Python SBMLlayout.getNodeIds Beispiele

Beispiel #1

Datei: demo_copasi.py Projekt: nrhawkins/libsbml-draw

    model_file = "/home/radix/repos/libsbml-draw/model_files/copasi.xml"
else:
    model_dir = "/Users/natalieh/repos/libsbml-draw/model_files/"
    model_file = "/Users/natalieh/repos/libsbml-draw/model_files/copasi.xml"
#model_file = Path(pkg_resources.resource_filename("libsbml_draw", "model_files/model.xml"))

print("model file: \n", model_file)

sl = SBMLlayout(model_file)

sl._describeModel()

## Draw Original copasi.xml
sl.drawNetwork()

print("node ids: ", sl.getNodeIds())
print("reaction ids: ", sl.getReactionIds())

sl.setNodeFontStyle("S1", "italic")
sl.setNodeColor("S1", "lightpink")
sl.setNodeColor("S2", "lightgreen")

sl.setNodeFontColor("S1", "white")
sl.setNodeFontStyle("S1", "italic")

sl.setReactionColor("_J0", "blue")
sl.setReactionCurveWidth("_J0", 1)

# Draw Pink and Green 
sl.drawNetwork()

Beispiel #2

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))

sl = SBMLlayout(str(model_file))

sl._describeModel()

print("node ids: ", sl.getNodeIds())
print("reaction ids: ", sl.getReactionIds())

sl.drawNetwork()

sl._describeReaction(0)

sl.setNodeEdgeWidth("all", 2)

out_file = "model_out.xml"
sl.writeSBMLFile("model_out.xml")

sl2 = SBMLlayout(out_file)

print("sl2 layoutSpecified: ", sl2._SBMLlayout__layoutSpecified)

Beispiel #3

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()
# layout.regenerateLayout()
# layout.regenerateLayout()
# layout.drawNetwork('compartment_network.png')

Beispiel #4

layout = SBMLlayout('2CompartmentModel.xml')
# print(layout.getNumberOfRoles())

layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
layout.regenerateLayout()
[layout.setCompartmentEdgeColor(i, 'grey') for i in layout.getCompartmentIds()]
[layout.setCompartmentLineWidth(i, 10) for i in layout.getCompartmentIds()]
[layout.setNodeEdgeWidth(i, 10) for i in layout.getNodeIds()]
[layout.setNodeFontSize(i, 40) for i in layout.getNodeIds()]
[
    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('compartment_network.png')

# layout.regenerateLayout()
# layout.regenerateLayout()
# layout.regenerateLayout()
# layout.regenerateLayout()