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')
sl.setReactionColor("_J0", "red", species="A")
sl.setReactionEdgeColor("_J3", "#0000ff30")
sl.setReactionEdgeColor("_J4", "pink", species="D")
# only applies to FancyArrowPatch arrowhead
sl.setReactionFillColor("_J2", "lightgreen")
sl.setReactionCurveWidth("_J0", 5, role_name="product")
sl.setReactionCurveWidth("_J4", 10)
sl.setReactionCurveWidth(["_J1", "_J2", "_J3"], 15)
sl.setNodeFillColor("A", "pink")
sl.setNodeEdgeColor("all", "green")
sl.setNodeEdgeWidth(["D", "X1", "C"], 3)
sl.setNodeFontWeight(["X0", "A", "B", "C", "D", "X1"], "bold")
sl.setNodeTextAnchor("X0", "right")
sl.setNodeTextAnchor("A", "left")
sl.setNodeVTextAnchor("B", "center")
sl.drawNetwork()
print("_J0 width: ", sl.getReactionCurveWidth("_J0"))
print("_J1 edge color: ", sl.getReactionEdgeColor("_J1"))
print("_J1 fill color: ", sl.getReactionFillColor("_J1"))
print("_J3 edge color: ", sl.getReactionEdgeColor("_J3"))
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)
sl2.drawNetwork()
sl.getArrowheadVert(1, 1)
centroid = sl.getNodeCentroid("X0")
print("centroid: ", centroid)
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
applyRender = True
sl = SBMLlayout(str(model_file), applyRender=applyRender)
sl._describeModel()
sl.setReactionCurveWidth("all", 5)
sl.setReactionCurveWidth("_J0", 7, role_name="product")
sl.setNodeEdgeColor("X1", "#ff0000")
sl.setNodeFillColor("X1", "#ff000030")
sl.setNodeEdgeWidth("X1", 3)
sl.setNodeFontWeight(["A", "B", "C", "D"], "bold")
sl.setReactionEdgeColor("_J0", "#ff0000", role_name="product")
sl.setReactionEdgeColor("_J1", "#ff00ff", role_name="substrate")
sl.setReactionEdgeColor("_J2", "#ff00ff", role_name="product")
sl.setReactionEdgeColor("_J5", "#00ff00", species="D")
sl.setReactionEdgeColor("_J3", "#ffff00", role_name="product")
sl.setReactionEdgeColor("_J4", "#00ffff")
model_file_name = "ftest_no_layout.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))