2.1.3. biggr_maps.map

Classes

Map
TextLabel
Node
MetaboliteNode
MultiMarkerNode
MidMarkerNode
Segment
Reaction
PlacementOptions
AutoReaction
AutoReactionWithOptionalMetabolites

Functions

node_from_dict(→ Node)
cubic_bezier_bt(t, b0, b1, b2, b3)
non_primary_scaling(x)
default_text_offset(x)

Module Contents

class biggr_maps.map.Map(name: str, description: str, homepage: str | None = None, schema: str | None = None, canvas: Tuple[float, float, float, float] | None = None)

name

description

homepage = None

schema = None

reactions

nodes

segments

labels

canvas = None

add_node(node: Node | None)

add_segment(segment: Segment)

add_reaction(reaction: Reaction)

add_label(label: TextLabel)

fit_canvas(spacing: float = 100, expand_only=False)

to_escher()

class biggr_maps.map.TextLabel(x: float, y: float, text: str)

identifier = None

x

y

text

to_escher()

class biggr_maps.map.Node(x: float | None = None, y: float | None = None)

identifier = None

node_type = None

x = None

y = None

to_escher()

copy()

class biggr_maps.map.MetaboliteNode(bigg_id: str, name: str, x: float | None = None, y: float | None = None, label_x: float | None = None, label_y: float | None = None, node_is_primary: bool = False)

Bases: Node

node_type = 'metabolite'

bigg_id

name

label_x = None

label_y = None

node_is_primary = False

class biggr_maps.map.MultiMarkerNode(x: float, y: float)

Bases: Node

node_type = 'multimarker'

class biggr_maps.map.MidMarkerNode(x: float, y: float)

Bases: Node

node_type = 'midmarker'

class biggr_maps.map.Segment(from_node: Node, to_node: Node, b1: Tuple[float, float] | None = None, b2: Tuple[float, float] | None = None)

identifier = None

from_node

to_node

b1 = None

b2 = None

to_escher()

biggr_maps.map.node_from_dict(d: Dict[str, Any]) → Node

class biggr_maps.map.Reaction(name: str, bigg_id: str, label_x: float, label_y: float, mid_marker: MidMarkerNode, plus_multi_marker: MultiMarkerNode | None, minus_multi_marker: MultiMarkerNode | None, reversibility: bool = True, gene_reaction_rule: str | None = None, genes: List[Dict[str, str]] | None = None)

identifier = None

name

bigg_id

label_x

label_y

reversibility = True

mid_marker

multi_markers

metabolites = []

segments = []

gene_reaction_rule = None

genes = None

add_segment(segment: Segment)

add_metabolite(node: MetaboliteNode, coefficient: float | int)

to_escher()

biggr_maps.map.cubic_bezier_bt(t, b0, b1, b2, b3)

biggr_maps.map.non_primary_scaling(x)

biggr_maps.map.default_text_offset(x)

class biggr_maps.map.PlacementOptions(delta=math.pi * 0.15, delta_tolerance=0.5, no_primary_length_f=None, scale=3.0, b1_scale=0.3, b2_scale=0.8, text_y_correction=6, text_offset_f=None, placement_f=None)

delta = 0.47123889803846897

delta_tolerance = 0.5

scale = 3.0

b1_scale = 0.3

b2_scale = 0.8

text_y_correction = 6

placement_f = None

class biggr_maps.map.AutoReaction(bigg_id: str, mid_marker: MidMarkerNode, angle: float, unit: float = 50, text_y_correction: float = 8, label_x: float | None = None, label_y: float | None = None, minus_multi_marker: MultiMarkerNode | MidMarkerNode | None = None, plus_multi_marker: MultiMarkerNode | MidMarkerNode | None = None, **kwargs)

Bases: Reaction

angle

unit = 50

alternating_side_placement(i, delta, plus_minus)

same_side_placement(n, delta, plus_minus, absolute_side=0)

calculate_placement(ref_node, node, plus_minus, angle_delta, n, b1_b2, placement_opts)

add_metabolite(node: MetaboliteNode, coefficient: float | int, b1_b2: Tuple[float | None, float | None] | None = None, placement_opts=None)

class biggr_maps.map.AutoReactionWithOptionalMetabolites(*args, **kwargs)

Bases: AutoReaction

optional_metabolites

finalized = False

add_optional_metabolite(node: MetaboliteNode, coefficient: float, b1_b2: Tuple[float | None, float | None] | None)