments.issubset(other.compartments)
        and self.influences.issubset(other.influences)
        and self.logical_operators.issubset(other.logical_operators)
        and self.submaps.issubset(other.submaps)
        and self.tags.issubset(other.tags)
    )

SimpleChemicalUnitOfInformation dataclass

SimpleChemicalUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Simple chemical unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'3dded47c-635d-45cf-abae-5b83e48cd779'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

SimpleChemicalUnitOfInformationLayout dataclass

SimpleChemicalUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Simple chemical unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'2f2857cc-2541-4e42-be4d-4a4056990ebc'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	12.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

Submap dataclass

Submap(*, id_: str = make_uuid4_as_str(), label: str | None = None, terminals: frozenset[Terminal] = frozenset())

Bases: SBGNModelElement

Submap.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'9e507ba6-b128-4d72-85a9-9ed83dcb4c50'
label	str | None	The label of the submap.	None
terminals	frozenset[Terminal]	The terminals of the submap.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

SubmapLayout dataclass

SubmapLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 80.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float = 2.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 80.0)

Bases: _SimpleMixin, SBGNNode

Submap layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'958ba947-95a9-4197-b093-221fb93d7ee6'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	80.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float	The stroke width of the node	2.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	80.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

Tag dataclass

Tag(*, id_: str = make_uuid4_as_str(), label: str | None = None, referred_element: TagReference | None = None)

Bases: SBGNModelElement

Tag.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'5377d23a-ff23-4f00-846e-d64515b0c512'
label	str | None	The label of the tag.	None
referred_element	TagReference | None	The element referred to by the tag.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

TagLayout dataclass

TagLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 35.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Tag layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'a03b8c58-dfb9-4921-8e67-d1aa16ba9b0e'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	35.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	35.0
direction	Direction	The direction the tag points to.	<Direction.RIGHT: 2>
angle	float	The angle of the pointed side.	70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = dataclasses.field(default=70.0, metadata={'description': 'The angle of the pointed side.'})

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

TagReference dataclass

TagReference(*, id_: str = make_uuid4_as_str(), referred_element: Activity | Compartment)

Bases: SBGNRole

Tag reference.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'6516c662-5d23-4eeb-b537-dacf9cdddb0a'
referred_element	Activity | Compartment	The activity or compartment being referenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

Terminal dataclass

Terminal(*, id_: str = make_uuid4_as_str(), label: str | None = None, referred_element: TerminalReference | None = None)

Bases: SBGNAuxiliaryUnit

Terminal.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'9f3c054b-0ef4-47b7-b142-a332b92671f8'
label	str | None	The label of the terminal.	None
referred_element	TerminalReference | None	The element referred to by the terminal.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

TerminalLayout dataclass

TerminalLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 35.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Terminal layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8a5188f9-bcbe-44af-bd03-89a31ca740cd'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	35.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	35.0
direction	Direction	The direction the terminal points to.	<Direction.RIGHT: 2>
angle	float	The angle of the notched side.	70.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
angle	float	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = dataclasses.field(default=70.0, metadata={'description': 'The angle of the notched side.'})

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

TerminalReference dataclass

TerminalReference(*, id_: str = make_uuid4_as_str(), referred_element: Activity | Compartment)

Bases: SBGNRole

Terminal reference.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'8c85e800-cc14-44d4-85fb-99843ba9f197'
referred_element	Activity | Compartment	The activity or compartment being referenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

UnitOfInformation dataclass

UnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: SBGNAuxiliaryUnit

Abstract base class for units of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'd9e74d66-99c4-4044-9637-02dba86f21cb'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

UnitOfInformationLayout dataclass

UnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0)

Bases: _SimpleMixin, SBGNNode

Unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'81eebb20-a689-473a-b51c-c6e0ea1621fa'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.

UnknownInfluence dataclass

UnknownInfluence(*, id_: str = make_uuid4_as_str(), source: BiologicalActivity | LogicalOperator, target: Activity)

Bases: Influence

Unknown influence.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'792cc74c-b759-4fdc-ae4a-0ce541abd67c'
source	BiologicalActivity | LogicalOperator	The source activity or logical operator.	required
target	Activity	The target activity being influenced.	required

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

UnknownInfluenceLayout dataclass

UnknownInfluenceLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, end_shorten: float = 0.0, fill: NoneValueType | Color | None = None, filter_: NoneValueType | Filter | None = None, path_fill: NoneValueType | Color | None = NoneValue, path_filter: NoneValueType | Filter | None = None, path_stroke: NoneValueType | Color | None = black, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, path_stroke_width: float | None = 1.25, path_transform: NoneValueType | tuple[Transformation, ...] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: NoneValueType | float | None = None, segments: tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...] = tuple(), source: LayoutElement | None = None, start_shorten: float = 0.0, target: LayoutElement | None = None, transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_filter: NoneValueType | Filter | None = None, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_stroke_width: float | None = 1.25, arrowhead_transform: NoneValueType | tuple[Transformation, ...] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Unknown influence layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'c065db0c-adfe-4e1a-b081-08fb5040ad7a'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
end_shorten	float	The length the end of the arc will be shorten by	0.0
fill	NoneValueType | Color | None	The fill color of the arc	None
filter_	NoneValueType | Filter | None	The filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fb1b7eb96a0>
path_filter	NoneValueType | Filter | None	The path filter of the arc	None
path_stroke	NoneValueType | Color | None	The path stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
path_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The path stroke dasharray of the arc	None
path_stroke_dashoffset	NoneValueType | float | None	The path stroke dashoffset of the arc	None
path_stroke_width	float | None	The path stroke width of the arc	1.25
path_transform	NoneValueType | tuple[Transformation, ...] | None	The path transform of the arc	None
stroke	NoneValueType | Color | None	The stroke color of the arc	None
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the arc	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the arc	None
stroke_width	NoneValueType | float | None	The stroke width of the arc	None
segments	tuple[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc, ...]	The path segments of the arc	<dynamic>
source	LayoutElement | None	The source of the arc	None
start_shorten	float	The length the start of the arc will be shorten by	0.0
target	LayoutElement | None	The target of the arc	None
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the arc	None
arrowhead_fill	NoneValueType | Color | None	The arrowhead fill color of the arc	Color(red=255, green=255, blue=255, alpha=1.0)
arrowhead_filter	NoneValueType | Filter | None	The arrowhead filter of the arc	None
arrowhead_stroke	NoneValueType | Color | None	The arrowhead stroke color of the arc	Color(red=0, green=0, blue=0, alpha=1.0)
arrowhead_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The arrowhead stroke dasharray of the arc	None
arrowhead_stroke_dashoffset	NoneValueType | float | None	The arrowhead stroke dashoffset of the arc	None
arrowhead_stroke_width	float | None	The arrowhead stroke width of the arc	1.25
arrowhead_transform	NoneValueType | tuple[Transformation, ...] | None	The arrowhead transform of the arc	None
arrowhead_height	float	The height of the arrowhead.	10.0
arrowhead_width	float	The width of the arrowhead.	10.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
arrowhead_base	Return the arrowhead base anchor point of the single-headed arc.
arrowhead_bbox	Return the bounding box of the single-headed arc arrowhead.
arrowhead_border	Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.
arrowhead_drawing_elements	Return the drawing elements of the single-headed arc arrowhead.
arrowhead_length	Return the length of the single-headed arc arrowhead.
arrowhead_tip	Return the arrowhead tip anchor point of the single-headed arc.
bbox	Compute and return the bounding box of the group layout element.
childless	Return a copy of the arc with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
end_point	Return the ending point of the arc.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
fraction	Return the position and angle on the arc at a given fraction (of the total arc length).
length	Return the total length of the arc path.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_children	Return the self children of the arc.
own_drawing_elements	Return the self drawing elements of the single-headed arc.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
path_drawing_elements	Return the drawing elements of the single-headed arc path.
points	Return the points of the arc path.
start_point	Return the starting point of the arc.
to_geometry	Return a list of geometry primitives from the drawing elements.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

arrowhead_base

arrowhead_base() -> Point

Return the arrowhead base anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_base(self) -> Point:
    """Return the arrowhead base anchor point of the single-headed arc."""
    arrowhead_length = self.arrowhead_length()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

arrowhead_bbox

arrowhead_bbox() -> Bbox

Return the bounding box of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_bbox(self) -> Bbox:
    """Return the bounding box of the single-headed arc arrowhead."""
    return get_drawing_elements_bbox(self.arrowhead_drawing_elements())

arrowhead_border

arrowhead_border(point: Point) -> Point

Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def arrowhead_border(self, point: Point) -> Point:
    """Return the point at the intersection of the drawing elements of the single-headed arc arrowhead and the line going through the center of these drawing elements and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    point = get_drawing_elements_border(self.arrowhead_drawing_elements(), point)
    if point is None:
        return self.arrowhead_tip()
    return point

arrowhead_drawing_elements

arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_drawing_elements(
    self,
) -> list[DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead."""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_arrowhead",
        elements=tuple(drawing_elements),
        fill=self.arrowhead_fill,
        filter_=self.arrowhead_filter,
        id_=f"{self.id_}_arrowhead",
        stroke=self.arrowhead_stroke,
        stroke_dasharray=self.arrowhead_stroke_dasharray,
        stroke_dashoffset=self.arrowhead_stroke_dashoffset,
        stroke_width=self.arrowhead_stroke_width,
        transform=self.arrowhead_transform,
    )
    transformation = self._get_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

arrowhead_length

arrowhead_length() -> float

Return the length of the single-headed arc arrowhead.

Source code in src/momapy/core/layout.py

def arrowhead_length(self) -> float:
    """Return the length of the single-headed arc arrowhead."""
    bbox = get_drawing_elements_bbox(self._arrowhead_border_drawing_elements())
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

arrowhead_tip

arrowhead_tip() -> Point

Return the arrowhead tip anchor point of the single-headed arc.

Source code in src/momapy/core/layout.py

def arrowhead_tip(self) -> Point:
    """Return the arrowhead tip anchor point of the single-headed arc."""
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.end_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

childless

childless() -> Self

Return a copy of the arc with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the arc with no children."""
    return dataclasses.replace(self, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

end_point

end_point() -> Point

Return the ending point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def end_point(self) -> Point:
    """Return the ending point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[-1]

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

fraction

fraction(fraction: float) -> tuple[Point, float]

Return the position and angle on the arc at a given fraction (of the total arc length).

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def fraction(self, fraction: float) -> tuple[Point, float]:
    """Return the position and angle on the arc at a given fraction (of the total arc length).

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    current_length = 0
    length_to_reach = fraction * self.length()
    for segment in self.segments:
        current_length += segment.length()
        if current_length >= length_to_reach:
            break
    segment_start_length = current_length - segment.length()
    segment_fraction = (length_to_reach - segment_start_length) / segment.length()
    position, angle = segment.get_position_and_angle_at_fraction(segment_fraction)
    return position, angle

length

length() -> float

Return the total length of the arc path.

Source code in src/momapy/core/layout.py

def length(self) -> float:
    """Return the total length of the arc path."""
    return sum([segment.length() for segment in self.segments])

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_children

own_children() -> list[LayoutElement]

Return the self children of the arc.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the arc."""
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the self drawing elements of the single-headed arc."""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path.

Source code in src/momapy/core/layout.py

def path_drawing_elements(self) -> list[Path]:
    """Return the drawing elements of the single-headed arc path."""
    arrowhead_length = self.arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten, "start")
            .shortened(self.end_shorten + arrowhead_length, "end")
        )
        actions = [
            MoveTo(segment.p1),
            self._make_path_action_from_segment(segment),
        ]
    else:
        first_segment = self.segments[0].shortened(self.start_shorten, "start")
        last_segment = self.segments[-1].shortened(
            self.end_shorten + arrowhead_length, "end"
        )
        actions = [
            MoveTo(first_segment.p1),
            self._make_path_action_from_segment(first_segment),
        ]
        for segment in self.segments[1:-1]:
            action = self._make_path_action_from_segment(segment)
            actions.append(action)
        actions.append(self._make_path_action_from_segment(last_segment))
    path = Path(
        actions=tuple(actions),
        class_=f"{type(self).__name__}_path",
        fill=self.path_fill,
        filter_=self.path_filter,
        id_=f"{self.id_}_path",
        stroke=self.path_stroke,
        stroke_dasharray=self.path_stroke_dasharray,
        stroke_dashoffset=self.path_stroke_dashoffset,
        stroke_width=self.path_stroke_width,
        transform=self.path_transform,
    )
    return [path]

points

points() -> list[Point]

Return the points of the arc path.

An arc with no segments has no points and returns an empty list.

Source code in src/momapy/core/layout.py

def points(self) -> list[Point]:
    """Return the points of the arc path.

    An arc with no segments has no points and returns an empty list.
    """
    if not self.segments:
        return []
    points = []
    for segment in self.segments:
        points.append(segment.p1)
    points.append(segment.p2)
    return points

start_point

start_point() -> Point

Return the starting point of the arc.

Raises:

Type	Description
ValueError	If the arc has no segments.

Source code in src/momapy/core/layout.py

def start_point(self) -> Point:
    """Return the starting point of the arc.

    Raises:
        ValueError: If the arc has no segments.
    """
    if not self.segments:
        raise ValueError("arc has no segments")
    return self.points()[0]

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

UnspecifiedEntityUnitOfInformation dataclass

UnspecifiedEntityUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: str | None = None)

Bases: UnitOfInformation

Unspecified entity unit of information.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'36d927d2-189a-4f5d-ad67-5d7576311658'
label	str | None	The label of the unit of information.	None

Methods:

Name	Description
descendants	Return every ModelElement reachable from self, excluding self.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from self, excluding self.

This reflectively walks the dataclass field-graph (i.e. reference reachability) across scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity. A model element referenced by several parents therefore appears once.

Note the deliberate contrast with LayoutElement.descendants, which instead walks the explicit children() tree (visual containment): there a layout element contained under two parents is reached through each, with no identity dedup.

Returns:

Type	Description
list[ModelElement]	The list of reachable ModelElement instances in visit
list[ModelElement]	order, without self.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["ModelElement"]:
    """Return every `ModelElement` reachable from `self`, excluding `self`.

    This reflectively walks the dataclass field-graph (i.e. *reference
    reachability*) across scalar `ModelElement` fields and
    `frozenset`/`tuple` containers, deduplicating by object identity. A
    model element referenced by several parents therefore appears once.

    Note the deliberate contrast with
    [`LayoutElement.descendants`][momapy.core.elements.LayoutElement.descendants],
    which instead walks the explicit `children()` tree (visual
    *containment*): there a layout element contained under two parents is
    reached through each, with no identity dedup.

    Returns:
        The list of reachable `ModelElement` instances in visit
        order, without `self`.
    """
    seen: set[int] = {id(self)}
    result: list[ModelElement] = []
    if dataclasses.is_dataclass(self):
        for field in dataclasses.fields(type(self)):
            _walk_model_graph(getattr(self, field.name), seen, result)
    return result

UnspecifiedEntityUnitOfInformationLayout dataclass

UnspecifiedEntityUnitOfInformationLayout(*, id_: str = make_uuid4_as_str(), layout_elements: tuple[LayoutElement, ...] = tuple(), group_fill: NoneValueType | Color | None = None, group_fill_rule: FillRule | None = None, group_filter: NoneValueType | Filter | None = None, group_font_family: str | None = None, group_font_size: float | None = None, group_font_style: FontStyle | None = None, group_font_weight: FontWeight | float | None = None, group_stroke: NoneValueType | Color | None = None, group_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, group_stroke_dashoffset: NoneValueType | float | None = None, group_stroke_width: NoneValueType | float | None = None, group_text_anchor: TextAnchor | None = None, group_transform: NoneValueType | tuple[Transformation, ...] | None = None, fill: NoneValueType | Color | None = white, filter_: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke: NoneValueType | Color | None = black, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, stroke_width: float | None = 1.25, transform: NoneValueType | tuple[Transformation, ...] | None = None, width: float = 18.0)

Bases: _SimpleMixin, SBGNNode

Unspecified entity unit of information layout.

Parameters:

Name	Type	Description	Default
id_	str	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	'ceba0879-0128-4dcb-9934-46150fe49c01'
layout_elements	tuple[LayoutElement, ...]	The sub-layout elements of the group layout. These are part of the children of the group layout	<dynamic>
group_fill	NoneValueType | Color | None	The fill color of the group layout	None
group_fill_rule	FillRule | None	The fill rule of the group layout	None
group_filter	NoneValueType | Filter | None	The filter of the group layout	None
group_font_family	str | None	The font family of the group layout	None
group_font_size	float | None	The font size of the group layout	None
group_font_style	FontStyle | None	The font style of the group layout	None
group_font_weight	FontWeight | float | None	The font weight of the group layout	None
group_stroke	NoneValueType | Color | None	The stroke color of the group layout	None
group_stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the group layout	None
group_stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the group layout	None
group_stroke_width	NoneValueType | float | None	The stroke width of the group layout	None
group_text_anchor	TextAnchor | None	The text anchor of the group layout	None
group_transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the group layout	None
fill	NoneValueType | Color | None	The fill color of the node	Color(red=255, green=255, blue=255, alpha=1.0)
filter_	NoneValueType | Filter | None	The filter of the node	None
height	float	The height of the node	12.0
label	TextLayout | None	The label of the node	None
position	Point	The position of the node	required
stroke	NoneValueType | Color | None	The stroke color of the node	Color(red=0, green=0, blue=0, alpha=1.0)
stroke_dasharray	NoneValueType | tuple[float, ...] | None	The stroke dasharray of the node	None
stroke_dashoffset	NoneValueType | float | None	The stroke dashoffset of the node	None
stroke_width	float | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation, ...] | None	The transform of the node	None
width	float	The width of the node	18.0

Methods:

Name	Description
anchor_point	Return an anchor point of the layout element.
angle	Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
bbox	Compute and return the bounding box of the group layout element.
border	Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.
center	Return the center anchor of the node.
childless	Return a copy of the node with no children.
children	Return the children of the group layout.
contains	Return True if another layout element is a descendant of the layout element, False otherwise.
descendants	Return the descendants of the layout element.
drawing_elements	Return the drawing elements of the group layout.
east	Return the east anchor of the node.
east_north_east	Return the east north east anchor of the node.
east_south_east	Return the east south east anchor of the node.
equals	Return True if the layout element is equal to another layout element, False otherwise.
flattened	Return a list containing copy of the layout element with no children and all its descendants with no children.
label_center	Return the label center anchor of the node.
north	Return the north anchor of the node.
north_east	Return the north east anchor of the node.
north_north_east	Return the north north east anchor of the node.
north_north_west	Return the north north west anchor of the node.
north_west	Return the north west anchor of the node.
own_angle	Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.
own_bbox	Compute and return the bounding box of the self drawing element of the group layout.
own_border	Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.
own_children	Return the self children of the node. A node has unique child that is its label.
own_drawing_elements	Return the node's own drawing elements.
own_to_geometry	Return a list of geometry primitives from the self drawing elements.
size	Return the size of the node.
south	Return the south anchor of the node.
south_east	Return the south east anchor of the node.
south_south_east	Return the south south east anchor of the node.
south_south_west	Return the south south west anchor of the node.
south_west	Return the south west anchor of the node.
to_geometry	Return a list of geometry primitives from the drawing elements.
west	Return the west anchor of the node.
west_north_west	Return the west north west anchor of the node.
west_south_west	Return the west south west anchor of the node.

Attributes:

Name	Type	Description
x	float	Return the x coordinate of the node.
y	float	Return the y coordinate of the node.

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element.

Source code in src/momapy/core/elements.py

def anchor_point(self, anchor_name: str) -> Point:
    """Return an anchor point of the layout element."""
    return getattr(self, anchor_name)()

angle

angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

bbox

bbox() -> Bbox

Compute and return the bounding box of the group layout element.

Source code in src/momapy/core/layout.py

def bbox(self) -> Bbox:
    """Compute and return the bounding box of the group layout element."""
    own_bbox = self.own_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = own_bbox.north_west().x
    min_y = own_bbox.north_west().y
    max_x = own_bbox.south_east().x
    max_y = own_bbox.south_east().y
    for bbox in bboxes:
        if bbox.north_west().x < min_x:
            min_x = bbox.north_west().x
        if bbox.north_west().y < min_y:
            min_y = bbox.north_west().y
        if bbox.south_east().x > max_x:
            max_x = bbox.south_east().x
        if bbox.south_east().y > max_y:
            max_y = bbox.south_east().y
    bbox = Bbox(
        Point(min_x / 2 + max_x / 2, min_y / 2 + max_y / 2),
        max_x - min_x,
        max_y - min_y,
    )
    return bbox

border

border(point: Point) -> Point | None

Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.drawing_elements(),
        point=point,
        center=self.center(),
    )

center

center() -> Point

Return the center anchor of the node.

Source code in src/momapy/core/layout.py

def center(self) -> Point:
    """Return the center anchor of the node."""
    return self.position

childless

childless() -> Self

Return a copy of the node with no children.

Source code in src/momapy/core/layout.py

def childless(self) -> typing_extensions.Self:
    """Return a copy of the node with no children."""
    return dataclasses.replace(self, label=None, layout_elements=tuple([]))

children

children() -> list[LayoutElement]

Return the children of the group layout.

These are the self children of the group layout (returned by the own_children method) and the other children of the group layout (given by the layout_elements attribute).

Source code in src/momapy/core/layout.py

def children(self) -> list[LayoutElement]:
    """Return the children of the group layout.

    These are the self children of the group layout (returned by the `own_children` method) and the other children of the group layout (given by the `layout_elements` attribute).
    """
    return self.own_children() + list(self.layout_elements)

contains

contains(other: LayoutElement) -> bool

Return True if another layout element is a descendant of the layout element, False otherwise.

Source code in src/momapy/core/elements.py

def contains(self, other: "LayoutElement") -> bool:
    """Return `True` if another layout element is a descendant of the layout element, `False` otherwise."""
    return other in self.descendants()

descendants

descendants() -> list[LayoutElement]

Return the descendants of the layout element.

This walks the explicit children() tree (i.e. visual containment) depth-first, returning every layout element in the contained subtree (without self).

Note the deliberate contrast with ModelElement.descendants and Model.descendants, which reflectively walk the dataclass field-graph (i.e. reference reachability) and deduplicate by object identity. A model element referenced by several parents therefore appears once across the model graph, whereas layout descendants are strictly the contained subtree and a layout element contained under two parents is reached through each.

Returns:

Type	Description
list[LayoutElement]	The list of descendant layout elements in visit order.

Source code in src/momapy/core/elements.py

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element.

    This walks the explicit `children()` tree (i.e. visual
    *containment*) depth-first, returning every layout element in the
    contained subtree (without `self`).

    Note the deliberate contrast with
    [`ModelElement.descendants`][momapy.core.elements.ModelElement.descendants]
    and [`Model.descendants`][momapy.core.model.Model.descendants],
    which reflectively walk the dataclass field-graph (i.e. *reference
    reachability*) and deduplicate by object identity. A model element
    referenced by several parents therefore appears once across the
    model graph, whereas layout descendants are strictly the contained
    subtree and a layout element contained under two parents is reached
    through each.

    Returns:
        The list of descendant layout elements in visit order.
    """
    descendants = []
    for child in self.children():
        descendants.append(child)
        descendants += child.descendants()
    return descendants

drawing_elements

drawing_elements() -> list[DrawingElement]

Return the drawing elements of the group layout.

The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.

Source code in src/momapy/core/layout.py

def drawing_elements(self) -> list[DrawingElement]:
    """Return the drawing elements of the group layout.

    The returned drawing elements are a group drawing element formed of the self drawing elements of the group layout and the drawing elements of its children.
    """
    drawing_elements = self.own_drawing_elements()
    for child in self.children():
        if child is not None:
            drawing_elements += child.drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}",
        fill=self.group_fill,
        fill_rule=self.group_fill_rule,
        filter_=self.group_filter,
        font_family=self.group_font_family,
        font_size=self.group_font_size,
        font_style=self.group_font_style,
        font_weight=self.group_font_weight,
        stroke=self.group_stroke,
        stroke_dasharray=self.group_stroke_dasharray,
        stroke_dashoffset=self.group_stroke_dashoffset,
        stroke_width=self.group_stroke_width,
        text_anchor=self.group_text_anchor,
        transform=self.group_transform,
    )
    return [group]

east

east() -> Point

Return the east anchor of the node.

Source code in src/momapy/core/layout.py

def east(self) -> Point:
    """Return the east anchor of the node."""
    return self.own_angle(0)

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node.

Source code in src/momapy/core/layout.py

def east_north_east(self) -> Point:
    """Return the east north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

east_south_east

east_south_east() -> Point

Return the east south east anchor of the node.

Source code in src/momapy/core/layout.py

def east_south_east(self) -> Point:
    """Return the east south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

equals

equals(other: LayoutElement, flattened: bool = False, unordered: bool = False) -> bool

Return True if the layout element is equal to another layout element, False otherwise.

Source code in src/momapy/core/elements.py

def equals(
    self, other: "LayoutElement", flattened: bool = False, unordered: bool = False
) -> bool:
    """Return `True` if the layout element is equal to another layout element, `False` otherwise."""
    if type(self) is type(other):
        if not flattened:
            return self == other
        else:
            if not unordered:
                return self.flattened() == other.flattened()
            else:
                return set(self.flattened()) == set(other.flattened())
    return False

flattened

flattened() -> list[LayoutElement]

Return a list containing copy of the layout element with no children and all its descendants with no children.

Source code in src/momapy/core/elements.py

def flattened(self) -> list["LayoutElement"]:
    """Return a list containing copy of the layout element with no children and all its descendants with no children."""
    flattened = [self.childless()]
    for child in self.children():
        flattened += child.flattened()
    return flattened

label_center

label_center() -> Point

Return the label center anchor of the node.

Source code in src/momapy/core/layout.py

def label_center(self) -> Point:
    """Return the label center anchor of the node."""
    return self.position

north

north() -> Point

Return the north anchor of the node.

Source code in src/momapy/core/layout.py

def north(self) -> Point:
    """Return the north anchor of the node."""
    return self.own_angle(90)

north_east

north_east() -> Point

Return the north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_east(self) -> Point:
    """Return the north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_east

north_north_east() -> Point

Return the north north east anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_east(self) -> Point:
    """Return the north north east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, -self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_north_west

north_north_west() -> Point

Return the north north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_north_west(self) -> Point:
    """Return the north north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node.

Source code in src/momapy/core/layout.py

def north_west(self) -> Point:
    """Return the north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

own_angle

own_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal.

Source code in src/momapy/core/layout.py

def own_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line passing through the center anchor point of the node and at a given angle from the horizontal."""
    return get_drawing_elements_angle(
        drawing_elements=self.own_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

own_bbox

own_bbox() -> Bbox

Compute and return the bounding box of the self drawing element of the group layout.

Source code in src/momapy/core/layout.py

def own_bbox(self) -> Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout."""
    primitives = self.own_to_geometry()
    if not primitives:
        return Bbox(Point(0.0, 0.0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return Bbox.union(bboxes)

own_border

own_border(point: Point) -> Point | None

Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

When there are multiple intersection points, the one closest to the given point is returned.

Source code in src/momapy/core/layout.py

def own_border(self, point: Point) -> Point | None:
    """Return the point on the border of the node that intersects the self drawing elements of the node with the line formed of the center anchor point of the node and the given point.

    When there are multiple intersection points, the one closest to the given point is returned.
    """
    return get_drawing_elements_border(
        drawing_elements=self.own_drawing_elements(),
        point=point,
        center=self.center(),
    )

own_children

own_children() -> list[LayoutElement]

Return the self children of the node. A node has unique child that is its label.

Source code in src/momapy/core/layout.py

def own_children(self) -> list[LayoutElement]:
    """Return the self children of the node. A node has unique child that is its label."""
    if self.label is not None:
        return [self.label]
    return []

own_drawing_elements

own_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements.

Source code in src/momapy/core/layout.py

def own_drawing_elements(self) -> list[DrawingElement]:
    """Return the node's own drawing elements."""
    drawing_elements = self._border_drawing_elements()
    group = Group(
        class_=f"{type(self).__name__}_own",
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter_=self.filter_,
        id_=f"{self.id_}_own",
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

own_to_geometry

own_to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the self drawing elements.

Source code in src/momapy/core/layout.py

def own_to_geometry(
    self,
) -> list[
    Segment | QuadraticBezierCurve | CubicBezierCurve | GeometryEllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return drawing_elements_to_geometry(self.own_drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node.

Source code in src/momapy/core/layout.py

def size(self) -> tuple[float, float]:
    """Return the size of the node."""
    return (self.width, self.height)

south

south() -> Point

Return the south anchor of the node.

Source code in src/momapy/core/layout.py

def south(self) -> Point:
    """Return the south anchor of the node."""
    return self.own_angle(270)

south_east

south_east() -> Point

Return the south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_east(self) -> Point:
    """Return the south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_east

south_south_east() -> Point

Return the south south east anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_east(self) -> Point:
    """Return the south south east anchor of the node."""
    line = Line(self.center(), self.center() + (self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_south_west

south_south_west() -> Point

Return the south south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_south_west(self) -> Point:
    """Return the south south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 4, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node.

Source code in src/momapy/core/layout.py

def south_west(self) -> Point:
    """Return the south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 2))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

to_geometry

to_geometry() -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]

Return a list of geometry primitives from the drawing elements.

Source code in src/momapy/core/elements.py

def to_geometry(
    self,
) -> list[Segment | QuadraticBezierCurve | CubicBezierCurve | EllipticalArc]:
    """Return a list of geometry primitives from the drawing elements."""
    return drawing_elements_to_geometry(self.drawing_elements())

west

west() -> Point

Return the west anchor of the node.

Source code in src/momapy/core/layout.py

def west(self) -> Point:
    """Return the west anchor of the node."""
    return self.own_angle(180)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node.

Source code in src/momapy/core/layout.py

def west_north_west(self) -> Point:
    """Return the west north west anchor of the node."""
    line = Line(self.center(), self.center() - (self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

west_south_west

west_south_west() -> Point

Return the west south west anchor of the node.

Source code in src/momapy/core/layout.py

def west_south_west(self) -> Point:
    """Return the west south west anchor of the node."""
    line = Line(self.center(), self.center() + (-self.width / 2, self.height / 4))
    angle = -line.get_angle_to_horizontal()
    return self.own_angle(angle, unit="radians")

x property

x: float

Return the x coordinate of the node.

y property

y: float

Return the y coordinate of the node.