from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "TCA_ecoli_glucose_BIOMD222_url.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
sl.drawNetwork("TCA_ecoli_glucose.pdf")
import pkg_resources
import pytest
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "BorisEJB.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file), autoComputeLayout=True)
sl._describeModel()
sl.drawNetwork("boris_ejb_override.pdf")
def test_write_file_raises():
with pytest.raises(ValueError):
sl.writeSBMLFile("ftest_layout_override.xml")
# This will write if allowed, and when it is read back in, it displays as
# a single blob of garbage because everything is plotted with the same centers
# sl.writeSBMLFile("test_layout_override.xml")
# slr = SBMLlayout("test_layout_override.xml", autoComputeLayout=False)
slr = SBMLlayout(str(model_file), autoComputeLayout=False)
elif platform.system() == "Linux":
model_dir = "/home/radix/repos/libsbml-draw/model_files/"
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
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "BorisEJB.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file), autoComputeLayout=True)
sl._describeModel()
sl.drawNetwork("Boris_EJB.png")
sl.drawNetwork("Boris_EJB.pdf")
sl2 = SBMLlayout(str(model_file))
sl2._describeModel()
sl2.drawNetwork()
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "simple-L2-render-local.xml"
#model_file_name = "simple-L2-render-local-L3V1.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.setCompartmentEdgeColor("vol1", "#0000ff")
sl.setCompartmentFillColor("vol1", "#ff000010")
sl.setCompartmentLineWidth("vol1", 5)
assert sl.getCompartmentEdgeColor("vol1") == "#0000ffff"
assert sl.getCompartmentFillColor("vol1") == "#ff000010"
assert sl.getCompartmentLineWidth("vol1") == 5
sl.drawNetwork("simple_render_local.png")
sl.writeSBMLFile("simple_render_local_out.xml")
slr = SBMLlayout("simple_render_local_out.xml")
#model_file = "C:\\tmp\\copasi.xml"
model_file = "C:\\tmp\\largerpathway.xml"
#doc = libsbml.readSBMLFromFile(model_file)
#model = doc.getModel()
#layout_plugin = model.getPlugin("layout")
#if layout_plugin:
# print("num layouts: ", layout_plugin.getNumLayouts())
sl = SBMLlayout(model_file)
sl._describeModel()
sl.drawNetwork()
#r = Render(model_file, sl.layout_number)
#r._describeRenderInfo()
#print("render: ", type(r))
#print("num layouts: ", r.layout_plugin.getNumLayouts())
#sl._applyRenderInformation(None)
#a0e0a030
reactionIds = sl.getReactionIds()
sl.setNodeColor("all", "#0000ff30")
sl.setReactionColor("all", "blue")
"model/data/" + MODEL_FILE_NAME))
sl = SBMLlayout(str(MODEL_FILE))
sl._describeModel()
assert sl.getNumberOfNodes() == 6
assert sl.getNumberOfReactions() == 5
assert sl.getNodeFontSize("ABCDEFG") == 12
assert sl.getNodeFontWeight("F") == "normal"
assert sl.getNodeFillColor("E") == "#a0e0a030"
sl.drawNetwork("larger_pathway.png")
# sl.setReactionCurveWidth("all", 12)
sl.drawNetwork()
sl.writeSBMLFile("ftest_larger_pathway.xml")
slr = SBMLlayout("ftest_larger_pathway.xml")
slr.drawNetwork()
assert sl.getNumberOfNodes() == 6
assert sl.getNumberOfReactions() == 5
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "modexmpl.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
sl.drawNetwork("ftest_line_endings.pdf")
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
#model_file_name = "GlycolysisOriginal_L3V1.xml"
#model_file_name = "GlycolysisOriginal-L3V1.xml"
model_file_name = "GlycolysisOriginal.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
print("node font size: ", sl.getNodeFontSize("ATP"))
sl.drawNetwork("GlycolysisOriginal.pdf")
#sl.drawNetwork(figsize=(20,20))
#sl.setNodeFontSize("all", 8)
#sl.drawNetwork()
#for node in sl._SBMLlayout__network.nodes.values():
# print("node id, name: ", node.id, node.name)
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "random_network.xml"
#model_file = Path(pkg_resources.resource_filename("libsbml_draw", "model/data/" + model_file_name))
sl = SBMLlayout(model_file_name, applyRender=False)
sl._describeModel()
sl.drawNetwork("random_4s_2r.pdf")
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))
applyRender = True
sl = SBMLlayout(str(model_file), applyRender=applyRender)
sl._describeModel()
sl.drawNetwork()
sl.lockNode("X0")
sl.lockNode("A")
sl.aliasNode("B")
sl.regenerateLayout()
sl.drawNetwork("model_simple_alias_B_lock_A_X0.pdf")
print("node ids: ", sl.getNodeIds())
print()
#print("string: ", sl._SBMLlayout__getSBMLWithLayoutString())
assert sl.getReactionCurveWidth("_J1")[0] == ("A", "SUBSTRATE", 5)
assert sl.getReactionCurveWidth("_J1")[1] == ("B", "PRODUCT", 5)
assert sl.getReactionCurveWidth("_J2")[0] == ('B', 'SUBSTRATE', 5)
assert sl.getReactionCurveWidth("_J2")[1] == ('D', 'PRODUCT', 5)
assert sl.getReactionCurveWidth("_J5")[0] == ('D', 'SUBSTRATE', 5)
assert sl.getReactionCurveWidth("_J5")[1] == ('X1', 'PRODUCT', 5)
assert sl.getReactionCurveWidth("_J3")[0] == ('A', 'SUBSTRATE', 5)
assert sl.getReactionCurveWidth("_J3")[1] == ('C', 'PRODUCT', 5)
assert sl.getReactionCurveWidth("_J4")[0] == ('C', 'SUBSTRATE', 5)
assert sl.getReactionCurveWidth("_J4")[1] == ('D', 'PRODUCT', 5)
sl.drawNetwork(scaling_factor=0.75)
assert sl.getNumberOfNodes() == 6
assert sl.getNumberOfReactions() == 6
sl.setNodeEdgeColor("X1", "#ff0000")
sl.setNodeFillColor("X1", "#ff000030")
sl.setNodeEdgeWidth("X1", 3)
assert sl.getNodeEdgeColor("X1") == "#ff0000ff"
assert sl.getNodeFillColor("X1") == "#ff000030"
assert sl.getNodeEdgeWidth("X1") == 3
assert sl.getNodeEdgeColor("A") == "#0000ff"
assert sl.getNodeFillColor("A") == "#c9e0fb"
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()
# layout.regenerateLayout()
# layout.drawNetwork('compartment_network.png')
#
# layout.writeSBMLFile('2CompartmentModelWithLayout.xml')
#
# from libsbml_draw.model.sbml_layout import SBMLlayout
#
# # Create a SBMLlayout object.
# layout = SBMLlayout('2CompartmentModel.xml')
#
sl = SBMLlayout(model_file)
# generate layout
if not sl.layoutSpecified:
sl._randomizeLayout()
sl._doLayoutAlgorithm()
# describe network
print("num nodes: ", sl.getNumberOfNodes())
print("num reactions: ", sl.getNumberOfReactions())
# create network
sl._createNetwork()
# draw network
sl.drawNetwork()
# print node id's
print("node ids: ", sl.getNodeIds())
if "copasi" in model_file:
# set node properties
sl.setNodeColor("S1", "pink")
sl.setNodeColor("S2", "green")
sl.setNodeColor("S1", "Verdana")
sl.setNodeColor("S1", "white")
sl.setNodeFontsize("S1", 18)
sl.setNodeFontstyle("S1", "italic")
sl.setNodeFontsize("S2", 24)
sl.setNodeFontstyle("S2", "oblique")
if platform.system() == "Windows":
model_dir = "C:\\Users\\nrhaw\\Documents\\repos\\libsbml-draw\\model_files\\"
elif platform.system() == "Linux":
model_dir = "/home/radix/repos/libsbml-draw/model_files/"
else:
model_dir = "/Users/natalieh/repos/libsbml-draw/model_files/"
model_file = model_dir + file_name
print("model file: \n", model_file)
sl = SBMLlayout(model_file)
sl._describeModel()
my_fig = sl.drawNetwork()
color1 = ["S6", "S7", "S5", "S4", "S8"]
color2 = ["S0", "S1", "S2", "S3", "S9", "S10", "S11"]
for node in color1:
sl.setNodeFillColor(node, "lightblue")
for node in color2:
sl.setNodeFillColor(node, "lightgreen")
for reaction in sl.getReactionIds():
sl.setReactionCurveWidth(reaction, 2)
sl.drawNetwork()
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "BIOMD0000000013_url.xml"
# Poolman2004_CalvinCycle
sl = SBMLlayout(model_file_name, applyRender=False)
sl._describeModel()
#sl.drawNetwork("plant_metabolism.pdf")
sl.aliasNode("ATP_ch")
sl.aliasNode("ADP_ch")
sl.aliasNode("GAP_ch")
sl.aliasNode("PGA_ch")
sl.regenerateLayout()
sl.drawNetwork("plant_metabolism_alias.pdf")
MODEL_FILE = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + MODEL_FILE_NAME))
print("model file: ", str(MODEL_FILE))
sl = SBMLlayout(str(MODEL_FILE))
#sl.describeModel()
sl.setReactionColor("all", "#0000ff50")
sl.setNodeColor("all", "#00ff0030")
#sl.setNodeFontSize("all", 24)
sl.drawNetwork("largerpathway.png")
#sl.drawNetwork(figsize=(12,12))
print("node ids: ", sl.getNodeIds())
print("reaction ids: ", sl.getReactionIds())
print()
for node in sl._SBMLlayout__network.nodes.values():
print("node fs: ", node.font_size, node.font_family)
sl.writeSBMLFile("largerpathway_out.xml")
#sl.drawNetwork(scaling_factor=.5)
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')
#
# layout.writeSBMLFile('2CompartmentModelWithLayout.xml')
#
# from libsbml_draw.model.sbml_layout import SBMLlayout
#
# # Create a SBMLlayout object.
# layout = SBMLlayout('2CompartmentModel.xml')
#
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()
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "TCA_ecoli_glucose_BIOMD222_url.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
sl.drawNetwork()
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "GlycolysisOriginal.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
assert sl.getNumberOfNodes() == 23
assert sl.getNumberOfReactions() == 11
sl.drawNetwork("GlycolysisOriginal.png")
assert sl.getNodeEdgeWidth("External_glucose") == 3
assert sl.getNodeEdgeWidth("Glucose") == 1
# in this case, bottom means top
assert sl.getNodeVTextAnchor("pyruvate") == "bottom"
assert sl.getNodeVTextAnchor("ADP") == "bottom"
assert sl.getNodeFillColor("NAD") == "#7fff55"
assert sl.getNodeFillColor("NADH") == "#d4ffaa"
assert sl.getNodeFillColor("ATP") == "#ff7faa"
assert sl.getNodeFillColor("ADP") == "#ffd4d4"
assert sl.getNodeEdgeColor("glycerate_3_phosphate") == "#969696"
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "rabies.xml"
sl = SBMLlayout(model_file_name, applyRender=False)
sl._describeModel()
sl.drawNetwork("rabies_China.pdf")
from pathlib import Path
import pkg_resources
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "modexmpl.xml"
model_file = Path(
pkg_resources.resource_filename("libsbml_draw",
"model/data/" + model_file_name))
sl = SBMLlayout(str(model_file))
sl._describeModel()
fig = sl.drawNetwork()
#fig = sl.drawNetwork(node_mutation_scale=5)
#sl.setArrowheadScale(1, 15)
#sl.setArrowheadScale(4, 15)
#fig = sl.drawNetwork(node_mutation_scale=5)
model_file = Path(pkg_resources.resource_filename(
"libsbml_draw", "model/data/" + model_file_name))
# https://stackoverflow.com/questions/33635439/matplotlib-patch-size-in-points
#print("validate: ", SBMLlayout._validate_sbml_filename(str(model_file)))
sl = SBMLlayout(str(model_file))
sl._describeModel()
#sl.drawNetwork("complicated_nodes.png", figsize=(6,6))
#sl.drawNetwork("complicated_nodes.png", figsize=(8,8))
sl.drawNetwork("complicated_nodes.png")
#sl.setNodeFontSize("all", 6)
#sl.drawNetwork()
#for node in sl.getNodeIds():
# centroid = sl.getNodeCentroid(node)
# print("centroid: ", centroid[0], ", ", centroid[1])
# print("width: ", sl.getNodeWidth(node))
# print("height: ", sl.getNodeHeight(node))
#for node in sl._SBMLlayout__network.nodes.values():
# print("edge_color: ", node.edge_color)
# print("fill_color: ", node.fill_color)
from libsbml_draw.model.sbml_layout import SBMLlayout
model_file_name = "BIOMD0000000091_url.xml"
# Proctor2005 - Actions of chaperones and their role in ageing
sl = SBMLlayout(model_file_name, applyRender=False)
sl._describeModel()
sl.drawNetwork("alzheimers_chaperones_aging.pdf")
