example1.py

An example layout.

#!/usr/bin/env python

#
# \file    example1.py
# \brief   SBML Layout example
# \author  Ralph Gauges
# 

# Copyright 2004 European Media Laboratories Research gGmbH
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of the License, or
# any later version.
#
# This library is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
# MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
# documentation provided hereunder is on an "as is" basis, and the
# European Media Laboratories Research gGmbH have no obligations to
# provide maintenance, support, updates, enhancements or modifications.
# In no event shall the European Media Laboratories Research gGmbH be
# liable to any party for direct, indirect, special, incidental or
# consequential damages, including lost profits, arising out of the use of
# this software and its documentation, even if the European Media
# Laboratories Research gGmbH have been advised of the possibility of such
# damage.  See the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# The original code contained here was initially developed by:
#
#     Ralph Gaugess
#     Bioinformatics Group
#     European Media Laboratories Research gGmbH
#     Schloss-Wolfsbrunnenweg 31c
#     69118 Heidelberg
#     Germany
#
#     http://www.eml-research.de/english/Research/BCB/
#     mailto:ralph.gauges@eml-r.villa-bosch.de
#
# Contributor(s):
#


from libsbml import *

def createDimensions(width, height):
  """Create a dimension object with given width and height"""
  dim = Dimensions()
  dim.setWidth(width)
  dim.setHeight(height)
  return dim

def createPoint(x, y):
  """Create a point object with given coordinates"""
  p = Point()
  p.setX(x)
  p.setY(y)
  return p

def createBoundingBox(id, x, y, width, height):
  """Create a bounding box object with given coordinates and dimensions"""
  bb = BoundingBox()
  bb.setX(x)
  bb.setY(y)
  bb.setWidth(width)
  bb.setHeight(height)
  return bb

# create the document

document=SBMLDocument(2,1)
# create the Model

model=document.createModel("TestModel")
document.enablePackage(LayoutExtension.getXmlnsL2(), "layout", True)

# create the Compartment

compartment=model.createCompartment()
compartment.setId("Compartment_1")
# create the Species

species1=model.createSpecies()
species1.setId("Species_1")
species1.setCompartment(compartment.getId())

species2=model.createSpecies()
species2.setId("Species_2")
species2.setCompartment(compartment.getId())

# create the Reactions

reaction1=model.createReaction()
reaction1.setId("Reaction_1")
reaction1.setReversible(False)

reference1=reaction1.createReactant()
reference1.setSpecies(species1.getId())
reference1.setId("SpeciesReference_1")

reference2=reaction1.createProduct()
reference2.setSpecies(species2.getId())
reference2.setId("SpeciesReference_2")

reaction2=model.createReaction()
reaction2.setId("Reaction_2")
reaction2.setReversible(False)

reference3=reaction1.createReactant()
reference3.setSpecies(species2.getId())
reference3.setId("SpeciesReference_3")

reference4=reaction1.createProduct()
reference4.setSpecies(species1.getId())
reference4.setId("SpeciesReference_4")

# create the Layout
mplugin = model.getPlugin("layout")
layout = mplugin.createLayout()

layout.setId("Layout_1")
layout.setDimensions(createDimensions(400.0,220.0))


# create the CompartmentGlyph

compartmentGlyph=layout.createCompartmentGlyph()
compartmentGlyph.setId("CompartmentGlyph_1")
compartmentGlyph.setCompartmentId(compartment.getId())
compartmentGlyph.setBoundingBox(createBoundingBox("bb1",5,5,390,210))


# create the SpeciesGlyphs

speciesGlyph1=layout.createSpeciesGlyph()
speciesGlyph1.setId("SpeciesGlyph_1")
speciesGlyph1.setSpeciesId(species1.getId())
speciesGlyph1.setBoundingBox(createBoundingBox("bb2",80,26,240,24))

textGlyph1=layout.createTextGlyph()
textGlyph1.setId("TextGlyph_01")
textGlyph1.setBoundingBox(createBoundingBox("bbA",92,26,228,24))
textGlyph1.setOriginOfTextId(speciesGlyph1.getId())
textGlyph1.setGraphicalObjectId(speciesGlyph1.getId())


speciesGlyph2=layout.createSpeciesGlyph()
speciesGlyph2.setId("SpeciesGlyph_2")
speciesGlyph2.setSpeciesId(species2.getId())
speciesGlyph2.setBoundingBox(createBoundingBox("bb3",80,170,240,24))

textGlyph2=layout.createTextGlyph()
textGlyph2.setId("TextGlyph_02")
textGlyph2.setBoundingBox(createBoundingBox("bbB",92,170,228,24))
textGlyph2.setOriginOfTextId(speciesGlyph2.getId())
textGlyph2.setGraphicalObjectId(speciesGlyph2.getId())

# create the ReactionGlyphs

reactionGlyph1=layout.createReactionGlyph()
reactionGlyph1.setId("ReactionGlyph_1")
reactionGlyph1.setReactionId(reaction1.getId())

reactionCurve1=reactionGlyph1.getCurve()
ls=reactionCurve1.createLineSegment()
ls.setStart(createPoint(165,105))
ls.setEnd(createPoint(165,115))

reactionGlyph2=layout.createReactionGlyph()
reactionGlyph2.setId("ReactionGlyph_1")
reactionGlyph2.setReactionId(reaction2.getId())

reactionCurve2=reactionGlyph2.getCurve()
ls=reactionCurve2.createLineSegment()
ls.setStart(createPoint(235,105))
ls.setEnd(createPoint(235,115))

# add the SpeciesReferenceGlyphs

speciesReferenceGlyph1=reactionGlyph1.createSpeciesReferenceGlyph()
speciesReferenceGlyph1.setId("SpeciesReferenceGlyph_1")
speciesReferenceGlyph1.setSpeciesGlyphId(speciesGlyph1.getId())
speciesReferenceGlyph1.setSpeciesReferenceId(reference1.getId())
speciesReferenceGlyph1.setRole(SPECIES_ROLE_SUBSTRATE)

speciesReferenceCurve1=speciesReferenceGlyph1.getCurve()
cb=speciesReferenceCurve1.createCubicBezier()
cb.setStart(createPoint(165,105))
cb.setBasePoint1(createPoint(165,90))
cb.setBasePoint2(createPoint(165,90))
cb.setEnd(createPoint(195,60))

speciesReferenceGlyph2=reactionGlyph1.createSpeciesReferenceGlyph()
speciesReferenceGlyph2.setId("SpeciesReferenceGlyph_2")
speciesReferenceGlyph2.setSpeciesGlyphId(speciesGlyph2.getId())
speciesReferenceGlyph2.setSpeciesReferenceId(reference2.getId())
speciesReferenceGlyph2.setRole(SPECIES_ROLE_PRODUCT)

speciesReferenceCurve2=speciesReferenceGlyph2.getCurve()
cb=speciesReferenceCurve2.createCubicBezier()
cb.setStart(createPoint(165,115))
cb.setBasePoint1(createPoint(165,130))
cb.setBasePoint2(createPoint(165,130))
cb.setEnd(createPoint(195,160))


speciesReferenceGlyph3=reactionGlyph2.createSpeciesReferenceGlyph()
speciesReferenceGlyph3.setId("SpeciesReferenceGlyph_3")
speciesReferenceGlyph3.setSpeciesGlyphId(speciesGlyph2.getId())
speciesReferenceGlyph3.setSpeciesReferenceId(reference3.getId())
speciesReferenceGlyph3.setRole(SPECIES_ROLE_SUBSTRATE)

speciesReferenceCurve3=speciesReferenceGlyph3.getCurve()
cb=speciesReferenceCurve3.createCubicBezier()
cb.setStart(createPoint(235,115))
cb.setBasePoint1(createPoint(235,130))
cb.setBasePoint2(createPoint(235,130))
cb.setEnd(createPoint(205,160))

speciesReferenceGlyph4=reactionGlyph2.createSpeciesReferenceGlyph()
speciesReferenceGlyph4.setId("SpeciesReferenceGlyph_4")
speciesReferenceGlyph4.setSpeciesGlyphId(speciesGlyph1.getId())
speciesReferenceGlyph4.setSpeciesReferenceId(reference4.getId())
speciesReferenceGlyph4.setRole(SPECIES_ROLE_PRODUCT)

speciesReferenceCurve4=speciesReferenceGlyph4.getCurve()
cb=speciesReferenceCurve4.createCubicBezier()
cb.setStart(createPoint(235,105))
cb.setBasePoint1(createPoint(235,90))
cb.setBasePoint2(createPoint(235,90))
cb.setEnd(createPoint(205,60))


writeSBML(document,"TestModel1-python.xml")