model_file_name = "glycolysis_BIOMD176.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
sl.drawNetwork()
sl.aliasNode("ATP")
sl.aliasNode("ADP")
sl.drawNetwork()
sl.regenerateLayout()
sl.drawNetwork()
loo = sl.getLayoutAlgorithmOptions()
print(loo.k)
#sl.setLayoutAlgorithm_grav()
#sl.drawNetwork("glycolysis_bm12.png")
#sl.drawNetwork("glycolysis_bm12.pdf")
setArrowheadScale funciton does not work, but changing the default
value does
Sometimes run into problems with a canvas which is too big (like in the schmerier 2008 model)
SBO term unexpected warning. Where does it come from
Gradient colours are cool. Would like to see them.
Font size should scale with scaling factor
'''
layout = SBMLlayout('Kholodenko2000.xml')
# print(layout.getNumberOfRoles())
layout.regenerateLayout()
[layout.setCompartmentEdgeColor(i, 'grey') for i in layout.getCompartmentIds()]
[layout.setNodeEdgeWidth(i, 10) for i in layout.getNodeIds()]
[layout.setNodeFontSize(i, 40) for i in layout.getNodeIds()]
[layout.setCompartmentLineWidth(i, 25) for i in layout.getCompartmentIds()]
# [layout.setReactionEdgeColor(i, edge_color='black') for i in layout.getReactionIds()]
[layout.setReactionCurveWidth(i, 10) for i in layout.getReactionIds()]
[layout.setArrowheadScale(i, 50) for i in range(layout.getNumberOfRoles())]
# [layout.setNodeColor(i, 'white') for i in layout.getNodeIds()]
# [layout.setNodeEdgeColor(i, 'black') for i in layout.getNodeIds()]
layout.drawNetwork('Kholodenko2000Layout.png', scaling_factor=1.5)
# layout.regenerateLayout()
# layout.regenerateLayout()
# layout.regenerateLayout()
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "model.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
s = SBMLlayout(str(model_file))
# s._describeModel()
s.setNodeFontSize('all', 15)
s.setReactionCurveWidth('all', 3)
s.setNodeColor('all', 'red')
s.setNodeFontColor('all', 'white')
s.drawNetwork()
s.regenerateLayout()
s.drawNetwork()
