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, anchors).

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 anchor is the layout that stands for the cluster on its own and must be passed as anchor= when calling add_mapping):

Model element	Members of the frozenset key	Anchor
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	Activity in an SBGN-AF map.
AndOperator	Logical AND operator.
AndOperatorLayout	Layout for AND operators.
BiologicalActivity	Biological activity.
BiologicalActivityLayout	Layout for biological activities.
Compartment	Compartment in an SBGN-AF map.
CompartmentLayout	Layout for compartments.
ComplexUnitOfInformation	Unit of information typing a biological activity as a complex.
ComplexUnitOfInformationLayout	Layout for complex units of information.
DelayOperator	Logical DELAY operator.
DelayOperatorLayout	Layout for DELAY operators.
EquivalenceArcLayout	Layout for equivalence arcs.
Influence	Influence between activities.
LogicArcLayout	Layout for logic arcs.
LogicalOperator	Logical operator.
LogicalOperatorInput	Input to a logical operator.
MacromoleculeUnitOfInformation	Unit of information typing a biological activity as a macromolecule.
MacromoleculeUnitOfInformationLayout	Layout for macromolecule units of information.
NecessaryStimulation	Necessary stimulation.
NecessaryStimulationLayout	Layout for necessary stimulations.
NegativeInfluence	Negative (inhibiting) influence.
NegativeInfluenceLayout	Layout for negative influences.
NotOperator	Logical NOT operator.
NotOperatorLayout	Layout for NOT operators.
NucleicAcidFeatureUnitOfInformation	Unit of information typing a biological activity as a nucleic acid feature.
NucleicAcidFeatureUnitOfInformationLayout	Layout for nucleic acid feature units of information.
OrOperator	Logical OR operator.
OrOperatorLayout	Layout for OR operators.
PerturbationUnitOfInformation	Unit of information typing a biological activity as a perturbation.
PerturbationUnitOfInformationLayout	Layout for perturbation units of information.
Phenotype	Phenotype activity.
PhenotypeLayout	Layout for phenotypes.
PositiveInfluence	Positive (stimulating) influence.
PositiveInfluenceLayout	Layout for positive influences.
SBGNAFLayout	SBGN-AF layout.
SBGNAFMap	SBGN-AF map.
SBGNAFModel	SBGN-AF model.
SimpleChemicalUnitOfInformation	Unit of information typing a biological activity as a simple chemical.
SimpleChemicalUnitOfInformationLayout	Layout for simple chemical units of information.
Submap	Submap element.
SubmapLayout	Layout for submaps.
Tag	Tag element.
TagLayout	Layout for tags.
TagReference	Reference to a tag.
Terminal	Terminal element.
TerminalLayout	Layout for terminals.
TerminalReference	Reference to a terminal.
UnitOfInformation	Unit of information for activities and compartments.
UnitOfInformationLayout	Class for unit of information layouts
UnknownInfluence	Influence of unspecified sign.
UnknownInfluenceLayout	Layout for unknown influences.
UnspecifiedEntityUnitOfInformation	Unit of information typing a biological activity as an unspecified entity.
UnspecifiedEntityUnitOfInformationLayout	Layout for unspecified entity units of information.

Activity dataclass

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

Bases: SBGNModelElement

Activity in an SBGN-AF map.

Activities represent biological activities or processes.

Attributes:

Name	Type	Description

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	'8d9ca32a-45df-438c-be7a-0aa9a4af2cfa'
label	str | None		None
compartment	Compartment | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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

Logical AND operator.

The output is active only when every input is active.

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	'266c5a05-6c29-46de-bc87-228b0c4ca609'
inputs	frozenset[LogicalOperatorInput]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, 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, direction: Direction = 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

Layout for AND 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	'95bb94dc-4773-4e9b-8c4d-de1a06905620'
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 width of the node	30.0
text	str		'AND'
font_family	str		'DejaVu Sans'
font_fill	Color | NoneValueType		Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType		<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
font_style	FontStyle		<FontStyle.NORMAL: 0>
font_weight	FontWeight | float		<FontWeight.NORMAL: 0>
direction	Direction		<Direction.HORIZONTAL: 1>
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

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x + self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y - self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y + self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x - self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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.

Represents a biological activity with associated units of information.

Attributes:

Name	Type	Description

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	'4a921d0d-ca3b-437f-becf-804cce8ff690'
label	str | None		None
compartment	Compartment | None		None
units_of_information	frozenset[UnitOfInformation]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0)

Bases: _SimpleMixin, SBGNNode

Layout for biological 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	'f475d054-edcc-4781-8439-55cc67d087c2'
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 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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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 in an SBGN-AF map.

Compartments represent distinct spatial regions where activities are located.

Attributes:

Name	Type	Description

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	'828435b0-be05-46dd-b826-feeb85c2eda9'
label	str | None		None
units_of_information	frozenset[UnitOfInformation]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 80.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 80.0, rounded_corners: float = 5.0, border_stroke_width: float | None = 3.25)

Bases: _SimpleMixin, SBGNNode

Layout for compartments.

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	'34cf0d83-1348-4b6d-a925-55c396bd8760'
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 | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float	The width width of the node	80.0
rounded_corners	float		5.0
border_stroke_width	float | None		3.25

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Unit of information typing a biological activity as a complex.

Rendered as an SBGN complex glyph embedded in the activity node.

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	'75344ec9-67ec-4947-baa6-c04a5a2de19b'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, cut_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Layout for complex 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	'a3cd5ec0-be2b-4aa4-8ba6-3c33874301d6'
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 width of the node	12.0
cut_corners	float		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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Logical DELAY operator.

The output mirrors the input after a delay; used to model time-shifted 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	'fdc9cd80-d4f8-43a4-8971-511e52f9a51c'
inputs	frozenset[LogicalOperatorInput]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, 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, direction: Direction = 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

Layout for DELAY 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	'17209f63-4599-4d6c-ad4c-7e8b06623318'
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 width of the node	30.0
text	str		'τ'
font_family	str		'DejaVu Sans'
font_fill	Color | NoneValueType		Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType		<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
font_style	FontStyle		<FontStyle.NORMAL: 0>
font_weight	FontWeight | float		<FontWeight.NORMAL: 0>
direction	Direction		<Direction.HORIZONTAL: 1>
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

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x + self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y - self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y + self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x - self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: SBGNSingleHeadedArc

Layout for equivalence arcs.

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	'05d2b5b4-3e62-486d-9431-f6dc454c4f2d'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.drawing_elements())

Influence dataclass

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

Bases: SBGNModelElement

Influence between activities.

Represents an influence from a source activity to a target activity.

Attributes:

Name	Type	Description

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	'efe6add0-eb6a-4947-815d-4c22374d02ae'
source	BiologicalActivity | LogicalOperator		required
target	Activity		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: SBGNSingleHeadedArc

Layout for logic arcs.

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	'4a2c6a39-155b-4951-9d71-e9c4ed7ebb92'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.drawing_elements())

LogicalOperator dataclass

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

Bases: SBGNModelElement

Logical operator.

Represents logical operations (AND, OR, NOT, DELAY) on activities.

Attributes:

Name	Type	Description

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	'38d10717-932e-4e00-9285-67326bc5f4ed'
inputs	frozenset[LogicalOperatorInput]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(), element: Union[BiologicalActivity, ForwardRef(LogicalOperator, module=modules[__name__])])

Bases: SBGNRole

Input to a logical operator.

Represents an input connection to a logical operator.

Attributes:

Name	Type	Description

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	'45367176-bcf4-4ed8-86fc-edf93ff841c5'
element	BiologicalActivity | ForwardRef		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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

Unit of information typing a biological activity as a macromolecule.

Rendered as an SBGN macromolecule glyph embedded in the activity node.

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	'c0a37493-3d5d-468c-bf82-79aa80bd7273'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, rounded_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Layout for macromolecule 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	'e07134ba-6144-40b1-9509-1e6d0203ff5c'
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 width of the node	12.0
rounded_corners	float		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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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.

The target requires the source to be active; without it the target cannot be active.

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	'8daec6d4-486d-457b-82b7-44ac796efb79'
source	BiologicalActivity | LogicalOperator		required
target	Activity		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, 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

Layout for necessary stimulations.

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	'3cd21fce-fc3c-4b33-973f-f55e3650d70d'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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		12.0
arrowhead_sep	float		3.0
arrowhead_triangle_height	float		10.0
arrowhead_triangle_width	float		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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.drawing_elements())

NegativeInfluence dataclass

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

Bases: Influence

Negative (inhibiting) influence.

The source decreases the activity of the target.

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	'996e3361-fcc1-4561-9b4b-1c45089a6079'
source	BiologicalActivity | LogicalOperator		required
target	Activity		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)

Bases: SBGNSingleHeadedArc

Layout for negative 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	'def0b7cb-0a27-491a-a54f-cf49ecfb797f'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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		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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.drawing_elements())

NotOperator dataclass

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

Bases: LogicalOperator

Logical NOT operator.

The output is active when its (single) input is inactive.

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	'b50cac62-096e-47b8-a3b3-967e41d37e09'
inputs	frozenset[LogicalOperatorInput]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, 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, direction: Direction = 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

Layout for NOT 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	'2f595ac9-b605-4318-b692-8f5b02e65c81'
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 width of the node	30.0
text	str		'NOT'
font_family	str		'DejaVu Sans'
font_fill	Color | NoneValueType		Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType		<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
font_style	FontStyle		<FontStyle.NORMAL: 0>
font_weight	FontWeight | float		<FontWeight.NORMAL: 0>
direction	Direction		<Direction.HORIZONTAL: 1>
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

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x + self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y - self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y + self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x - self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Unit of information typing a biological activity as a nucleic acid feature.

Rendered as an SBGN nucleic acid feature glyph embedded in the activity node.

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	'e7e03c2d-87c1-4818-886f-568993bc52ae'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, rounded_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Layout for nucleic acid feature 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	'a7f75974-ee1e-4c70-870f-66116ffacb0c'
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 width of the node	12.0
rounded_corners	float		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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Logical OR operator.

The output is active when at least one input is active.

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	'3584b3c6-1bd6-45df-87d6-1d802f2b2e68'
inputs	frozenset[LogicalOperatorInput]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, 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, direction: Direction = 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

Layout for OR 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	'88adf88a-40e8-46b1-b217-209ce2b794af'
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 width of the node	30.0
text	str		'OR'
font_family	str		'DejaVu Sans'
font_fill	Color | NoneValueType		Color(red=0, green=0, blue=0, alpha=1.0)
font_stroke	Color | NoneValueType		<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
font_style	FontStyle		<FontStyle.NORMAL: 0>
font_weight	FontWeight | float		<FontWeight.NORMAL: 0>
direction	Direction		<Direction.HORIZONTAL: 1>
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

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.Point:
    """Get the east (right) anchor point.

    Returns:
        Point on the east side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x + self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Get the base point of the left connector.

    Returns:
        Point where the left connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y - self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the left connector.

    Returns:
        Point at the end of the left connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the north (top) anchor point.

    Returns:
        Point on the north side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y - self.height / 2 - self.left_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.Point:
    """Get the base point of the right connector.

    Returns:
        Point where the right connector attaches to the shape.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x, self.y + self.height / 2)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the tip point of the right connector.

    Returns:
        Point at the end of the right connector line.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Get the south (bottom) anchor point.

    Returns:
        Point on the south side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(
            self.x, self.y + self.height / 2 + self.right_connector_length
        )
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.Point:
    """Get the west (left) anchor point.

    Returns:
        Point on the west side of the element.
    """
    if self.direction == momapy.core.elements.Direction.VERTICAL:
        return momapy.geometry.Point(self.x - self.width / 2, self.y)
    else:
        return momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Unit of information typing a biological activity as a perturbation.

Denotes an external influence (drug, stimulus, mutation) acting on the system.

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	'0683539b-23ac-4fb6-aa36-afc2c46f9984'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Layout for perturbation 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	'913579b1-2c1b-48da-99f6-215f1be172aa'
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 width of the node	12.0
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.	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 west 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) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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 activity.

Represents an observable characteristic of the system — a system-level outcome produced by the combination of biological activities rather than an individual activity itself.

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	'c38e7f34-a00a-4730-8380-8c797303ba4a'
label	str | None		None
compartment	Compartment | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 30.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Layout for phenotypes.

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	'e6091809-2682-467d-80c4-9b1c9412d4b5'
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 width of the node	60.0
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.	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 west 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) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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 (stimulating) influence.

The source increases the activity of the target.

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	'37f8fe09-f32a-48eb-a476-5005af13c394'
source	BiologicalActivity | LogicalOperator		required
target	Activity		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Layout for positive 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	'd4a235f7-64cb-4564-9f7c-f2f6ca61032d'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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		10.0
arrowhead_width	float		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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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.

Represents the visual layout of an 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	'308b6691-2d28-4eb3-8fbc-7454c18a8d7e'
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 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 west 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 another given layout is a sublayout of the 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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, flattened=False, unordered=False)

Return true if another given layout is a sublayout of the layout, false otherwise

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

def is_sublayout(self, other, flattened=False, unordered=False):
    """Return `true` if another given layout is a sublayout of the layout, `false` otherwise"""

    def _is_sublist(list1, list2, unordered=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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

SBGN-AF map.

Represents a complete SBGN Activity Flow map with model and layout.

Attributes:

Name	Type	Description

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	'99cb6672-aa75-41a2-9f35-a1092989067b'
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 layout elements mapped to the given model element
is_submap	Return true if another given map is a submap of the Map, false otherwise

get_mapping

get_mapping(map_element: MapElement)

Return the layout elements mapped to the given model element

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

def get_mapping(
    self,
    map_element: "MapElement",
):
    """Return the layout elements mapped to the given model element"""
    return self.layout_model_mapping.get_mapping(map_element)

is_submap

is_submap(other)

Return true if another given map is a submap of the Map, false otherwise

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

def is_submap(self, other):
    """Return `true` if another given map is a submap of the `Map`, `false` otherwise"""
    if (
        self.model is None
        or self.layout is None
        or self.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.

Represents a complete SBGN Activity Flow model.

Attributes:

Name	Type	Description

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	'1a038c0a-9a3b-48c6-ae18-9f64fb358853'
activities	frozenset[Activity]	Build an immutable unordered collection of unique elements.	<dynamic>
compartments	frozenset[Compartment]	Build an immutable unordered collection of unique elements.	<dynamic>
influences	frozenset[Influence]	Build an immutable unordered collection of unique elements.	<dynamic>
logical_operators	frozenset[LogicalOperator]	Build an immutable unordered collection of unique elements.	<dynamic>
submaps	frozenset[Submap]	Build an immutable unordered collection of unique elements.	<dynamic>
tags	frozenset[Tag]	Build an immutable unordered collection of unique elements.	<dynamic>

Methods:

Name	Description
descendants	Return every ModelElement reachable from this Model.
is_submodel	Check if another model is a submodel of this model.

descendants

descendants() -> list[ModelElement]

Return every ModelElement reachable from this Model.

Walks 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.

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`.

    Walks 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.

    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 another model is a submodel of this model.

Parameters:

Name	Type	Description	Default
other	SBGNAFModel	Another SBGN-AF model to compare against.	required

Returns:

Type	Description
bool	True if other is a submodel of this model, False otherwise.

Source code in src/momapy/sbgn/af/model.py

def is_submodel(self, other: "SBGNAFModel") -> bool:
    """Check if another model is a submodel of this model.

    Args:
        other: Another SBGN-AF model to compare against.

    Returns:
        True if other is a submodel of this model, 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

Unit of information typing a biological activity as a simple chemical.

Rendered as an SBGN simple chemical glyph embedded in the activity node.

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	'481b0540-398b-452d-9590-6e09df6510e9'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Layout for simple chemical 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	'f5fc51e7-bb7b-4c11-942b-b76dbb5829c0'
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 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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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 element.

Submaps represent embedded or referenced sub-diagrams.

Attributes:

Name	Type	Description

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	'41ef7cfe-317a-4723-9e41-b8df68bb9cb4'
label	str | None		None
terminals	frozenset[Terminal]	Build an immutable unordered collection of unique elements.	<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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 80.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 80.0, border_stroke_width: float | None = 2.25)

Bases: _SimpleMixin, SBGNNode

Layout for submaps.

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	'f5f60a5a-b27e-4242-8644-f4ee8d95e361'
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 | None	The stroke width of the node	1.25
transform	NoneValueType | tuple[Transformation] | None	The transform of the node	None
width	float	The width width of the node	80.0
border_stroke_width	float | None		2.25

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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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, refers_to: TagReference | None = None)

Bases: SBGNModelElement

Tag element.

Tags provide identifiers that can be referenced from other locations.

Attributes:

Name	Type	Description

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	'c595a574-9c7d-47da-b1c1-6f0c5588eaf8'
label	str | None		None
refers_to	TagReference | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 35.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: TagLayout

Layout for tags.

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	'99c43830-0754-4dc3-9c72-07d4d999370c'
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 width of the node	35.0
direction	Direction		<Direction.RIGHT: 4>
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.	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 west 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) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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(), element: Activity | Compartment)

Bases: SBGNRole

Reference to a tag.

Attributes:

Name	Type	Description

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	'ecae9604-c540-40d9-b636-1c67d78d9c51'
element	Activity | Compartment		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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, refers_to: TerminalReference | None = None)

Bases: SBGNModelElement

Terminal element.

Terminals represent connection points to submaps.

Attributes:

Name	Type	Description

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	'c2c6a30b-6ec0-4462-b372-00aab7982274'
label	str | None		None
refers_to	TerminalReference | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 35.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Layout for terminals.

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	'b2930a7d-8394-4034-80be-b03ec3fb6ba6'
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 width of the node	35.0
direction	Direction		<Direction.RIGHT: 4>
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.	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 west 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) -> momapy.geometry.Point:
    """Return an anchor point of the layout element"""
    return getattr(self, anchor_name)()

angle class-attribute instance-attribute

angle: float = 70.0

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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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(), element: Activity | Compartment)

Bases: SBGNRole

Reference to a terminal.

Attributes:

Name	Type	Description

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	'395384aa-2b36-4ff8-851f-0b4a2718e810'
element	Activity | Compartment		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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: SBGNModelElement

Unit of information for activities and compartments.

Units of information provide additional information about activities or compartments.

Attributes:

Name	Type	Description

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	'31db5f8b-81ad-45e5-a837-b13967184c36'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Class for unit of information layouts

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	'9f1563df-d65e-426b-ace7-8f6ffabfc87f'
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 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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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

Influence of unspecified sign.

Used when the regulatory effect of the source on the target is not known.

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	'8630041c-eb94-40b0-9805-1770505c22c3'
source	BiologicalActivity | LogicalOperator		required
target	Activity		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, arrowhead_fill: NoneValueType | Color | None = white, arrowhead_stroke: NoneValueType | Color | None = black, arrowhead_stroke_width: float | None = 1.25, *, 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_filter: NoneValueType | Filter | None = None, path_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, path_stroke_dashoffset: NoneValueType | float | None = None, 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_filter: NoneValueType | Filter | None = None, arrowhead_stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: NoneValueType | float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Layout for unknown 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	'8f367a75-bed2-4275-b3ec-20298deb7962'
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 fill filter of the arc	None
path_fill	NoneValueType | Color | None	The path fill color of the arc	<momapy.drawing.NoneValueType object at 0x7fbe12e88d70>
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		10.0
arrowhead_width	float		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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Bbox:
    """Return the bounding box of the single-headed arc arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.arrowhead_drawing_elements()
    )

arrowhead_border

arrowhead_border(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) -> momapy.geometry.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 = momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the single-headed arc arrowhead"""
    drawing_elements = self._arrowhead_border_drawing_elements()
    group = momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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

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

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

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

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

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

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

Return the total length of the arc path

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

def length(self):
    """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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the single-headed arc"""
    drawing_elements = (
        self.path_drawing_elements() + self.arrowhead_drawing_elements()
    )
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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[momapy.drawing.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 = [
            momapy.drawing.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 = [
            momapy.drawing.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 = momapy.drawing.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

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

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

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

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.drawing_elements())

UnspecifiedEntityUnitOfInformation dataclass

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

Bases: UnitOfInformation

Unit of information typing a biological activity as an unspecified entity.

Used when the underlying entity class is unknown or deliberately abstract.

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	'28032779-72ca-4d3b-aa55-724f264fb270'
label	str | None		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.

Walks scalar ModelElement fields and frozenset/tuple containers, deduplicating by object identity.

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`.

    Walks scalar `ModelElement` fields and `frozenset`/`tuple`
    containers, deduplicating by object identity.

    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(fill: NoneValueType | Color | None = white, stroke: NoneValueType | Color | None = black, stroke_width: float | None = 1.25, *, 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, filter: NoneValueType | Filter | None = None, height: float = 12.0, label: TextLayout | None = None, position: Point, stroke_dasharray: NoneValueType | tuple[float, ...] | None = None, stroke_dashoffset: NoneValueType | float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Layout for unspecified entity 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	'a00b50f6-590e-4172-aefc-5f3c96bf1080'
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 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 west 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) -> momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 = momapy.geometry.Bbox(
        momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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

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

def descendants(self) -> list["LayoutElement"]:
    """Return the descendants of the layout element"""
    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[momapy.drawing.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 = momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the east north east anchor of the node"""
    line = momapy.geometry.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 west anchor of the node

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

def east_south_east(self) -> momapy.geometry.Point:
    """Return the east south east west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the north west anchor of the node"""
    line = momapy.geometry.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",
) -> momapy.geometry.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 momapy.drawing.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) -> momapy.geometry.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 momapy.geometry.Bbox(momapy.geometry.Point(0, 0), 0, 0)
    bboxes = [p.bbox() for p in primitives]
    return momapy.geometry.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: momapy.geometry.Point) -> momapy.geometry.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 momapy.drawing.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[momapy.drawing.DrawingElement]:
    """Return the node's own drawing elements"""
    drawing_elements = self._border_drawing_elements()
    group = momapy.drawing.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the self drawing elements."""
    return momapy.drawing.drawing_elements_to_geometry(self.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south east anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south south west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the south west anchor of the node"""
    line = momapy.geometry.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[
    momapy.geometry.Segment
    | momapy.geometry.QuadraticBezierCurve
    | momapy.geometry.CubicBezierCurve
    | momapy.geometry.EllipticalArc
]:
    """Return a list of geometry primitives from the drawing elements."""
    return momapy.drawing.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) -> momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west north west anchor of the node"""
    line = momapy.geometry.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) -> momapy.geometry.Point:
    """Return the west south west anchor of the node"""
    line = momapy.geometry.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