AF

momapy.sbgn.af

Classes for SBGN AF maps

Classes:

Name	Description
Activity	Class for activities
AndOperator	Class for and operators
AndOperatorLayout	Class for and operator layouts
BiologicalActivity	Class for biological activities
BiologicalActivityLayout	Class for biological activity layouts
Compartment	Class for compartments
CompartmentLayout	Class for compartment layouts
ComplexUnitOfInformation	Class for complex units of information
ComplexUnitOfInformationLayout	Class for complex unit of information layouts
DelayOperator	Class for delay operators
DelayOperatorLayout	Class for delay operator layouts
EquivalenceArcLayout	Class for equivalence arc layouts
Influence	Class for influences
LogicArcLayout	Class for logic arc layouts
LogicalOperator	Class for logical operators
LogicalOperatorInput	Class for inputs of logical operators
MacromoleculeUnitOfInformation	Class for marcomolecule units of information
MacromoleculeUnitOfInformationLayout	Class for macromolecule unit of information layouts
NecessaryStimulation	Class for necessary stimulations
NecessaryStimulationLayout	Class for necessary stimulation layouts
NegativeInfluence	Class for negative influences
NegativeInfluenceLayout	Class for negative influence layouts
NotOperator	Class for not operators
NotOperatorLayout	Class for not operator layouts
NucleicAcidFeatureUnitOfInformation	Class for nucleic acid feature units of information
NucleicAcidFeatureUnitOfInformationLayout	Class for nucleic acid feature unit of information layouts
OrOperator	Class for or operators
OrOperatorLayout	Class for or operator layouts
PerturbationUnitOfInformation	Class for perturbation units of information
PerturbationUnitOfInformationLayout	Class for perturbation unit of information layouts
Phenotype	Class for phenotypes
PhenotypeLayout	Class for phenotype layouts
PositiveInfluence	Class for positive influences
PositiveInfluenceLayout	Class for positive influence layouts
SBGNAFLayout	Class for SBGN-AF layouts
SBGNAFMap	Class for SBGN-AF maps
SBGNAFModel	Class for SBGN-AF models
SimpleChemicalUnitOfInformation	Class for simple chemical units of information
SimpleChemicalUnitOfInformationLayout	Class for simple chemical unit of information layouts
Submap	Class for submaps
SubmapLayout	Class for submap layouts
Tag	Class for tags
TagLayout	Class for tag layouts
TagReference	Class for references of tags
Terminal	Class for terminals
TerminalLayout	Class for terminal layouts
TerminalReference	Class for references of terminals
UnitOfInformation	Base class for units of information
UnknownInfluence	Class for unknown influences
UnknownInfluenceLayout	Class for unknown influence layouts
UnspecifiedEntityUnitOfInformation	Class for unspecified entity units of information
UnspecifiedEntityUnitOfInformationLayout	Class for unspecified entity unit of information layouts

Attributes:

Name	Type	Description
SBGNAFLayoutBuilder		Class for SBGN-AF layout builders
SBGNAFMapBuilder		Class for SBGN-AF map builders
SBGNAFModelBuilder		Class for SBGN-AF model builders

Activity dataclass

Activity(*, id_: str = make_uuid4_as_str())

Bases: SBGNModelElement

Class for activities

AndOperator dataclass

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

Bases: LogicalOperator

Class for and operators

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, 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

Class for and operator layouts

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_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_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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size 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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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(), units_of_information: frozenset[UnitOfInformation] = frozenset())

Bases: Activity

Class for biological activities

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0)

Bases: _SimpleMixin, SBGNNode

Class for biological activity layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None)

Bases: SBGNModelElement

Class for compartments

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: 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

Class for compartment layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None)

Bases: UnitOfInformation

Class for complex units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, cut_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Class for complex unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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

Class for delay operators

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, 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

Class for delay operator layouts

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_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_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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size 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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: SBGNSingleHeadedArc

Class for equivalence arc layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

Influence dataclass

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

Bases: SBGNModelElement

Class for influences

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: SBGNSingleHeadedArc

Class for logic arc layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

LogicalOperator dataclass

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

Bases: SBGNModelElement

Class for logical operators

LogicalOperatorInput dataclass

LogicalOperatorInput(*, id_: str = make_uuid4_as_str(), element: Union[BiologicalActivity, LogicalOperator])

Bases: SBGNRole

Class for inputs of logical operators

MacromoleculeUnitOfInformation dataclass

MacromoleculeUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: Optional[str] = None)

Bases: UnitOfInformation

Class for marcomolecule units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, rounded_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Class for macromolecule unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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

Class for necessary stimulations

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: 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

Class for necessary stimulation layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

NegativeInfluence dataclass

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

Bases: Influence

Class for negative influences

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0)

Bases: SBGNSingleHeadedArc

Class for negative influence layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

NotOperator dataclass

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

Bases: LogicalOperator

Class for not operators

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, 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

Class for not operator layouts

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_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_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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size 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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None)

Bases: UnitOfInformation

Class for nucleic acid feature units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, rounded_corners: float = 5.0)

Bases: _SimpleMixin, SBGNNode

Class for nucleic acid feature unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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

Class for or operators

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 30.0, 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

Class for or operator layouts

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_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_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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
size	Return the size 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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None)

Bases: UnitOfInformation

Class for perturbation units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Class for perturbation unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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())

Bases: Activity

Class for phenotypes

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 60.0, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Class for phenotype layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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

Class for positive influences

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Class for positive influence layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float)

Bases: SBGNLayout

Class for SBGN-AF layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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

SBGNAFLayoutBuilder module-attribute

SBGNAFLayoutBuilder = get_or_make_builder_cls(SBGNAFLayout)

Class for SBGN-AF layout builders

SBGNAFMap dataclass

SBGNAFMap(*, id_: str = make_uuid4_as_str(), model: Optional[SBGNAFModel] = None, layout: Optional[SBGNAFLayout] = None, layout_model_mapping: LayoutModelMapping | None = None)

Bases: SBGNMap

Class for SBGN-AF maps

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 | tuple[ModelElement, ModelElement])

Return the layout elements mapped to the given model element

Source code in src/momapy/core.py

def get_mapping(
    self,
    map_element: MapElement | tuple[ModelElement, ModelElement],
):
    """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.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)
    )

SBGNAFMapBuilder module-attribute

SBGNAFMapBuilder = get_or_make_builder_cls(SBGNAFMap, builder_namespace={'new_model': _sbgnaf_map_builder_new_model, 'new_layout': _sbgnaf_map_builder_new_layout})

Class for SBGN-AF map builders

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

Class for SBGN-AF models

Methods:

Name	Description
is_submodel	Return true if the another given SBGN-AF model is a submodel of the SBGN-AF model, false otherwise

is_submodel

is_submodel(other: SBGNAFModel) -> bool

Return true if the another given SBGN-AF model is a submodel of the SBGN-AF model, false otherwise

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

def is_submodel(self, other: "SBGNAFModel") -> bool:
    """Return `true` if the another given SBGN-AF model is a submodel of the SBGN-AF 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(other.submaps)
        and self.tags.issubset(other.tags)
    )

SBGNAFModelBuilder module-attribute

SBGNAFModelBuilder = get_or_make_builder_cls(SBGNAFModel)

Class for SBGN-AF model builders

SimpleChemicalUnitOfInformation dataclass

SimpleChemicalUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: Optional[str] = None)

Bases: UnitOfInformation

Class for simple chemical units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Class for simple chemical unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None, terminals: frozenset[Terminal] = frozenset())

Bases: SBGNModelElement

Class for submaps

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 80.0, border_stroke_width: float | None = 2.25)

Bases: _SimpleMixin, SBGNNode

Class for submap layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Optional[str] = None, refers_to: Optional[TagReference] = None)

Bases: SBGNModelElement

Class for tags

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: TagLayout

Class for tag layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Union[Activity, Compartment])

Bases: SBGNRole

Class for references of tags

Terminal dataclass

Terminal(*, id_: str = make_uuid4_as_str(), label: Optional[str] = None, refers_to: Optional[TerminalReference] = None)

Bases: SBGNModelElement

Class for terminals

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 35.0, direction: Direction = RIGHT, angle: float = 70.0)

Bases: _SimpleMixin, SBGNNode

Class for terminal layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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: Union[Activity, Compartment])

Bases: SBGNRole

Class for references of terminals

UnitOfInformation dataclass

UnitOfInformation(*, id_: str = make_uuid4_as_str(), label: Optional[str] = None)

Bases: SBGNModelElement

Base class for units of information

UnknownInfluence dataclass

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

Bases: Influence

Class for unknown influences

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, path_stroke_dashoffset: float | None = None, path_transform: NoneValueType | tuple[Transformation] | None = None, stroke: NoneValueType | Color | None = None, stroke_dasharray: NoneValueType | tuple[float] | None = None, stroke_dashoffset: float | None = None, stroke_width: float | None = None, segments: tuple[Segment | BezierCurve | 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: tuple[float, ...] | None = None, arrowhead_stroke_dashoffset: float | None = None, arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, arrowhead_height: float = 10.0, arrowhead_width: float = 10.0)

Bases: SBGNSingleHeadedArc

Class for unknown influence layouts

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
path_drawing_elements	Return the drawing elements of the single-headed arc path
points	Return the points of the arc path
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_children	Return the self children of the arc
self_drawing_elements	Return the self drawing elements of the single-headed arc
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
start_point	Return the starting point of the arc
to_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element

anchor_point

anchor_point(anchor_name: str) -> Point

Return an anchor point of the layout element

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

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.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.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.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.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
    position, angle = segment.get_position_and_angle_at_fraction(fraction)
    return position, angle

length

length()

Return the total length of the arc path

Source code in src/momapy/core.py

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

path_drawing_elements

path_drawing_elements() -> list[Path]

Return the drawing elements of the single-headed arc path

Source code in src/momapy/core.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.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

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_children

self_children() -> list[LayoutElement]

Return the self children of the arc

Source code in src/momapy/core.py

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

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the self drawing elements of the single-headed arc

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

start_point

start_point() -> Point

Return the starting point of the arc

Source code in src/momapy/core.py

def start_point(self) -> momapy.geometry.Point:
    """Return the starting point of the arc"""
    return self.points()[0]

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

UnspecifiedEntityUnitOfInformation dataclass

UnspecifiedEntityUnitOfInformation(*, id_: str = make_uuid4_as_str(), label: Optional[str] = None)

Bases: UnitOfInformation

Class for unspecified entity units of information

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: tuple[float, ...] | None = None, group_stroke_dashoffset: float | None = None, group_stroke_width: 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: tuple[float, ...] | None = None, stroke_dashoffset: float | None = None, transform: NoneValueType | tuple[Transformation] | None = None, width: float = 12.0)

Bases: _SimpleMixin, SBGNNode

Class for unspecified entity unit of information layouts

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
self_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.
self_bbox	Compute and return the bounding box of the self drawing element of the group layout
self_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.
self_children	Return the self children of the node. A node has unique child that is its label
self_drawing_elements	Return the node's own drawing elements
self_to_shapely	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
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_shapely	Return a shapely collection of geometries reproducing the drawing elements of the layout element
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.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

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.py

def angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.py

def bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the group layout element"""
    self_bbox = self.self_bbox()
    bboxes = [child.bbox() for child in self.children()]
    min_x = self_bbox.north_west().x
    min_y = self_bbox.north_west().y
    max_x = self_bbox.south_east().x
    max_y = self_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

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.py

def border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.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.py

def childless(self) -> typing.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 self_children method) and the other children of the group layout (given by the layout_elements attribute)

Source code in src/momapy/core.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 `self_children` method) and the other children of the group layout (given by the `layout_elements` attribute)
    """
    return self.self_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.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.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.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.self_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__}_group",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_group",
        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.py

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

east_north_east

east_north_east() -> Point

Return the east north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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.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.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.py

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

north_east

north_east() -> Point

Return the north east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

north_west

north_west() -> Point

Return the north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

self_angle

self_angle(angle: float, unit: Literal['degrees', 'radians'] = 'degrees') -> Point

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.py

def self_angle(
    self,
    angle: float,
    unit: typing.Literal["degrees", "radians"] = "degrees",
) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        angle=angle,
        unit=unit,
        center=self.center(),
    )

self_bbox

self_bbox() -> Bbox

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

Source code in src/momapy/core.py

def self_bbox(self) -> momapy.geometry.Bbox:
    """Compute and return the bounding box of the self drawing element of the group layout"""
    bounds = self.self_to_shapely().bounds
    return momapy.geometry.Bbox.from_bounds(bounds)

self_border

self_border(point: Point) -> Point

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.py

def self_border(self, point: momapy.geometry.Point) -> momapy.geometry.Point:
    """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.self_drawing_elements(),
        point=point,
        center=self.center(),
    )

self_children

self_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.py

def self_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 []

self_drawing_elements

self_drawing_elements() -> list[DrawingElement]

Return the node's own drawing elements

Source code in src/momapy/core.py

def self_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_=type(self).__name__,
        elements=tuple(drawing_elements),
        fill=self.fill,
        filter=self.filter,
        id_=self.id_,
        stroke=self.stroke,
        stroke_dasharray=self.stroke_dasharray,
        stroke_dashoffset=self.stroke_dashoffset,
        stroke_width=self.stroke_width,
        transform=self.transform,
    )
    return [group]

self_to_shapely

self_to_shapely() -> GeometryCollection

Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout

Source code in src/momapy/core.py

def self_to_shapely(self) -> shapely.GeometryCollection:
    """Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout"""
    return momapy.drawing.drawing_elements_to_shapely(self.drawing_elements())

size

size() -> tuple[float, float]

Return the size of the node

Source code in src/momapy/core.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.py

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

south_east

south_east() -> Point

Return the south east anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

south_west

south_west() -> Point

Return the south west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_angle(angle, unit="radians")

to_shapely

to_shapely(to_polygons: bool = False) -> GeometryCollection

Return a shapely collection of geometries reproducing the drawing elements of the layout element

Source code in src/momapy/core.py

def to_shapely(self, to_polygons: bool = False) -> shapely.GeometryCollection:
    """Return a shapely collection of geometries reproducing the drawing elements of the layout element"""
    geom_collection = []
    for drawing_element in self.drawing_elements():
        geom_collection += drawing_element.to_shapely(to_polygons=to_polygons).geoms
    return shapely.GeometryCollection(geom_collection)

west

west() -> Point

Return the west anchor of the node

Source code in src/momapy/core.py

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

west_north_west

west_north_west() -> Point

Return the west north west anchor of the node

Source code in src/momapy/core.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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.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 = -momapy.geometry.get_angle_to_horizontal_of_line(line)
    return self.self_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