stonpy.sbgn module

class stonpy.sbgn.Arc(id=None, clazz=None, source=None, target=None, start=None, end=None, nexts=None, glyphs=None, ports=None)

Bases: object

add_glyph(glyph)

add_next(next_)

add_port(port)

property cardinality

to_tuple()

class stonpy.sbgn.ArcClass(value)

Bases: Enum

Enumeration with all possible values for the class attribute of Arcs in SBGN-ML.

ABSOLUTE_INHIBITION = 'absolute inhibition'

ABSOLUTE_STIMULATION = 'absolute stimulation'

ASSIGNMENT = 'assignment'

CATALYSIS = 'catalysis'

CONSUMPTION = 'consumption'

EQUIVALENCE_ARC = 'equivalence arc'

INHIBITION = 'inhibition'

INTERACTION = 'interaction'

LOGIC_ARC = 'logic arc'

MODULATION = 'modulation'

NECESSARY_STIMULATION = 'necessary stimulation'

NEGATIVE_INFLUENCE = 'negative influence'

POSITIVE_INFLUENCE = 'positive influence'

PRODUCTION = 'production'

STIMULATION = 'stimulation'

UNKNOWN_INFLUENCE = 'unknown influence'

class stonpy.sbgn.ArcPoint(x=None, y=None, points=None)

Bases: Point

add_point(point)

class stonpy.sbgn.Arcgroup(value)

Bases: Enum

Enumeration with all possible values for the class attribute of Arcs in SBGN-ML.

INTERACTION = 'interaction'

class stonpy.sbgn.Bbox(x=None, y=None, w=None, h=None)

Bases: object

to_tuple()

class stonpy.sbgn.Clone(label=None)

Bases: object

to_tuple()

class stonpy.sbgn.End(x=None, y=None, points=None)

Bases: ArcPoint

class stonpy.sbgn.Glyph(id=None, clazz=None, label=None, clone=None, bbox=None, orientation=None, glyphs=None, ports=None, compartmentRef=None, compartmentOrder=None, entity=None)

Bases: object

add_glyph(glyph)

add_port(port)

property subunits

property svs

property tags

to_tuple()

property uis

class stonpy.sbgn.GlyphClass(value)

Bases: Enum

Enumeration with all possible values for the class attribute of Glyphs in SBGN-ML. This includes both top-level glyphs and sub-glyphs.

AND = 'and'

ANNOTATION = 'annotation'

ASSOCIATION = 'association'

BIOLOGICAL_ACTIVITY = 'biological activity'

CARDINALITY = 'cardinality'

COMPARTMENT = 'compartment'

COMPLEX = 'complex'

COMPLEX_MULTIMER = 'complex multimer'

DELAY = 'delay'

DISSOCIATION = 'dissociation'

ENTITY = 'entity'

EXISTENCE = 'existence'

IMPLICIT_XOR = 'implicit xor'

INTERACTION = 'interaction'

LOCATION = 'location'

MACROMOLECULE = 'macromolecule'

MACROMOLECULE_MULTIMER = 'macromolecule multimer'

NOT = 'not'

NUCLEIC_ACID_FEATURE = 'nucleic acid feature'

NUCLEIC_ACID_FEATURE_MULTIMER = 'nucleic acid feature multimer'

OBSERVABLE = 'observable'

OMITTED_PROCESS = 'omitted process'

OR = 'or'

OUTCOME = 'outcome'

PERTURBATION = 'perturbation'

PERTURBING_AGENT = 'perturbing agent'

PHENOTYPE = 'phenotype'

PROCESS = 'process'

SIMPLE_CHEMICAL = 'simple chemical'

SIMPLE_CHEMICAL_MULTIMER = 'simple chemical multimer'

SOURCE_AND_SINK = 'source and sink'

STATE_VARIABLE = 'state variable'

STOICHIOMETRY = 'stoichiometry'

SUBMAP = 'submap'

TAG = 'tag'

TERMINAL = 'terminal'

UNCERTAIN_PROCESS = 'uncertain process'

UNIT_OF_INFORMATION = 'unit of information'

UNSPECIFIED_ENTITY = 'unspecified entity'

VARIABLE_VALUE = 'variable value'

class stonpy.sbgn.Label(text=None, bbox=None)

Bases: object

to_tuple()

class stonpy.sbgn.Language(value)

Bases: Enum

Enum representing the three languages of SBGN.

AF = 'activity flow'

ER = 'entity relationship'

PD = 'process description'

class stonpy.sbgn.Map(id=None, language=None, glyphs=None, arcs=None, arcgroups=None)

Bases: object

add_arc(arc)

add_arcgroup(arcgroup)

add_glyph(glyph)

to_tuple()

class stonpy.sbgn.Next(x=None, y=None, points=None)

Bases: ArcPoint

class stonpy.sbgn.Orientation(value)

Bases: Enum

An enumeration.

DOWN = 'down'

HORIZONTAL = 'horizontal'

LEFT = 'left'

RIGHT = 'right'

UP = 'up'

VERTICAL = 'vertical'

class stonpy.sbgn.Point(x=None, y=None)

Bases: object

to_tuple()

class stonpy.sbgn.Port(id=None, x=None, y=None, owner=None)

Bases: Point

class stonpy.sbgn.Start(x=None, y=None, points=None)

Bases: ArcPoint

stonpy.sbgn.cast_arc(old, dids)

stonpy.sbgn.cast_arcgroup(old, dids)

stonpy.sbgn.cast_bbox(old)

stonpy.sbgn.cast_clone(old)

stonpy.sbgn.cast_end(old)

stonpy.sbgn.cast_glyph(old, dids)

stonpy.sbgn.cast_label(old)

stonpy.sbgn.cast_map(old)

stonpy.sbgn.cast_next(old)

stonpy.sbgn.cast_point(old)

stonpy.sbgn.cast_port(old)

stonpy.sbgn.cast_start(old)

stonpy.sbgn.read(file_name)