sbmlutils.layout.layout

Utilities for the creation and work with layout models.

Module Contents

Classes

SpeciesGlyph	SpeciesGlyph.
CompartmentGlyph	CompartmentGlyph.
ReactionGlyph	ReactionGlyph.
Layout	Layout.

Attributes

LAYOUT_VERSION
LAYOUT_ROLE_SUBSTRATE
LAYOUT_ROLE_PRODUCT
LAYOUT_ROLE_SIDESUBSTRATE
LAYOUT_ROLE_SIDEPRODUCT
LAYOUT_ROLE_MODIFIER
LAYOUT_ROLE_ACTIVATOR
LAYOUT_ROLE_INHIBITOR
LAYOUT_ROLE_UNDEFINED

sbmlutils.layout.layout.LAYOUT_VERSION = 1

sbmlutils.layout.layout.LAYOUT_ROLE_SUBSTRATE = 'substrate'

sbmlutils.layout.layout.LAYOUT_ROLE_PRODUCT = 'product'

sbmlutils.layout.layout.LAYOUT_ROLE_SIDESUBSTRATE = 'sidesubstrate'

sbmlutils.layout.layout.LAYOUT_ROLE_SIDEPRODUCT = 'sideproduct'

sbmlutils.layout.layout.LAYOUT_ROLE_MODIFIER = 'modifier'

sbmlutils.layout.layout.LAYOUT_ROLE_ACTIVATOR = 'activator'

sbmlutils.layout.layout.LAYOUT_ROLE_INHIBITOR = 'inhibitor'

sbmlutils.layout.layout.LAYOUT_ROLE_UNDEFINED = 'undefined'

class sbmlutils.layout.layout.SpeciesGlyph(sid, species, x, y, z=0, w=50, h=20, d=0, text=None, name=None, sboTerm=None, metaId=None)

Bases: sbmlutils.factory.Sbase

SpeciesGlyph.

Parameters:

• sid (str) –

• species (str) –

• x (float) –

• y (float) –

• z (float) –

• w (float) –

• h (float) –

• d (float) –

• text (Optional[str]) –

• name (Optional[str]) –

• sboTerm (Optional[str]) –

• metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)

Set fields.

Parameters:

• obj (libsbml.SpeciesGlyph) –

• layout (libsbml.Layout) –

• model (libsbml.Model) –

Return type:

None

class sbmlutils.layout.layout.CompartmentGlyph(sid, compartment, x, y, z=0, w=200, h=200, d=0, text=None, name=None, sboTerm=None, metaId=None)

Bases: sbmlutils.factory.Sbase

CompartmentGlyph.

Parameters:

• sid (str) –

• compartment (str) –

• x (float) –

• y (float) –

• z (float) –

• w (float) –

• h (float) –

• d (float) –

• text (Optional[str]) –

• name (Optional[str]) –

• sboTerm (Optional[str]) –

• metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)

Set fields.

Parameters:

• obj (libsbml.SpeciesGlyph) –

• layout (libsbml.Layout) –

• model (libsbml.Model) –

Return type:

None

class sbmlutils.layout.layout.ReactionGlyph(sid, reaction, x, y, z=0, species_glyphs=None, w=20, h=20, d=0, text=None, name=None, sboTerm=None, metaId=None)

Bases: sbmlutils.factory.Sbase

ReactionGlyph.

Parameters:

• sid (str) –

• reaction (str) –

• x (float) –

• y (float) –

• z (float) –

• species_glyphs (Optional[Dict[str, str]]) –

• w (float) –

• h (float) –

• d (float) –

• text (Optional[str]) –

• name (Optional[str]) –

• sboTerm (Optional[str]) –

• metaId (Optional[str]) –

_set_glyph_fields(obj, layout, model)

Parameters:

• obj (libsbml.ReactionGlyph) –

• layout (libsbml.Layout) –

• model (libsbml.Model) –

Return type:

None

_create_curve(layout, srg, r_glyph_id, s_glyph_id, role, direction)

Heuristic for creating the curves.

Parameters:

• layout (libsbml.Layout) –

• srg (libsbml.SpeciesReferenceGlyph) –

• r_glyph_id (str) –

• s_glyph_id (str) –

• role (str) –

• direction (str) –

Returns:

Return type:

None

class sbmlutils.layout.layout.Layout(sid, width, height, compartment_glyphs=None, species_glyphs=None, reaction_glyphs=None, depth=0, name=None, sboTerm=None, metaId=None)

Bases: sbmlutils.factory.Sbase

Layout.

Parameters:

• sid (str) –

• width (float) –

• height (float) –

• compartment_glyphs (Optional[List[CompartmentGlyph]]) –

• species_glyphs (Optional[List[SpeciesGlyph]]) –

• reaction_glyphs (Optional[List[ReactionGlyph]]) –

• depth (int) –

• name (Optional[str]) –

• sboTerm (Optional[str]) –

• metaId (Optional[str]) –

create_sbml(model)

Create SBML in model.

Parameters:

model (libsbml.Model) –

Return type:

libsbml.Layout

_set_fields(sbase, model)

Parameters:

• sbase (libsbml.Layout) –

• model (libsbml.Model) –

Return type:

None