Ejemplos de SBMLlayout en Python

Ejemplo n.º 1

Archivo: mtest_font_size_api.py Proyecto: nrhawkins/libsbml-draw

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()

assert sl.getNodeFontSize("X0") == 10

sl.setNodeFontSize("X0", 24)

assert sl.getNodeFontSize("X0") == 24

sl.drawNetwork()

sl.regenerateLayout()

sl.drawNetwork()

Ejemplo n.º 2

Archivo: test_load_separately.py Proyecto: nrhawkins/libsbml-draw

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()

sl.loadSBMLFile(str(model_file))


def test_model_load_file_separately():
    assert sl.getNumberOfNodes() == 6
    assert sl.getNumberOfReactions() == 6

Ejemplo n.º 3

Archivo: test_fr_alg_options.py Proyecto: nrhawkins/libsbml-draw

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))

fr_alg = sl.getLayoutAlgorithmOptions()


def test_fr_alg_options_defaults():

    assert fr_alg.k == 20
    assert fr_alg.gravity == 0
    assert fr_alg.baryx == 500
    assert fr_alg.baryy == 500
    assert fr_alg.autobary == 1
    assert fr_alg.padding == 20


sl2 = SBMLlayout(str(model_file))

sl2.setLayoutAlgorithm_k(15)
sl2.setLayoutAlgorithm_gravity(20)
sl2.setLayoutAlgorithm_baryx(100)

Ejemplo n.º 4

Archivo: demo_render_sbml.py Proyecto: nrhawkins/libsbml-draw

import platform

from libsbml_draw.model.sbml_layout import SBMLlayout

if platform.system() == "Windows":
    model_file = "C:\\Users\\nrhaw\\Documents\\repos\\libsbml-draw\\model_files\\render_sbml_pink_green.xml"
elif platform.system() == "Linux":
    model_file = "/home/radix/repos/libsbml-draw/model_files/render_sbml.xml"
else:
    model_file = "/Users/natalieh/repos/libsbml-draw/model_files/render_sbml.xml"

sl = SBMLlayout(model_file)

#sl.describeModel()

sl.drawNetwork()

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

Ejemplo n.º 5

#import libsbml

from libsbml_draw.model.sbml_layout import SBMLlayout
#from libsbml_draw.model.render import Render

#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()

Ejemplo n.º 6

  Node5 = 0;
  Node6 = 0;
  Node7 = 0;
  Node8888888 = 0;
  Node9 = 0;
  Node10 = 0;
  Node11 = 0;
  Node12 = 0;
  Node13 = 0;
  Node14 = 0;
end
''')

from libsbml_draw.model.sbml_layout import SBMLlayout

sl = SBMLlayout(r.getSBML())

sl._describeModel()

sl.drawNetwork()

#sl.drawNetwork(figsize=(8,8))

#sl.drawNetwork(figsize=(8,8), node_mutation_scale=5)

#sl.drawNetwork("complicated_nodes_antimony.png", show=False)

# plt.show?
# import IPython.display as display
# display.Image("complicated_nodes_antimony.png", width=300)

Ejemplo n.º 7

Archivo: mtest_render_input.py Proyecto: nrhawkins/libsbml-draw

from pathlib import Path
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")

Ejemplo n.º 8

Archivo: demo_upconvert_check.py Proyecto: nrhawkins/libsbml-draw

from pathlib import Path
import pkg_resources

from libsbml_draw.model.sbml_layout import SBMLlayout

model_file_name = "simple-L2-render-local-L3V1-fixed.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.writeSBMLFile("fixed.xml")

Ejemplo n.º 9

from pathlib import Path
import pkg_resources

from libsbml_draw.model.sbml_layout import SBMLlayout

#model_file_name = "complicated_nodes-L3V1.xml"
model_file_name = "complicated_nodes.xml"

model_file = Path(
    pkg_resources.resource_filename("libsbml_draw",
                                    "model/data/" + model_file_name))

sl = SBMLlayout(str(model_file))

sl._describeModel()

sl.drawNetwork("complicated_nodes.png")

Ejemplo n.º 10

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)

Ejemplo n.º 11

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()

Ejemplo n.º 12

Archivo: test_layout_boris.py Proyecto: nrhawkins/libsbml-draw

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=False)


def test_boris_model_default_layout():
    assert sl.getNumberOfNodes() == 8
    assert sl.getNumberOfReactions() == 10


model_file_name = "test_layout_override.xml"

model_file = Path(pkg_resources.resource_filename(
        "libsbml_draw", "model/data/" + model_file_name))

slr = SBMLlayout(str(model_file), autoComputeLayout=False)


def test_boris_model_back_in():
    assert slr.getNumberOfNodes() == 8
    assert slr.getNumberOfReactions() == 10

Ejemplo n.º 13

  Node5 = 0;
  Node6 = 0;
  Node7 = 0;
  Node8888888 = 0;
  Node9 = 0;
  Node10 = 0;
  Node11 = 0;
  Node12 = 0;
  Node13 = 0;
  Node14 = 0;
end
''')

from libsbml_draw.model.sbml_layout import SBMLlayout

sl = SBMLlayout(r.getSBML())

sl._describeModel()

sl.drawNetwork()

assert sl.getNumberOfNodes() == 12
assert sl.getNumberOfReactions() == 8

slsl = SBMLlayout()

slsl.loadSBMLString(r.getSBML())

slsl._describeModel()

slsl.drawNetwork()

Ejemplo n.º 14

from pathlib import Path
import pkg_resources

from libsbml_draw.model.sbml_layout import SBMLlayout

MODEL_FILE_NAME = "largerpathway.xml"

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():

Ejemplo n.º 15

Archivo: mtest_line_endings.py Proyecto: nrhawkins/libsbml-draw

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")

Ejemplo n.º 16

Archivo: demo_loadSBML.py Proyecto: nrhawkins/libsbml-draw

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()

sl.loadSBMLFile(str(model_file))

sl._describeModel()

sl.drawNetwork()

sl_str = sl.getSBMLString()

ss = SBMLlayout()

ss.loadSBMLString(sl_str)

ss._describeModel()

ss.drawNetwork()

Ejemplo n.º 17

Archivo: demo_glycolysis_bm12.py Proyecto: nrhawkins/libsbml-draw

from pathlib import Path
import pkg_resources

from libsbml_draw.model.sbml_layout import SBMLlayout

#chance glycolysis 1960
#model_file_name = "chance_glycolysis_1960.xml"
#model_file_name = "repressilator_BIOMD12.xml"

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()

Ejemplo n.º 18

from pathlib import Path
import pkg_resources

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"

Ejemplo n.º 19

regenerate layout causes network properties to revert 
back to default

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)

Ejemplo n.º 20

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")

Ejemplo n.º 21

"""
"""
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()

sl.loadSBMLFile(str(model_file))

sl._describeModel()

sl.drawNetwork()

ss = SBMLlayout()

sbmlString = sl.getSBMLString()

ss.loadSBMLString(sbmlString)

ss._describeModel()

ss.drawNetwork()

Ejemplo n.º 22

Archivo: mtest_layout_override.py Proyecto: nrhawkins/libsbml-draw

from pathlib import Path
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)

Ejemplo n.º 23

Archivo: demo_TCA_ecoli_glucose.py Proyecto: nrhawkins/libsbml-draw

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()

Ejemplo n.º 24

#from libsbml import readSBMLFromFile, read`SBMLFromString

#import libsbml_draw.c_api.sbnw_c_api as sbnw
from libsbml_draw.model.sbml_layout import SBMLlayout

#model_file = "C:\\tmp\\model.xml"
#model_file = "C:\\tmp\\copasi.xml"
#model_file = "C:\\tmp\\render_sbml.xml"
#model_file = "C:\\tmp\\largerpathway.xml"
model_file = "C:\\tmp\\simple-L2-render-global.xml"

# read model
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())

Ejemplo n.º 25

Archivo: mtest_biomodels_rabies_china.py Proyecto: nrhawkins/libsbml-draw

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")

Ejemplo n.º 26

Archivo: test_font_size_api.py Proyecto: nrhawkins/libsbml-draw

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.setNodeFontSize("X0", 24)


def test_font_size_api_singles():

    assert sl.getNodeFontSize("A") == 10
    assert sl.getNodeFontSize("X0") == 24


sl2 = SBMLlayout(str(model_file))
sl2.setNodeFontSize("all", 18)


def test_font_size_api_all():

    assert sl2.getNodeFontSize("X0") == 18
    assert sl2.getNodeFontSize("A") == 18
    assert sl2.getNodeFontSize("B") == 18
    assert sl2.getNodeFontSize("C") == 18

Ejemplo n.º 27

Archivo: demo_copasi.py Proyecto: nrhawkins/libsbml-draw

if platform.system() == "Windows":
    model_dir = "C:\\Users\\nrhaw\\Documents\\repos\\libsbml-draw\\model_files\\"
    # model_file = "C:\\tmp\\copasi.xml"
    model_file = model_dir + "copasi.xml"
    #model_file = model_dir + "render_sbml_pink_green.xml"
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")

Ejemplo n.º 28

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")

Ejemplo n.º 29

Archivo: demo_complicated_nodes.py Proyecto: nrhawkins/libsbml-draw

import pkg_resources

from libsbml_draw.model.sbml_layout import SBMLlayout

#model_file_name = "complicated_nodes-L3V1.xml"
model_file_name = "complicated_nodes.xml"

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)

Ejemplo n.º 30

from libsbml_draw.model.sbml_layout import SBMLlayout

file_name = "veronica-network.xml"

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():