Core

momapy.sbgn.core

Base classes defining core SBGN map elements

Classes:

Name	Description
`SBGNAuxiliaryUnit`	Base class for SBGN auxiliary units
`SBGNDoubleHeadedArc`	Base class for SBGN double-headed arcs
`SBGNLayout`	Base class for SBGN layouts
`SBGNMap`	Base class for SBGN maps
`SBGNModel`	Base class for SBGN models
`SBGNModelElement`	Base class for SBGN model elements
`SBGNNode`	Base class for SBGN nodes
`SBGNRole`	Base class for SBGN roles
`SBGNSingleHeadedArc`	Base class for SBGN single-headed arcs

SBGNAuxiliaryUnit `dataclass`

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

Bases: SBGNModelElement

Base class for SBGN auxiliary units

SBGNDoubleHeadedArc `dataclass`

SBGNDoubleHeadedArc(path_fill: NoneValueType | Color | None = NoneValue, path_stroke: NoneValueType | Color | None = black, path_stroke_width: float | None = 1.25, end_arrowhead_fill: NoneValueType | Color | None = white, end_arrowhead_stroke: NoneValueType | Color | None = black, end_arrowhead_stroke_width: float | None = 1.25, start_arrowhead_fill: NoneValueType | Color | None = white, start_arrowhead_stroke: NoneValueType | Color | None = black, start_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, end_arrowhead_filter: NoneValueType | Filter | None = None, end_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, end_arrowhead_stroke_dashoffset: float | None = None, end_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None, start_arrowhead_filter: NoneValueType | Filter | None = None, start_arrowhead_stroke_dasharray: tuple[float, ...] | None = None, start_arrowhead_stroke_dashoffset: float | None = None, start_arrowhead_transform: NoneValueType | tuple[Transformation] | None = None)

Bases: DoubleHeadedArc

Base class for SBGN double-headed arcs

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
`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_arrowhead_base`	Return the base anchor point of the double-headed arc end arrowhead
`end_arrowhead_bbox`	Return the bounding box of the double-headed arc start arrowhead
`end_arrowhead_border`	Return the point at the intersection of the drawing elements of the double-headed arc end arrowhead and the line going through the center of these drawing elements and the given point.
`end_arrowhead_length`	Return the length of the double-headed arc end arrowhead
`end_arrowhead_tip`	Return the tip anchor point of the double-headed arc end arrowhead
`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 double-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 double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead
`self_to_shapely`	Compute and return a shapely collection of geometries reproducing the self drawing elements of the group layout
`start_arrowhead_base`	Return the base anchor point of the double-headed arc start arrowhead
`start_arrowhead_bbox`	Return the bounding box of the double-headed arc start arrowhead
`start_arrowhead_border`	Return the point at the intersection of the drawing elements of the double-headed arc start arrowhead and the line going through the center of these drawing elements and the given point.
`start_arrowhead_drawing_elements`	Return the drawing elements of the double-headed arc start arrowhead
`start_arrowhead_length`	Return the length of the double-headed arc start arrowhead
`start_arrowhead_tip`	Return the tip anchor point of the double-headed arc start arrowhead
`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)()

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_arrowhead_base

end_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc end arrowhead"""
    arrowhead_length = self.end_arrowhead_length()
    if arrowhead_length == 0:
        return self.end_point()
    segment = self.segments[-1]
    segment_length = segment.length()
    if segment_length == 0:
        return self.end_arrowhead_tip() - (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.end_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

end_arrowhead_bbox

end_arrowhead_bbox()

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def end_arrowhead_bbox(self):
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.end_arrowhead_drawing_elements()
    )

end_arrowhead_border

end_arrowhead_border(point)

Return the point at the intersection of the drawing elements of the double-headed arc end 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 end_arrowhead_border(self, point):
    """Return the point at the intersection of the drawing elements of the double-headed arc end 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.end_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.end_arrowhead_tip()
    return point

end_arrowhead_length

end_arrowhead_length() -> float

Return the length of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc end arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._end_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return bbox.east().x

end_arrowhead_tip

end_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc end arrowhead

Source code in src/momapy/core.py

def end_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc end arrowhead"""
    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)

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 double-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 double-headed arc path"""
    start_arrowhead_length = self.start_arrowhead_length()
    end_arrowhead_length = self.end_arrowhead_length()
    if len(self.segments) == 1:
        segment = (
            self.segments[0]
            .shortened(self.start_shorten + start_arrowhead_length, "start")
            .shortened(self.end_shorten + end_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_arrowhead_length, "start"
        )
        last_segment = self.segments[-1].shortened(
            self.end_shorten + end_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 double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead

Source code in src/momapy/core.py

def self_drawing_elements(self) -> list[momapy.drawing.DrawingElement]:
    """Return the self drawing elements of the double-headed arc. These include the drawing elements of the arc path, the start arrowhead, and the end arrowhead"""
    drawing_elements = (
        self.path_drawing_elements()
        + self.start_arrowhead_drawing_elements()
        + self.end_arrowhead_drawing_elements()
    )

    group = momapy.drawing.Group(
        class_=type(self).__name__,
        elements=tuple(drawing_elements),
        id_=self.id_,
        fill=self.fill,
        filter=self.filter,
        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_arrowhead_base

start_arrowhead_base() -> Point

Return the base anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_base(self) -> momapy.geometry.Point:
    """Return the base anchor point of the double-headed arc start arrowhead"""
    arrowhead_length = self.start_arrowhead_length()
    if arrowhead_length == 0:
        return self.start_point()
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return self.start_arrowhead_tip() + (arrowhead_length, 0)
    fraction = 1 - (arrowhead_length + self.start_shorten) / segment_length
    return segment.get_position_at_fraction(fraction)

start_arrowhead_bbox

start_arrowhead_bbox() -> Bbox

Return the bounding box of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_bbox(self) -> momapy.geometry.Bbox:
    """Return the bounding box of the double-headed arc start arrowhead"""
    return momapy.drawing.get_drawing_elements_bbox(
        self.start_arrowhead_drawing_elements()
    )

start_arrowhead_border

start_arrowhead_border(point) -> Point

Return the point at the intersection of the drawing elements of the double-headed arc start 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 start_arrowhead_border(self, point) -> momapy.geometry.Point:
    """Return the point at the intersection of the drawing elements of the double-headed arc start 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.start_arrowhead_drawing_elements(), point
    )
    if point.isnan():
        return self.start_arrowhead_tip()
    return point

start_arrowhead_drawing_elements

start_arrowhead_drawing_elements() -> list[DrawingElement]

Return the drawing elements of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_drawing_elements(
    self,
) -> list[momapy.drawing.DrawingElement]:
    """Return the drawing elements of the double-headed arc start arrowhead"""
    drawing_elements = self._start_arrowhead_border_drawing_elements()
    group = momapy.drawing.Group(
        class_=f"{type(self).__name__}_start_arrowhead",
        elements=tuple(drawing_elements),
        id_=f"{self.id_}_start_arrowhead",
        fill=self.start_arrowhead_fill,
        filter=self.start_arrowhead_filter,
        stroke=self.start_arrowhead_stroke,
        stroke_dasharray=self.start_arrowhead_stroke_dasharray,
        stroke_dashoffset=self.start_arrowhead_stroke_dashoffset,
        stroke_width=self.start_arrowhead_stroke_width,
        transform=self.start_arrowhead_transform,
    )
    transformation = self._get_start_arrowhead_transformation()
    group = group.transformed(transformation)
    return [group]

start_arrowhead_length

start_arrowhead_length() -> float

Return the length of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_length(self) -> float:
    """Return the length of the double-headed arc start arrowhead"""
    bbox = momapy.drawing.get_drawing_elements_bbox(
        self._start_arrowhead_border_drawing_elements()
    )
    if math.isnan(bbox.width):
        return 0.0
    return abs(bbox.west().x)

start_arrowhead_tip

start_arrowhead_tip() -> Point

Return the tip anchor point of the double-headed arc start arrowhead

Source code in src/momapy/core.py

def start_arrowhead_tip(self) -> momapy.geometry.Point:
    """Return the tip anchor point of the double-headed arc start arrowhead"""
    segment = self.segments[0]
    segment = momapy.geometry.Segment(segment.p2, segment.p1)
    segment_length = segment.length()
    if segment_length == 0:
        return segment.p2
    fraction = 1 - self.start_shorten / segment_length
    return segment.get_position_at_fraction(fraction)

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)

SBGNLayout `dataclass`

SBGNLayout(*, 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: Layout

Base class for SBGN 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

SBGNMap `dataclass`

SBGNMap(*, id_: str = make_uuid4_as_str(), model: SBGNModel, layout: SBGNLayout, layout_model_mapping: LayoutModelMapping | None = None)

Bases: Map

Base class for SBGN 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)
    )

SBGNModel `dataclass`

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

Bases: Model

Base class for SBGN models

SBGNModelElement `dataclass`

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

Bases: ModelElement

Base class for SBGN model elements

SBGNNode `dataclass`

SBGNNode(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, 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)

Bases: Node

Base class for SBGN nodes

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

SBGNRole `dataclass`

SBGNRole(*, id_: str = make_uuid4_as_str(), element: SBGNModelElement)

Bases: SBGNModelElement

Base class for SBGN roles

SBGNSingleHeadedArc `dataclass`

SBGNSingleHeadedArc(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: SingleHeadedArc

Base class for SBGN single-headed arcs

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)

Core

momapy.sbgn.core

SBGNAuxiliaryUnit dataclass

SBGNDoubleHeadedArc dataclass

anchor_point

bbox

childless

children

contains

descendants

drawing_elements

end_arrowhead_base

end_arrowhead_bbox

end_arrowhead_border

end_arrowhead_length

end_arrowhead_tip

end_point

equals

flattened

fraction

length

path_drawing_elements

points

self_bbox

self_children

self_drawing_elements

self_to_shapely

start_arrowhead_base

start_arrowhead_bbox

start_arrowhead_border

start_arrowhead_drawing_elements

start_arrowhead_length

start_arrowhead_tip

start_point

to_shapely

SBGNLayout dataclass

anchor_point

angle

bbox

border

center

childless

children

contains

descendants

drawing_elements

east

east_north_east

east_south_east

equals

flattened

is_sublayout

label_center

north

north_east

north_north_east

north_north_west

north_west

self_angle

self_bbox

self_border

self_children

self_drawing_elements

self_to_shapely

size

south

south_east

south_south_east

south_south_west

south_west

to_shapely

west

west_north_west

west_south_west

x property

y property

SBGNMap dataclass

get_mapping

is_submap

SBGNModel dataclass

SBGNAuxiliaryUnit `dataclass`

SBGNDoubleHeadedArc `dataclass`

SBGNLayout `dataclass`

x `property`

y `property`

SBGNMap `dataclass`

SBGNModel `dataclass`

SBGNModelElement `dataclass`

SBGNNode `dataclass`

x `property`

y `property`

SBGNRole `dataclass`

SBGNSingleHeadedArc `dataclass`