class ArrowDesigner(WindowedPlugin):
"""
The ArrowDesigner plugin that subclasses WindowedPlugin.
"""
metadata = PluginMetadata(
name='ArrowDesigner',
author='Gary Geng',
version='0.0.1',
short_desc='Arrow tip designer for reactions.',
long_desc='Arrow tip designer for reactions.',
category=PluginCategory.APPEARANCE,
)
def __init__(self):
super().__init__()
self.arrow_tip = api.get_arrow_tip()
def create_window(self, dialog):
"""
Called when creating a window. Create the designer window as well as control buttons.
"""
window = wx.Window(dialog, size=(500, 500))
sizer = wx.BoxSizer(wx.VERTICAL)
self.designer = DesignerWindow(window, self.arrow_tip)
save_btn = wx.Button(window, label='Save')
save_btn.Bind(wx.EVT_BUTTON, self.OnSave)
restore_btn = wx.Button(window, label='Restore default')
restore_btn.Bind(wx.EVT_BUTTON, self.OnRestore)
sizerflags = wx.SizerFlags().Align(wx.ALIGN_CENTER_HORIZONTAL).Border(
wx.TOP, 20)
sizer.Add(self.designer, sizerflags)
sizer.Add(save_btn, sizerflags)
sizer.Add(restore_btn, sizerflags)
dialog.SetSizer(sizer)
return window
def OnSave(self, evt):
"""
Handler for the "save" button. Save the new arrow tip.
"""
api.set_arrow_tip(self.arrow_tip)
def OnRestore(self, evt):
"""
Update the arrow point to be set to default values.
"""
default_tip = api.get_default_arrow_tip()
api.set_arrow_tip(default_tip)
self.designer.update_arrow_tip(default_tip)
class ExportAntimony(WindowedPlugin):
metadata = PluginMetadata(
name='ExportAntimony',
author='Jin Xu',
version='0.0.2',
short_desc='Export Antimony.',
long_desc='Export the Antimony String from the network on canvas.',
category=PluginCategory.ANALYSIS)
def create_window(self, dialog):
"""
Create a window to do the antimony export.
Args:
self
dialog
"""
self.window = wx.Panel(dialog, pos=(5, 100), size=(300, 320))
export_btn = wx.Button(self.window, -1, 'Export', (5, 5))
export_btn.Bind(wx.EVT_BUTTON, self.Export)
save_btn = wx.Button(self.window, -1, 'Save', (100, 5))
save_btn.Bind(wx.EVT_BUTTON, self.Save)
wx.StaticText(self.window, -1, 'Antimony string:', (5, 30))
self.antimonyText = wx.TextCtrl(self.window,
-1,
"", (10, 50),
size=(260, 220),
style=wx.TE_MULTILINE)
self.antimonyText.SetInsertionPoint(0)
return self.window
def Export(self, evt):
"""
Handler for the "Export" button.
Get the network on canvas and change it to an Antimony string.
"""
isReversible = True
netIn = 0
numNodes = api.node_count(netIn)
if numNodes == 0:
wx.MessageBox("Please import a network on canvas", "Message",
wx.OK | wx.ICON_INFORMATION)
else:
allNodes = api.get_nodes(netIn)
id = allNodes[0].id[0:-2]
numReactions = api.reaction_count(netIn)
antStr = ''
allReactions = api.get_reactions(netIn)
for i in range(numReactions):
antStr = antStr + 'J' + str(i) + ': '
rct_num = len(allReactions[i].sources)
prd_num = len(allReactions[i].targets)
for j in range(rct_num - 1):
antStr = antStr + id + '_' + str(
allReactions[i].sources[j])
antStr = antStr + ' + '
antStr = antStr + id + '_' + str(
allReactions[i].sources[rct_num - 1])
antStr = antStr + ' -> '
for j in range(prd_num - 1):
antStr = antStr + id + '_' + str(
allReactions[i].targets[j])
antStr = antStr + ' + '
antStr = antStr + id + '_' + str(
allReactions[i].targets[prd_num - 1])
antStr = antStr + '; E' + str(i) + '*(k' + str(i)
for j in range(rct_num):
antStr = antStr + '*' + id + '_' + str(
allReactions[i].sources[j])
if isReversible:
antStr = antStr + ' - k' + str(i) + 'r'
for j in range(prd_num):
antStr = antStr + '*' + id + '_' + str(
allReactions[i].targets[j])
antStr = antStr + ')'
antStr = antStr + ';\n'
self.antimonyText.SetValue(antStr)
def Save(self, evt):
"""
Handler for the "Save" button.
Save the Antimony string to a file.
"""
self.dirname = "" #set directory name to blank
dlg = wx.FileDialog(self.window,
"Save As",
self.dirname,
wildcard="Antimony files (*.ant)|*.ant",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
# Grab the content to be saved
itcontains = self.antimonyText.GetValue()
# Open the file for write, write, close
self.filename = dlg.GetFilename()
self.dirname = dlg.GetDirectory()
filehandle = open(os.path.join(self.dirname, self.filename), 'w')
filehandle.write(itcontains)
filehandle.close()
# Get rid of the dialog to keep things tidy
dlg.Destroy()
class IMPORTSBML(WindowedPlugin):
metadata = PluginMetadata(
name='ImportSBML',
author='Jin Xu',
version='0.0.2',
short_desc='Import SBML.',
long_desc='Import an SBML String from a file and visualize it as a network on canvas.',
category=PluginCategory.ANALYSIS
)
def create_window(self, dialog):
"""
Create a window to import SBML.
Args:
self
dialog
"""
self.window = wx.Panel(dialog, pos=(5,100), size=(300, 320))
self.sbmlStr = ''
import_btn = wx.Button(self.window, -1, 'Import', (5, 5))
import_btn.Bind(wx.EVT_BUTTON, self.Import)
visualize_btn = wx.Button(self.window, -1, 'Visualize', (100, 5))
visualize_btn.Bind(wx.EVT_BUTTON, self.Visualize)
wx.StaticText(self.window, -1, 'SBML string:', (5,30))
self.SBMLText = wx.TextCtrl(self.window, -1, "", (10, 50), size=(260, 220), style=wx.TE_MULTILINE)
self.SBMLText.SetInsertionPoint(0)
return self.window
def Import(self, evt):
"""
Handler for the "Import" button.
Open the SBML file and show it in the TextCtrl box.
"""
self.dirname="" #set directory name to blank
dlg = wx.FileDialog(self.window, "Choose a file to open", self.dirname, wildcard="SBML files (*.xml)|*.xml", style=wx.FD_OPEN | wx.FD_FILE_MUST_EXIST) #open the dialog boxto open file
if dlg.ShowModal() == wx.ID_OK: #if positive button selected....
self.filename = dlg.GetFilename() #get the filename of the file
self.dirname = dlg.GetDirectory() #get the directory of where file is located
f = open(os.path.join(self.dirname, self.filename), 'r') #traverse the file directory and find filename in the OS
self.sbmlStr = f.read()
self.SBMLText.SetValue(f.read()) #open the file from location as read
self.SBMLText.WriteText(self.sbmlStr)
f.close
dlg.Destroy()
def Visualize(self, evt):
"""
Handler for the "Visualize" button.
Visualize the SBML string to a network shown on the canvas.
"""
def hex_to_rgb(value):
value = value.lstrip('#')
return tuple(int(value[i:i+2], 16) for i in (0, 2, 4))
if len(self.sbmlStr) == 0:
wx.MessageBox("Please import an SBML file.", "Message", wx.OK | wx.ICON_INFORMATION)
else:
net_index = 0
api.clear_network(net_index)
comp_id_list = []
comp_dimension_list = []
comp_position_list = []
spec_id_list =[]
spec_dimension_list =[]
spec_position_list = []
#set the default values without render info:
comp_fill_color = (158, 169, 255)
comp_border_color = (0, 29, 255)
comp_border_width = 2.0
spec_fill_color = (255, 204, 153)
spec_border_color = (255, 108, 9)
spec_border_width = 2.0
reaction_line_color = (129, 123, 255)
reaction_line_width = 3.0
### from here for layout ###
document = readSBMLFromString(self.sbmlStr)
model_layout = document.getModel()
mplugin = (model_layout.getPlugin("layout"))
if mplugin is None:
wx.MessageBox("There is no layout information, so positions are randomly assigned.", "Message", wx.OK | wx.ICON_INFORMATION)
#
# Get the first Layout object via LayoutModelPlugin object.
#
else:
layout = mplugin.getLayout(0)
if layout is None:
wx.MessageBox("There is no layout information, so positions are randomly assigned.", "Message", wx.OK | wx.ICON_INFORMATION)
else:
numCompGlyphs = layout.getNumCompartmentGlyphs()
numSpecGlyphs = layout.getNumSpeciesGlyphs()
for i in range(numCompGlyphs):
compGlyph = layout.getCompartmentGlyph(i)
temp_id = compGlyph.getCompartmentId()
comp_id_list.append(temp_id)
boundingbox = compGlyph.getBoundingBox()
height = boundingbox.getHeight()
width = boundingbox.getWidth()
pos_x = boundingbox.getX()
pos_y = boundingbox.getY()
comp_dimension_list.append([width,height])
comp_position_list.append([pos_x,pos_y])
for i in range(numSpecGlyphs):
specGlyph = layout.getSpeciesGlyph(i)
spec_id = specGlyph.getSpeciesId()
spec_id_list.append(spec_id)
boundingbox = specGlyph.getBoundingBox()
height = boundingbox.getHeight()
width = boundingbox.getWidth()
pos_x = boundingbox.getX()
pos_y = boundingbox.getY()
spec_dimension_list.append([width,height])
spec_position_list.append([pos_x,pos_y])
rPlugin = layout.getPlugin("render")
if (rPlugin != None and rPlugin.getNumLocalRenderInformationObjects() > 0):
info = rPlugin.getRenderInformation(0)
color_list = []
for j in range ( 0, info.getNumColorDefinitions()):
color = info.getColorDefinition(j)
color_list.append([color.getId(),color.createValueString()])
for j in range (0, info.getNumStyles()):
style = info.getStyle(j)
group = style.getGroup()
typeList = style.createTypeString()
if 'COMPARTMENTGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getFill():
comp_fill_color = hex_to_rgb(color_list[k][1])
if color_list[k][0] == group.getStroke():
comp_border_color = hex_to_rgb(color_list[k][1])
comp_border_width = group.getStrokeWidth()
elif 'SPECIESGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getFill():
spec_fill_color = hex_to_rgb(color_list[k][1])
if color_list[k][0] == group.getStroke():
spec_border_color = hex_to_rgb(color_list[k][1])
spec_border_width = group.getStrokeWidth()
elif 'REACTIONGLYPH' in typeList:
for k in range(len(color_list)):
if color_list[k][0] == group.getStroke():
reaction_line_color = hex_to_rgb(color_list[k][1])
reaction_line_width = group.getStrokeWidth()
model = simplesbml.loadSBMLStr(self.sbmlStr)
numFloatingNodes = model.getNumFloatingSpecies()
FloatingNodes_ids = model.getListOfFloatingSpecies()
numBoundaryNodes = model.getNumBoundarySpecies()
BoundaryNodes_ids = model.getListOfBoundarySpecies()
numRxns = model.getNumReactions()
Rxns_ids = model.getListOfReactionIds()
numComps = model.getNumCompartments()
Comps_ids = model.getListOfCompartmentIds()
numNodes = numFloatingNodes + numBoundaryNodes
for i in range(numComps):
temp_id = Comps_ids[i]
vol= model.getCompartmentVolume(i)
if len(comp_id_list) != 0:
#if mplugin is not None:
for j in range(numComps):
if comp_id_list[j] == temp_id:
dimension = comp_dimension_list[j]
position = comp_position_list[j]
else:# no layout info about compartment,
# then the whole size of the canvas is the compartment size
dimension = [4000,2500]
position = [0,0]
api.add_compartment(net_index, id=temp_id, volume = vol,
size=Vec2(dimension[0],dimension[1]),position=Vec2(position[0],position[1]),
fill_color = api.Color(comp_fill_color[0],comp_fill_color[1],comp_fill_color[2]),
border_color = api.Color(comp_border_color[0],comp_border_color[1],comp_border_color[2]),
border_width = comp_border_width)
comp_node_list = [0]*numComps
for i in range(numComps):
comp_node_list[i] = []
if len(comp_id_list) != 0:
#if mplugin is not None:
for i in range (numFloatingNodes):
temp_id = FloatingNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
for j in range(numNodes):
if temp_id == spec_id_list[j]:
dimension = spec_dimension_list[j]
position = spec_position_list[j]
nodeIdx_temp = api.add_node(net_index, id=temp_id, floatingNode = True,
size=Vec2(dimension[0],dimension[1]), position=Vec2(position[0],position[1]),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range (numBoundaryNodes):
temp_id = BoundaryNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
for j in range(numNodes):
if temp_id == spec_id_list[j]:
dimension = spec_dimension_list[j]
position = spec_position_list[j]
nodeIdx_temp = api.add_node(net_index, id=temp_id, floatingNode = False,
size=Vec2(dimension[0],dimension[1]), position=Vec2(position[0],position[1]),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
else: # there is no layout information, assign position randomly and size as default
comp_id_list = Comps_ids
for i in range (numFloatingNodes):
temp_id = FloatingNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
nodeIdx_temp = api.add_node(net_index, id=temp_id, size=Vec2(60,40), floatingNode = True,
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800)),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range (numBoundaryNodes):
temp_id = BoundaryNodes_ids[i]
comp_id = model.getCompartmentIdSpeciesIsIn(temp_id)
nodeIdx_temp = api.add_node(net_index, id=temp_id, size=Vec2(60,40), floatingNode = False,
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800)),
fill_color=api.Color(spec_fill_color[0],spec_fill_color[1],spec_fill_color[2]),
border_color=api.Color(spec_border_color[0],spec_border_color[1],spec_border_color[2]),
border_width=spec_border_width)
for j in range(numComps):
if comp_id == comp_id_list[j]:
comp_node_list[j].append(nodeIdx_temp)
for i in range(numComps):
temp_id = Comps_ids[i]
for j in range(numComps):
if comp_id_list[j] == temp_id:
node_list_temp = comp_node_list[j]
for j in range(len(node_list_temp)):
api.set_compartment_of_node(net_index=net_index, node_index=node_list_temp[j], comp_index=i)
#handle_positions, center_pos was set as the default
numNodes = api.node_count(net_index)
allNodes = api.get_nodes(net_index)
for i in range (numRxns):
src = []
dst = []
temp_id = Rxns_ids[i]
kinetics = model.getRateLaw(i)
rct_num = model.getNumReactants(i)
prd_num = model.getNumProducts(i)
for j in range(rct_num):
rct_id = model.getReactant(temp_id,j)
for k in range(numNodes):
if allNodes[k].id == rct_id:
src.append(allNodes[k].index)
for j in range(prd_num):
prd_id = model.getProduct(temp_id,j)
for k in range(numNodes):
if allNodes[k].id == prd_id:
dst.append(allNodes[k].index)
api.add_reaction(net_index, id=temp_id, reactants=src, products=dst, rate_law = kinetics,
fill_color=api.Color(reaction_line_color[0],reaction_line_color[1],reaction_line_color[2]),
line_thickness=reaction_line_width)
Version 0.01: Author: Gary Geng (2020)
"""
# pylint: disable=maybe-no-member
from rkviewer.utils import opacity_mul
from rkviewer.canvas.state import ArrowTip
import wx
from typing import List, Tuple
from rkplugin import api
from rkplugin.plugins import PluginMetadata, WindowedPlugin
from rkplugin.api import Vec2
metadata = PluginMetadata(name='ArrowDesigner',
author='Gary Geng',
version='0.0.1',
short_desc='Arrow tip designer for reactions.',
long_desc='Arrow tip designer for reactions.')
class DesignerWindow(wx.Window):
"""
Defining the designer window.
"""
def __init__(self, parent, arrow_tip: ArrowTip):
"""
Creates the designer window for the arraw to design.
Args:
self: the Designer Window to initialize.
class AlignCircle(WindowedPlugin):
metadata = PluginMetadata(name='AlignCircle',
author='Evan Yip (2021)',
version='0.0.1',
short_desc='Align Circle',
long_desc='Aligns the nodes into a circle',
category=PluginCategory.UTILITIES)
def __init__(self):
"""
Initialize the AlignCircle
Args:
self
"""
# allows the align circle class to inherit
# the methods of the Windowed Plugin Class
super().__init__()
def create_window(self, dialog):
"""
Create a window to do the structural analysis.
Args:
self
dialog
"""
# Making the window
window = wx.Panel(dialog, pos=(5, 100), size=(300, 155))
wx.StaticText(window, -1, 'Select nodes to arrange in circle',
(15, 10))
# Use default radius
wx.StaticText(window, -1, 'Use default radius:', (15, 30))
self.defaultCheck = wx.CheckBox(window, -1, pos=(150, 30))
self.defaultCheck.SetValue(True)
# Making radius setable
wx.StaticText(window, -1, 'Input desired radius:', (15, 55))
self.radiusText = wx.TextCtrl(window,
-1,
'0', (150, 55),
size=(120, 22))
self.radiusText.SetInsertionPoint(0)
self.radiusText.Bind(wx.EVT_TEXT, self.OnText_radius) # binding test
self.radiusValue = float(self.radiusText.GetValue())
# Making the toggle button
apply_btn = wx.ToggleButton(window,
-1,
'Apply', (100, 85),
size=(80, 22))
apply_btn.SetValue(False)
# Binding the method to the button
apply_btn.Bind(wx.EVT_TOGGLEBUTTON, self.Apply)
return window
def find_center(self, num_nodes, nodes):
"""
Takes in the number of nodes and list of node indices and
computes the optimal centerpoint for the circle
Parameters: num_nodes(int) - number of nodes,
node_indices(list) - list of nodes indices
Returns: center(tuple)
"""
# Max dimension of the node size
max_dim = 0 # will consider this the diameter of a circle node
for i in nodes:
# Get node
node = api.get_node_by_index(0, i)
for dim in node.size:
if dim > max_dim:
max_dim = dim
# Approximate circumference estimate
spacing = max_dim / 4
circum_estimate = num_nodes * (max_dim + spacing)
# Computing radius
r = circum_estimate / (2 * np.pi) + max_dim
center = (r, r)
return center
def cart(self, r, theta):
"""
Converts from polar coordinates to cartesian coordinates
Parameters: r(double), theta(double in radians)
Returns: (x,y) cartesian coordinate tuple
"""
x = r * math.cos(theta)
y = r * math.sin(theta)
return x, y
def get_new_position(self, node_index, r, theta):
"""
Takes in the node index and outputs the new position for that node
Parameters: r(double), theta(double in radians)
Returns: (x,y) cartesian coordinate tuple
"""
node = api.get_node_by_index(0, node_index)
size = node.size # (width, height)
# accounting for slight offset, converting to cartesian
nodeCenter = self.cart(r - size[0], theta)
# accounting for node position being specified by top left corner
x = r + nodeCenter[0] - size[0] / 2
y = r + nodeCenter[1] + size[1] / 2
return Vec2(x, y)
def OnText_radius(self, event):
"""
Catches exception if self.radiusText can not be converted
to a floating point number. Opens a window.
"""
update = event.GetString()
if update != '':
try:
self.radiusValue = float(self.radiusText.GetValue())
except:
wx.MessageBox(
"Please enter a floating point number"
"for the desired radius", "Message",
wx.OK | wx.ICON_INFORMATION)
def CheckSelection(self, nodes):
"""
Verifies that there are selected nodes. Raises window if
no nodes are selected, but apply button is pressed
"""
if nodes == 0:
wx.MessageBox("Please select desired nodes to arrange"
"in circle", "Message", wx.OK | wx.ICON_INFORMATION)
return True
def Apply(self, event):
"""
If apply button is clicked, the nodes will be arranged in a circle
using either a default radius or a user input radius.
"""
def translate_nodes(node_indices, r, phi):
"""
Takes in list of node indices, desired radius, and phi
and moves the current node
to its new position
"""
# Iterate through the nodes and change their position.
node_num = 0
for i in node_ind:
theta = node_num * phi # angle position for node
newPos = self.get_new_position(i, r, theta)
if newPos[0] < 0 or newPos[1] < 0:
wx.MessageBox("Please increase radius size", "Message",
wx.OK | wx.ICON_INFORMATION)
return
api.move_node(0, i, newPos, False)
node_num += 1 # updating node number
# Get button and checkbox state
btn_state = event.GetEventObject().GetValue()
# chk_state = self.OnDefaultCheck()
chk_state = self.defaultCheck.GetValue()
# If the button is pressed, arrange the nodes into a circle
if btn_state is True:
# Get number of nodes selected
node_len = len(api.selected_node_indices())
# get list of node indices
node_ind = api.selected_node_indices()
# If no nodes selected raise error
select = self.CheckSelection(node_len)
if select is True:
return
# If default radius is checked
if chk_state is True:
# Compute the expected center of the circle
center = self.find_center(node_len, node_ind)
# Compute the angle step between each node
phi = 2 * math.pi / node_len
r = center[0] # radius
translate_nodes(node_ind, r, phi)
else:
r = self.radiusValue
center = Vec2(r, r)
phi = 2 * math.pi / node_len # angle step between each node
translate_nodes(node_ind, r, phi) # translating nodes
# Making the reactions straight lines
rxns = api.get_reaction_indices(0)
for rxn in rxns:
api.update_reaction(net_index=0,
reaction_index=rxn,
use_bezier=False)
# Setting button state back to False (unclicked)
event.GetEventObject().SetValue(False)
class LayoutNetworkX(WindowedPlugin):
metadata = PluginMetadata(
name='Auto Layout',
author='Carmen and Herbert M Sauro',
version='0.5.2',
short_desc='Auto Layout using networkX.',
long_desc='Rearrange a random network into a neat auto layout',
category=PluginCategory.UTILITIES,
)
def create_window(self, dialog):
'''
Create a window with several inputs and buttons.
Args:
self
dialog
'''
# TODO: k, gravity, useMagnetism, useBoundary, useGrid
self.window = wx.Panel(dialog, pos=(5,100), size=(350, 220))
self.sizer = wx.FlexGridSizer(cols=2, vgap=10, hgap=0)
self.sizer.AddGrowableCol(0, 0.6)
self.sizer.AddGrowableCol(1, 0.4)
self.sizer.Add((0, 10))
self.sizer.Add((0, 10))
self.MaxIterText = wx.TextCtrl(self.window, -1, "100", size=(100, -1))
self.MaxIterText.SetInsertionPoint(0)
self.MaxIterText.Bind(wx.EVT_TEXT, self.OnText_MaxIter)
self.MaxIterValue = int(self.MaxIterText.GetValue())
self.AddField('Max Number of Iterations', self.MaxIterText)
self.kText = wx.TextCtrl(self.window, -1, "70", size=(100, -1))
self.kText.SetInsertionPoint(0)
self.kText.Bind(wx.EVT_TEXT, self.OnText_k)
self.kValue = float(self.kText.GetValue())
self.AddField('k (float > 0)', self.kText)
self.scaleText = wx.TextCtrl(self.window, -1, "550", size=(100, -1))
self.scaleText.SetInsertionPoint(0)
self.scaleText.Bind(wx.EVT_TEXT, self.OnText_scale)
self.scaleValue = float(self.scaleText.GetValue())
self.AddField('Scale of Layout', self.scaleText)
self.useCentroid = False
self.centroidCheckBox = wx.CheckBox(self.window)
self.centroidCheckBox.Bind(wx.EVT_CHECKBOX, self.OnCheckUseCentroid)
self.AddField('Also Arrange Centroids', self.centroidCheckBox)
# add spacer left of button
self.sizer.Add((0, 0))
apply_btn = wx.Button(self.window, -1, 'Run', (220, 130))
apply_btn.Bind(wx.EVT_BUTTON, self.Apply)
self.sizer.Add(apply_btn)
self.window.SetPosition (wx.Point(10,10))
self.window.SetSizer(self.sizer)
return self.window
def AddField(self, text, field):
self.sizer.Add(wx.StaticText(self.window, label=text), wx.SizerFlags().Border(wx.LEFT, 20))
self.sizer.Add(field)
def OnText_MaxIter(self, evt):
try:
update = evt.GetString()
if update != '':
self.MaxIterValue = int(self.MaxIterText.GetValue())
except ValueError:
wx.MessageBox('Value must be a number', 'Error', wx.OK | wx.ICON_INFORMATION)
def OnText_k(self, evt):
try:
update = evt.GetString()
if update != '':
self.kValue = float(self.kText.GetValue())
except ValueError:
wx.MessageBox('Value must be a number', 'Error', wx.OK | wx.ICON_INFORMATION)
def OnText_scale(self, evt):
try:
update = evt.GetString()
if update != '':
self.scaleValue = float(self.scaleText.GetValue())
except ValueError:
wx.MessageBox('Value must be a number', 'Error', wx.OK | wx.ICON_INFORMATION)
def OnCheckUseCentroid(self, evt):
cb = evt.GetEventObject()
self.useCentroid = cb.GetValue()
def Apply(self, evt):
if api.node_count(0) == 0:
return
G = nx.Graph()
nodesInd = np.array(list(api.get_node_indices(0)))
reactionsInd = np.array(list(api.get_reaction_indices(0)))
originalPos = {}
def generateGraph():
# add nodes and centroids as "nodes" for networkX
nodes = np.array(list(api.get_node_indices(0)))
#reactionsInd = np.array(list(api.get_reaction_indices(0)))
cStr = np.empty_like(reactionsInd, dtype=str)
cStr[:,] = "c"
centroidId = np.char.add(cStr, reactionsInd.astype(str))
G.add_nodes_from(centroidId)
nStr = np.empty_like(nodes, dtype=str)
nStr[:,] = "n"
nodesId = np.array(list(np.char.add(nStr, nodesInd.astype(str))))
G.add_nodes_from(nodesId)
'''
for n in nodes:
centroidsTo = np.array(list(api.get_reactions_as_product(0, n))) # Gets the reactions in which it is a product -> TO
cStr = np.empty_like(centroidsTo, dtype=str)
cStr[:,] = "c"
centroidsToIn = np.char.add(cStr, centroidsTo.astype(str)) # centroids from which the node is product
centroidsFrom = np.array(list(api.get_reactions_as_reactant(0, n))) # reactions in which it is a reactanr -> FROM
cStr = np.empty_like(centroidsFrom, dtype=str)
cStr[:,] = "c"
centroidsFromIn = np.char.add(cStr, centroidsFrom.astype(str)) # centroids to which the node is reactant
nS = np.empty_like(centroidsToIn, dtype = str)
nS[:,] = "n"
numS = np.empty_like(centroidsToIn, dtype = int)
numS[:,] = n
nodeIndArrayTo = np.char.add(nS, numS.astype(str))
nS = np.empty_like(centroidsFromIn, dtype = str)
nS[:,] = "n"
numS = np.empty_like(centroidsFromIn, dtype = int)
numS[:,] = n
nodeIndArrayFrom = np.char.add(nS, numS.astype(str))
edgesTo = np.array(list(zip(centroidsToIn, nodeIndArrayTo)))
edgesFrom = np.array(list(zip(nodeIndArrayFrom, centroidsFromIn)))
G.add_edges_from(edgesTo)
G.add_edges_from(edgesFrom)
'''
# Add edges from reactant to centroid and centroid to product (undirected)
edges = list()
for reaction in api.get_reactions(0):
for s in reaction.sources:
edges.append(('n' + str(s), 'c' + str(reaction.index)))
for t in reaction.targets:
edges.append(('c' + str(reaction.index), 'n' + str(t)))
G.add_edges_from(edges)
cn = 0
for rea in api.get_reactions(0):
cent = api.compute_centroid(0, rea.sources, rea.targets)
#originalPos[centroidId[cn]] = list([cent.x, cent.y])
originalPos['c' + str(rea)] = list([random.randint(0,600), random.randint(0,600)])
cn = cn + 1
for nod in api.get_nodes(0):
#originalPos[nodesId[cn]] = list([nod.position.x, nod.position.y])
# random.randint(0,500), nod.position.y+random.randint (0,500)])
originalPos['n' + str(nod)] = list([random.randint(0,600), random.randint (0,600)])
cn = cn + 1
generateGraph()
#print(nx.to_dict_of_lists(G))
#nodeIds = list (api.get_node_indices(0))
with api.group_action():
for t in range(1):
pos = (nx.fruchterman_reingold_layout(G, k = self.kValue, iterations = self.MaxIterValue, scale = self.scaleValue, pos = originalPos, weight=1))
positions = np.array(list(pos.values()))
minX = 0
minY = 0
for p in positions:
if p[0] < minX:
minX = p[0]
if p[1] < minY:
minY = p[1]
positions = positions - np.array([minX, minY])
centroids = positions[0: len(reactionsInd)]
nodes = positions[len(reactionsInd): len(positions)]
count = 0
for n in nodes:
newX = float(n[0])
newY = float(n[1])
api.move_node(0, nodesInd[count], position = Vec2(newX, newY), allowNegativeCoordinates=True)
count = count + 1
if self.useCentroid:
count = 0
for c in centroids:
newX = float(c[0])
newY = float(c[1])
r = api.get_reaction_by_index(0, reactionsInd[count])
handles = api.default_handle_positions(0, r.index)
api.update_reaction(0, r.index, center_pos=Vec2(newX, newY), handle_positions=handles)
count = count + 1
else:
for index in api.get_reaction_indices(0):
api.update_reaction(0, index, center_pos=None)
handles = api.default_handle_positions(0, index)
api.update_reaction(0, index, handle_positions=handles)
'''
for r in api.get_reactions(0):
currCentroid = centroids[r.index]
newX = float(currCentroid[0])
newY = float(currCentroid[1])
api.update_reaction(0, r.index, center_pos=(Vec2(newX, newY)))
#api.update_reaction(0, r.index, center_pos=None)
handles = api.default_handle_positions(0, r.index)
api.set_reaction_center_handle(0, r.index, handles[0])
count = 1
for s in r.sources:
api.set_reaction_node_handle(0, r.index, s, True, handles[count])
count += 1
for t in r.targets:
api.set_reaction_node_handle(0, r.index, t, False, handles[count])
count += 1
'''
ws = api.window_size()
offset = Vec2(ws.x/4, ws.y/4)
api.translate_network(0, offset, check_bounds = True)
class AddReaction(WindowedPlugin):
metadata = PluginMetadata(
name='AddReaction',
author='Jin Xu and Herbert Sauro',
version='0.0.1',
short_desc='Add Reactions.',
long_desc='Add different reactions including UniUni, BiUni, UniBi and BiBi.',
category=PluginCategory.UTILITIES,
)
def __init__(self):
"""
Initialize the StructuralAnalysis Plugin.
Args:
self
"""
super().__init__()
self.uniuniState = False
self.biuniState = False
self.unibiState = False
self.bibiState = False
self.src = []
self.dest = []
def create_window(self, dialog):
"""
Create a window to do the structural analysis.
Args:
self
dialog
"""
window = wx.Panel(dialog, pos=(5,100), size=(150, 190))
wx.StaticText(window, -1, 'Select reaction type', (15,10))
wx.StaticText(window, -1, 'then select nodes:', (15,25))
self.UniUni_btn = wx.ToggleButton(window, -1, 'UniUni', (36, 22+25), size=(62,22))
self.UniUni_btn.Bind(wx.EVT_TOGGLEBUTTON, self.UniUni)
self.BiUni_btn = wx.ToggleButton(window, -1, 'BiUni', (36, 47+25), size=(62,22))
self.BiUni_btn.Bind(wx.EVT_TOGGLEBUTTON, self.BiUni)
self.UniBi_btn = wx.ToggleButton(window, -1, 'UniBi', (36, 72+25), size=(62,22))
self.UniBi_btn.Bind(wx.EVT_TOGGLEBUTTON, self.UniBi)
self.BiBi_btn = wx.ToggleButton(window, -1, 'BiBi', (36, 97+25), size=(62,22))
self.BiBi_btn.Bind(wx.EVT_TOGGLEBUTTON, self.BiBi)
window.SetPosition (wx.Point(10,10))
return window
def on_did_create_dialog(self):
# Set position of popup window to top-left corner of screen
self.dialog.SetPosition((240, 250))
def on_will_close_window(self, evt):
# print ("***** Window Closed *****")
evt.Skip()
def getUniqueName(self, base: str, names: list) -> str:
increment = 0
# keep incrementing until you find a unique Id
while True:
suffix = '_{}'.format(increment)
cur_id = base + suffix
if cur_id in names:
increment += 1
continue
else:
# loop finished normally; done
return cur_id
def addReaction (self, src, dest):
# THis method is callde for all reactions
names = []
# Get a unique reaction name
for r in api.get_reactions (0):
names.append (r.id)
reactionId = self.getUniqueName('reaction', names)
r_idx = api.add_reaction(0, reactionId, src, dest, fill_color=api.Color(129, 123, 255))
def on_selection_did_change(self, evt):
"""
Overrides base class event handler to update number of items selected.
Args:
self
node_indices(List[int]): List of node indices changed.
reaction_indices (List[int]): List of reaction indices changed.
compartment_indices (List[int]): List of compartment indices changed.
"""
if len (list(evt.node_indices)) == 0:
self.src = []
self.dest = []
return
if (not self.uniuniState) and (not self.biuniState) and \
(not self.unibiState) and (not self.bibiState):
return
self.node_clicked = list(evt.node_indices)
try:
if self.uniuniState:
if len(self.src) == 0:
self.src.append (self.node_clicked[0])
return
if len (self.dest) == 0:
self.dest.append (self.node_clicked[0])
self.addReaction (self.src, self.dest)
return
if self.biuniState:
if len(self.src) == 0:
self.src.append (self.node_clicked[0])
return
if len (self.src) == 1:
self.src.append (self.node_clicked[0])
return
if (len (self.src) <= 2) and len (self.dest) == 0:
self.dest.append (self.node_clicked[0])
self.addReaction (self.src, self.dest)
return
if self.unibiState:
if len(self.src) == 0:
self.src.append (self.node_clicked[0])
return
if len (self.dest) == 0:
self.dest.append (self.node_clicked[0])
return
if (len (self.src) <= 1) and len (self.dest) == 1:
self.dest.append (self.node_clicked[0])
self.addReaction (self.src, self.dest)
return
if self.bibiState:
if len(self.src) == 0:
self.src.append (self.node_clicked[0])
return
if len (self.src) == 1:
self.src.append (self.node_clicked[0])
return
if len (self.dest) == 0:
self.dest.append (self.node_clicked[0])
return
if (len (self.src) <= 2) and len (self.dest) == 1:
self.dest.append (self.node_clicked[0])
self.addReaction (self.src, self.dest)
return
except:
pass #wx.MessageBox("Error: Try again", "Message", wx.OK | wx.ICON_INFORMATION)
def UniUni(self, evt):
"""
Handler for the "UniUni" button. add a UniUni reaction.
"""
state = evt.GetEventObject().GetValue()
if state == True:
self.src = []
self.dest = []
# This code is to make the buttons work as a radionbutton
self.uniuniState = True
self.biuniState = False
self.unibiState = False
self.bibiState = False
self.BiUni_btn.SetValue (False)
self.UniBi_btn.SetValue (False)
self.BiBi_btn.SetValue (False)
else:
self.uniuniState = False
def BiUni(self, evt):
"""
Handler for the "BiUni" button. add a BiUni reaction.
"""
state = evt.GetEventObject().GetValue()
if state == True:
self.src = []
self.dest = []
# This code is to make the buttons work as a radionbutton
self.uniuniState = False
self.biuniState = True
self.unibiState = False
self.bibiState = False
self.UniUni_btn.SetValue (False)
self.UniBi_btn.SetValue (False)
self.BiBi_btn.SetValue (False)
else:
self.biuniState = False
def UniBi(self, evt):
"""
Handler for the "UniBi" button. add a UniBi reaction.
"""
state = evt.GetEventObject().GetValue()
if state == True:
self.src = []
self.dest = []
# This code is to make the buttons work as a radionbutton
self.uniuniState = False
self.biuniState = False
self.unibiState = True
self.bibiState = False
self.UniUni_btn.SetValue (False)
self.BiUni_btn.SetValue (False)
self.BiBi_btn.SetValue (False)
else:
self.unibiState = False
def BiBi(self, evt):
"""
Handler for the "UniBi" button. add a UniBi reaction.
"""
state = evt.GetEventObject().GetValue()
if state == True:
self.src = []
self.dest = []
# This code is to make the buttons work as a radionbutton
self.uniuniState = False
self.biuniState = False
self.unibiState = False
self.bibiState = True
self.UniUni_btn.SetValue (False)
self.BiUni_btn.SetValue (False)
self.UniBi_btn.SetValue (False)
else:
self.bibiState = False
class StructuralAnalysis(WindowedPlugin):
metadata = PluginMetadata(
name='StructuralAnalysis',
author='Jin Xu',
version='0.0.1',
short_desc='Structural Analysis.',
long_desc=
'StructuralAnalysis Plugin is to calculate and visualize the stoichiometry matrix and conserved moieties for the network.',
category=PluginCategory.ANALYSIS)
def __init__(self):
"""
Initialize the StructuralAnalysis Plugin.
Args:
self
"""
super().__init__()
self.index_list = []
def create_window(self, dialog):
"""
Create a window to do the structural analysis.
Args:
self
dialog
"""
topPanel = wx.Panel(dialog, pos=(0, 0), size=(700, 500))
# Create two panels size by side
panel1 = wx.Panel(topPanel, -1, pos=(0, 100), size=(200, 100))
panel2 = wx.Panel(topPanel, -1, pos=(100, 100), size=(450, 100))
sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(panel1, 0, wx.EXPAND | wx.ALL, border=10)
sizer.Add(panel2, 0, wx.EXPAND | wx.ALL, border=10)
topPanel.SetSizer(sizer)
# Add a notebook to the second panel
nb = wx.Notebook(panel2)
# Create the tabs
self.tab1 = TabOne(nb)
self.tab2 = TabTwo(nb)
nb.AddPage(self.tab1, "Stoichiometry")
nb.AddPage(self.tab2, "Moiety Conservation Laws")
# Make sure the second panel fills the right side.
sizer = wx.BoxSizer()
sizer.Add(nb, 1, wx.EXPAND)
panel2.SetSizer(sizer)
Compute_btn = wx.Button(panel1, -1, 'Compute Conservation Laws',
(20, 20))
Compute_btn.Bind(wx.EVT_BUTTON, self.Compute)
wx.StaticText(panel1, -1, 'Select a row from the table of', (20, 100))
wx.StaticText(panel1, -1, 'Moiety Conservation Laws', (20, 120))
wx.StaticText(panel1, -1, 'and pick a color:', (20, 140))
Picker = wx.ColourPickerCtrl(panel1, pos=(20, 160))
Picker.Bind(wx.EVT_COLOURPICKER_CHANGED, self.color_callback)
wx.StaticText(panel1, -1, 'Unhighlight the nodes:', (20, 240))
Clear_Btn = wx.Button(panel1, -1, 'Clear', (20, 260))
Clear_Btn.Bind(wx.EVT_BUTTON, self.unhighlight)
return topPanel
def on_did_create_dialog(self):
# Set position of popup window to top-left corner of screen
self.dialog.SetPosition((240, 250))
def Compute(self, evt):
"""
Handler for the "Compute" button.
Get the network on canvas.
Calculate the Stoichiometry Matrix and Conservation Matrix for the randon network.
"""
#self.index_list=[]
def nullspace(A, atol=1e-13, rtol=0):
A = _np.atleast_2d(A)
u, s, vh = _np.linalg.svd(A)
tol = max(atol, rtol * s[0])
nnz = (s >= tol).sum()
ns = vh[nnz:].conj().T
return ns
def rref(B, tol=1e-8, debug=False):
A = B.copy()
rows, cols = A.shape
r = 0
pivots_pos = []
row_exchanges = _np.arange(rows)
for c in range(cols):
if debug:
print("Now at row", r, "and col", c, "with matrix:")
print(A)
## Find the pivot row:
pivot = _np.argmax(_np.abs(A[r:rows, c])) + r
m = _np.abs(A[pivot, c])
if debug: print("Found pivot", m, "in row", pivot)
if m <= tol:
## Skip column c, making sure the approximately zero terms are
## actually zero.
A[r:rows, c] = _np.zeros(rows - r)
if debug:
print("All elements at and below (", r, ",", c,
") are zero.. moving on..")
else:
## keep track of bound variables
pivots_pos.append((r, c))
if pivot != r:
## Swap current row and pivot row
A[[pivot, r], c:cols] = A[[r, pivot], c:cols]
row_exchanges[[pivot, r]] = row_exchanges[[r, pivot]]
if debug:
print("Swap row", r, "with row", pivot, "Now:")
print(A)
## Normalize pivot row
A[r, c:cols] = A[r, c:cols] / A[r, c]
## Eliminate the current column
v = A[r, c:cols]
## Above (before row r):
if r > 0:
ridx_above = _np.arange(r)
A[ridx_above,
c:cols] = A[ridx_above, c:cols] - _np.outer(
v, A[ridx_above, c]).T
if debug:
print("Elimination above performed:")
print(A)
## Below (after row r):
if r < rows - 1:
ridx_below = _np.arange(r + 1, rows)
A[ridx_below,
c:cols] = A[ridx_below, c:cols] - _np.outer(
v, A[ridx_below, c]).T
if debug:
print("Elimination below performed:")
print(A)
r += 1
## Check if done
if r == rows:
break
return (A, pivots_pos, row_exchanges)
netIn = 0
numNodes = api.node_count(netIn)
if numNodes == 0:
wx.MessageBox("Please import a network on canvas", "Message",
wx.OK | wx.ICON_INFORMATION)
else:
allNodes = api.get_nodes(netIn)
id = allNodes[0].id[0:-2]
self.default_color = allNodes[0].fill_color
largest_node_index = 0
for i in range(numNodes):
if allNodes[i].index > largest_node_index:
largest_node_index = allNodes[i].index
row = largest_node_index + 1
numReactions = api.reaction_count(netIn)
#print("numReactions:", numReactions)
col = numReactions
self.st = _np.zeros((row, col))
allReactions = api.get_reactions(netIn)
for i in range(numReactions):
for j in range(len(allReactions[i].sources)):
#print(allReactions[i].sources[j])
for m in range(row):
if allReactions[i].sources[j] == m:
self.st.itemset((m, i), -1)
for j in range(len(allReactions[i].targets)):
#print(allReactions[i].targets[j])
for m in range(row):
if allReactions[i].targets[j] == m:
self.st.itemset((m, i), 1)
stt = _np.transpose(self.st)
m = _np.transpose(nullspace(stt))
moi_mat = rref(m)[0]
# set all the values of non-existing nodes to zero
for i in range(moi_mat.shape[0]):
for j in range(moi_mat.shape[1]):
if _np.array_equal(self.st[j, :],
_np.zeros(self.st.shape[1])):
moi_mat.itemset((i, j), 0.)
for i in range(self.st.shape[1]):
self.tab1.grid_st.SetColLabelValue(i, "J" + str(i))
for i in range(self.st.shape[0]):
self.tab1.grid_st.SetRowLabelValue(i, id + "_" + str(i))
for row in range(self.st.shape[0]):
for col in range(self.st.shape[1]):
self.tab1.grid_st.SetCellValue(
row, col, "%d" % self.st.item(row, col))
for i in range(moi_mat.shape[1]):
self.tab2.grid_moi.SetColLabelValue(i, id + "_" + str(i))
CSUM_id = 0
for i in range(moi_mat.shape[0]):
a = moi_mat[i, :]
a = [0 if a_ < 0.005 else a_
for a_ in a] # some elements are very small
if _np.array_equal(
a, _np.zeros(moi_mat.shape[1])
): # delete the row if all the elements are zero
CSUM_id = CSUM_id
else:
self.tab2.grid_moi.SetRowLabelValue(
CSUM_id, "CSUM" + str(CSUM_id))
for j in range(moi_mat.shape[1]):
self.tab2.grid_moi.SetCellValue(
CSUM_id, j, format(moi_mat[i][j], ".2f")) #
CSUM_id += 1
def printSelectedCells(self, top_left, bottom_right):
"""
Based on code from http://ginstrom.com/scribbles/2008/09/07/getting-the-selected-cells-from-a-wxpython-grid/
"""
cells = []
rows_start = top_left[0]
rows_end = bottom_right[0]
cols_start = top_left[1]
cols_end = bottom_right[1]
rows = range(rows_start, rows_end + 1)
cols = range(cols_start, cols_end + 1)
cells.extend([(row, col) for row in rows for col in cols])
#self.index_list = []
for cell in cells:
row, col = cell
value = self.tab2.grid_moi.GetCellValue(row, col)
#print(value)
if value != "0.00" and value != "+0.00" and value != "-0.00" and value != "":
self.index_list.append(int(col))
#print("selected nodes:", self.index_list)
def color_callback(self, evt):
"""
Get whatever cells are currently selected
"""
cells = self.tab2.grid_moi.GetSelectedCells()
if not cells:
if self.tab2.grid_moi.GetSelectionBlockTopLeft():
top_left = self.tab2.grid_moi.GetSelectionBlockTopLeft()[0]
bottom_right = self.tab2.grid_moi.GetSelectionBlockBottomRight(
)[0]
self.printSelectedCells(top_left, bottom_right)
#else:
# print (self.currentlySelectedCell)
else:
print("no cells are selected")
"""
Callback for the color picker control; sets the color of every node/reaction selected.
"""
wxcolor = evt.GetColour()
color = Color.from_rgb(wxcolor.GetRGB())
# start group action context for undo purposes
with api.group_action():
# color selected nodes
#for index in api.selected_node_indices():
if len(self.index_list) == 0:
wx.MessageBox("Please select a row and pick a color again",
"Message", wx.OK | wx.ICON_INFORMATION)
try:
for index in self.index_list:
api.update_node(api.cur_net_index(),
index,
fill_color=color,
border_color=color)
except:
wx.MessageBox("Please select a row and pick a color again",
"Message", wx.OK | wx.ICON_INFORMATION)
def unhighlight(self, evt):
"""
Callback for the color picker control; sets the color of every node/reaction selected.
"""
# start group action context for undo purposes
with api.group_action():
# color selected nodes
#for index in api.selected_node_indices():
try:
for index in self.index_list:
api.update_node(api.cur_net_index(),
index,
fill_color=self.default_color,
border_color=self.default_color)
except:
wx.MessageBox("There is no highlighted nodes", "Message",
wx.OK | wx.ICON_INFORMATION)
class RandomNetwork(WindowedPlugin):
metadata = PluginMetadata(
name='RandomNetwork',
author='Jin Xu, Herbert M Sauro',
version='0.0.1',
short_desc='Random network.',
long_desc='Display a random network with certain number of species and reactions as input.',
category=PluginCategory.UTILITIES
)
def __init__(self):
"""
Initialize the RandomNetwork.
Args:
self
"""
super().__init__()
def create_window(self, dialog):
"""
Create a window with several inputs and buttons.
Args:
self
dialog
"""
window = wx.Panel(dialog, pos=(5,100), size=(300, 320))
numSpecs = wx.StaticText(window, -1, 'Number of Species:', (20,20))
self.numSpecsText = wx.TextCtrl(window, -1, str(DefaultValues.maxSpecies), (160, 20), size=(100, -1))
self.numSpecsText.SetInsertionPoint(0)
self.numSpecsText.Bind(wx.EVT_TEXT, self.OnText_numSpecs)
self.numSpecsValue = int(self.numSpecsText.GetValue())
numRxns = wx.StaticText(window, -1, 'Number of Reactions:', (20,50))
self.numRxnsText = wx.TextCtrl(window, -1, str(DefaultValues.maxReactions), (160, 50), size=(100, -1))
self.numRxnsText.SetInsertionPoint(0)
self.numRxnsText.Bind(wx.EVT_TEXT, self.OnText_numRxns)
self.numRxnsValue = int(self.numRxnsText.GetValue())
probUniUni = wx.StaticText(window, -1, 'Probability of UniUni:', (20,90))
self.probUniUniText = wx.TextCtrl(window, -1, str(DefaultValues.probUniUniValue), (160, 90), size=(100, -1))
self.probUniUniText.SetInsertionPoint(0)
self.probUniUniText.Bind(wx.EVT_TEXT, self.OnText_UniUni)
self.probUniUniValue = float(self.probUniUniText.GetValue())
probBiUni = wx.StaticText(window, -1, 'Probability of BiUni:', (20,120))
self.probBiUniText = wx.TextCtrl(window, -1, str(DefaultValues.probBiUniValue), (160, 120), size=(100, -1))
self.probBiUniText.SetInsertionPoint(0)
self.probBiUniText.Bind(wx.EVT_TEXT, self.OnText_BiUni)
self.probBiUniValue = float(self.probBiUniText.GetValue())
probUniBi = wx.StaticText(window, -1, 'Probability of UniBi:', (20,150))
self.probUniBiText = wx.TextCtrl(window, -1, str(DefaultValues.probUniBiValue), (160, 150), size=(100, -1))
self.probUniBiText.SetInsertionPoint(0)
self.probUniBiText.Bind(wx.EVT_TEXT, self.OnText_UniBi)
self.probUniBiValue = float(self.probUniBiText.GetValue())
probBiBi = wx.StaticText(window, -1, 'Probability of BiBi:', (20,180))
self.probBiBiText = wx.TextCtrl(window, -1, str(DefaultValues.probBiBiValue), (160, 180), size=(100, -1))
self.probBiBiText.SetInsertionPoint(0)
self.probBiBiText.Bind(wx.EVT_TEXT, self.OnText_BiBi)
self.probBiBiValue = float(self.probBiBiText.GetValue())
randomSeed = wx.StaticText(window, -1, 'Random seed:', (20,210))
randomSeed = wx.StaticText(window, -1, '0 means no seed setup', (20,230))
self.randomSeedText = wx.TextCtrl(window, -1, str(DefaultValues.randomSeed), (160, 210), size=(100, -1))
self.randomSeedText.SetInsertionPoint(0)
self.randomSeedText.Bind(wx.EVT_TEXT, self.OnText_randomSeed)
self.randomSeedValue = float(self.randomSeedText.GetValue())
apply_btn = wx.Button(window, -1, 'Apply', (160, 250))
apply_btn.Bind(wx.EVT_BUTTON, self.Apply)
return window
def OnText_numSpecs(self, evt):
update = evt.GetString()
if update != '':
try:
self.numSpecsValue = int(self.numSpecsText.GetValue())
except:
wx.MessageBox("Please enter an integer for the number of species.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_numRxns(self, evt):
update = evt.GetString()
if update != '':
try:
self.numRxnsValue = int(self.numRxnsText.GetValue())
except:
wx.MessageBox("Please enter an integer for the number of reactions.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_UniUni(self, evt):
update = evt.GetString()
if update != '':
try:
self.probUniUniValue = float(self.probUniUniText.GetValue())
except:
wx.MessageBox("Please enter a floating point number for the probability of UniUni.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_BiUni(self, evt):
update = evt.GetString()
if update != '':
#DefaultValues.probBiUniValue = float(self.probBiUniText.GetValue())
try:
self.probBiUniValue = float(self.probBiUniText.GetValue())
except:
wx.MessageBox("Please enter a floating point number for the probability of BiUni.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_UniBi(self, evt):
update = evt.GetString()
if update != '':
try:
self.probUniBiValue = float(self.probUniBiText.GetValue())
except:
wx.MessageBox("Please enter a floating point number for the probability of UniBi.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_BiBi(self, evt):
update = evt.GetString()
if update != '':
try:
self.probBiBiValue = float(self.probBiBiText.GetValue())
except:
wx.MessageBox("Please enter a floating point number for the probability of BiBi.", "Message", wx.OK | wx.ICON_INFORMATION)
def OnText_randomSeed(self, evt):
update = evt.GetString()
if update != '':
try:
self.randomSeedValue = float(self.randomSeedText.GetValue())
except:
wx.MessageBox("Please enter a valid random seed other than zero.", "Message", wx.OK | wx.ICON_INFORMATION)
def Apply(self, evt):
"""
Handler for the "apply" button. apply the random network.
"""
if self.randomSeedValue != 0:
_random.seed(self.randomSeedValue)
class _TReactionType:
UNIUNI = 0
BIUNI = 1
UNIBI = 2
BIBI = 3
def _pickReactionType():
rt = _random.random()
if rt < self.probUniUniValue:
return _TReactionType.UNIUNI
elif rt < self.probUniUniValue + self.probBiUniValue:
return _TReactionType.BIUNI
elif rt < self.probUniUniValue + self.probBiUniValue + self.probUniBiValue:
return _TReactionType.UNIBI
else:
return _TReactionType.BIBI
# Generates a reaction network in the form of a reaction list
# reactionList = [nSpecies, reaction, reaction, ....]
# reaction = [reactionType, [list of reactants], [list of products], rateConsta>
# Disallowed reactions:
# S1 -> S1
# S1 + S2 -> S2 # Can't have the same reactant and product
# S1 + S1 -> S1
def _generateReactionList (nSpecies, nReactions):
reactionList = []
for r in range(nReactions):
rateConstant = _random.random()
rt = _pickReactionType()
if rt == _TReactionType.UNIUNI:
# UniUni
reactant = _random.randint (0, nSpecies-1)
product = _random.randint (0, nSpecies-1)
# Disallow S1 -> S1 type of reaction
while product == reactant:
product = _random.randint (0, nSpecies-1)
reactionList.append ([rt, [reactant], [product], rateConstant])
if rt == _TReactionType.BIUNI:
# BiUni
# Pick two reactants
reactant1 = _random.randint (0, nSpecies-1)
reactant2 = _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactants
species = range (nSpecies)
# Remove reactant1 and 2 from the species list
species = _np.delete (species, [reactant1, reactant2], axis=0)
# Then pick a product from the reactants that are left
product = species[_random.randint (0, len (species)-1)]
reactionList.append ([rt, [reactant1, reactant2], [product], rateConstant])
if rt == _TReactionType.UNIBI:
# UniBi
reactant1 = _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactant
species = range (nSpecies)
# Remove reactant1 from the species list
species = _np.delete (species, [reactant1], axis=0)
# Then pick a product from the reactants that are left
product1 = species[_random.randint (0, len (species)-1)]
product2 = species[_random.randint (0, len (species)-1)]
reactionList.append ([rt, [reactant1], [product1, product2], rateConstant])
if rt == _TReactionType.BIBI:
# BiBi
reactant1 = _random.randint (0, nSpecies-1)
reactant2= _random.randint (0, nSpecies-1)
# pick a product but only products that don't include the reactant
species = range (nSpecies)
# Remove reactant1 and 2 from the species list
species = _np.delete (species, [reactant1, reactant2], axis=0)
# Then pick a product from the reactants that are left
product1 = species[_random.randint (0, len (species)-1)]
product2 = species[_random.randint (0, len (species)-1)]
element = [rt, [reactant1, reactant2], [product1, product2], rateConstant]
reactionList.append (element)
reactionList.insert (0, nSpecies)
return reactionList
# Includes boundary and floating species
# Returns a list:
# [New Stoichiometry matrix, list of floatingIds, list of boundaryIds]
def _getFullStoichiometryMatrix (reactionList):
nSpecies = reactionList[0]
reactionListCopy = _copy.deepcopy (reactionList)
reactionListCopy.pop (0)
st = _np.zeros ((nSpecies, len(reactionListCopy)))
for index, r in enumerate (reactionListCopy):
if r[0] == _TReactionType.UNIUNI:
# UniUni
reactant = reactionListCopy[index][1][0]
st[reactant, index] = -1
product = reactionListCopy[index][2][0]
st[product, index] = 1
if r[0] == _TReactionType.BIUNI:
# BiUni
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
reactant2 = reactionListCopy[index][1][1]
st[reactant2, index] = -1
product = reactionListCopy[index][2][0]
st[product, index] = 1
if r[0] == _TReactionType.UNIBI:
# UniBi
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
product1 = reactionListCopy[index][2][0]
st[product1, index] = 1
product2 = reactionListCopy[index][2][1]
st[product2, index] = 1
if r[0] == _TReactionType.BIBI:
# BiBi
reactant1 = reactionListCopy[index][1][0]
st[reactant1, index] = -1
reactant2 = reactionListCopy[index][1][1]
st[reactant2, index] = -1
product1 = reactionListCopy[index][2][0]
st[product1, index] = 1
product2 = reactionListCopy[index][2][1]
st[product2, index] = 1
return st
def _getRateLaw (floatingIds, boundaryIds, reactionList, isReversible):
nSpecies = reactionList[0]
# Remove the first element which is the nSpecies
reactionListCopy = _copy.deepcopy (reactionList)
reactionListCopy.pop (0)
antStr_tot = []
for index, r in enumerate (reactionListCopy):
antStr= ''
antStr = antStr + 'J' + str (index) + ': '
if r[0] == _TReactionType.UNIUNI:
# UniUni
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0])
antStr = antStr + ')'
if r[0] == _TReactionType.BIUNI:
# BiUni
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0]) + '*S' + str (reactionListCopy[index][1][1])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0])
antStr = antStr + ')'
if r[0] == _TReactionType.UNIBI:
# UniBi
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0]) + '*S' + str (reactionListCopy[index][2][1])
antStr = antStr + ')'
if r[0] == _TReactionType.BIBI:
# BiBi
antStr = antStr + '(k' + str (index) + '*S' + str (reactionListCopy[index][1][0]) + '*S' + str (reactionListCopy[index][1][1])
if isReversible:
antStr = antStr + ' - k' + str (index) + 'r' + '*S' + str (reactionListCopy[index][2][0]) + '*S' + str (reactionListCopy[index][2][1])
antStr = antStr + ')'
antStr_tot.append(antStr)
return antStr_tot
test_prob = self.probUniUniValue + self.probBiUniValue + self.probUniBiValue + self.probBiBiValue
if test_prob != 1:
wx.MessageBox("The sum of probabilities should be one!", "Message", wx.OK | wx.ICON_INFORMATION)
else:
net_index = 0
api.clear_network(net_index)
rl = _generateReactionList (self.numSpecsValue, self.numRxnsValue)
st = _getFullStoichiometryMatrix (rl)
antStr = _getRateLaw (st[1], st[2], rl, isReversible=True)
numNodes = st.shape[0]
numRxns = st.shape[1]
nodeIdx = []
for i in range (numNodes):
nodeIdx.append (api.add_node(net_index, 'node_{}'.format(i), size=Vec2(60,40), fill_color=api.Color(255, 204, 153),
border_color=api.Color(255, 108, 9),
position=Vec2(40 + math.trunc (_random.random()*800), 40 + math.trunc (_random.random()*800))))
for i in range (numRxns):
src = []
dest = []
for j in range(numNodes):
if (st.item(j,i) == -1):
src.append(nodeIdx[j])
if (st.item(j,i) == 1):
dest.append(nodeIdx[j])
r_idx = api.add_reaction(net_index, 'reaction_{}'.format(i), src, dest, fill_color=api.Color(91, 176, 253))
# Need to remove orphan nodes
for i in range (numNodes):
if _np.array_equal(st[i,:], _np.zeros(numRxns)):
api.delete_node(net_index, nodeIdx[i])
class ExportSBML(WindowedPlugin):
metadata = PluginMetadata(
name='ExportSBML',
author='Jin Xu',
version='0.0.2',
short_desc='Export SBML.',
long_desc=
'Export the SBML String from the network on canvas and save it to a file.',
category=PluginCategory.ANALYSIS)
def create_window(self, dialog):
"""
Create a window to export the SBML.
Args:
self
dialog
"""
self.window = wx.Panel(dialog, pos=(5, 100), size=(300, 320))
export_btn = wx.Button(self.window, -1, 'Export', (5, 5))
export_btn.Bind(wx.EVT_BUTTON, self.Export)
save_btn = wx.Button(self.window, -1, 'Save', (100, 5))
save_btn.Bind(wx.EVT_BUTTON, self.Save)
wx.StaticText(self.window, -1, 'SBML string:', (5, 30))
self.SBMLText = wx.TextCtrl(self.window,
-1,
"", (10, 50),
size=(260, 220),
style=wx.TE_MULTILINE)
self.SBMLText.SetInsertionPoint(0)
return self.window
def Export(self, evt):
"""
Handler for the "Export" button.
Get the network on canvas and change it to an SBML string.
"""
isReversible = True
netIn = 0
numNodes = api.node_count(netIn)
numReactions = api.reaction_count(netIn)
if numNodes == 0: #or numReactions == 0 :
wx.MessageBox("Please import a network on canvas", "Message",
wx.OK | wx.ICON_INFORMATION)
else:
allNodes = api.get_nodes(netIn)
allReactions = api.get_reactions(netIn)
allcompartments = api.get_compartments(netIn)
numCompartments = len(allcompartments)
#######################################
# Creates an SBMLNamespaces object with the given SBML level, version
# package name, package version.
#
# (NOTE) By default, the name of package (i.e. "layout") will be used
# if the argument for the prefix is missing or empty. Thus the argument
# for the prefix can be added as follows:
#
# SBMLNamespaces sbmlns(3,1,"layout",1,"LAYOUT")
#
sbmlns = SBMLNamespaces(3, 1, "layout", 1)
# create the document
document = SBMLDocument(sbmlns)
# set the "required" attribute of layout package to "true"
document.setPkgRequired("layout", False)
# create the Model
model = document.createModel()
model.setId("Model_layout")
document.setModel(model)
# create the Compartment and species
if numCompartments != 0:
for i in range(numCompartments):
compartment = model.createCompartment()
comp_id = allcompartments[i].id
compartment.setId(comp_id)
compartment.setConstant(True)
for j in range(len(allcompartments[i].nodes)):
spec_id = allNodes[allcompartments[i].nodes[j]].id
species = model.createSpecies()
species.setId(spec_id)
species.setCompartment(comp_id)
species.setInitialConcentration(1.0)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
if allNodes[allcompartments[i].
nodes[j]].floatingNode == False:
species.setBoundaryCondition(True)
else: #set default compartment
compartment = model.createCompartment()
comp_id = "c_0"
compartment.setId(comp_id)
compartment.setConstant(True)
for i in range(numNodes):
spec_id = allNodes[i].id
species = model.createSpecies()
species.setId(spec_id)
species.setCompartment(comp_id)
species.setInitialConcentration(1.0)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
if allNodes[i].floatingNode == False:
species.setBoundaryCondition(True)
species.setConstant(True)
# create reactions:
for i in range(numReactions):
reaction_id = allReactions[i].id
rct = [] # id list of the rcts
prd = []
rct_num = len(allReactions[i].sources)
prd_num = len(allReactions[i].targets)
for j in range(rct_num):
rct.append(allNodes[allReactions[i].sources[j]].id)
for j in range(prd_num):
prd.append(allNodes[allReactions[i].targets[j]].id)
kinetic_law = ''
parameter_list = []
kinetic_law = kinetic_law + 'E' + str(i) + '*(k' + str(i)
parameter_list.append('E' + str(i))
parameter_list.append('k' + str(i))
for j in range(rct_num):
kinetic_law = kinetic_law + '*' + rct[j]
reaction = model.createReaction()
reaction.setId(allReactions[i].id)
reaction.setReversible(False)
reaction.setFast(False)
if isReversible:
reaction.setReversible(True)
kinetic_law = kinetic_law + ' - k' + str(i) + 'r'
parameter_list.append('k' + str(i) + 'r')
for j in range(prd_num):
kinetic_law = kinetic_law + '*' + prd[j]
kinetic_law = kinetic_law + ')'
for j in range(len(parameter_list)):
parameters = model.createParameter()
parameters.setId(parameter_list[j])
parameters.setValue(0.1)
parameters.setConstant(True)
kinetics = reaction.createKineticLaw()
kinetics.setFormula(kinetic_law)
for j in range(rct_num):
reference = reaction.createReactant()
reference.setSpecies(rct[j])
ref_id = "SpecRef_" + reaction_id + "_rct" + str(j)
reference.setId(ref_id)
reference.setStoichiometry(1.)
reference.setConstant(False)
for j in range(prd_num):
reference = reaction.createProduct()
reference.setSpecies(prd[j])
ref_id = "SpecRef_" + reaction_id + "_prd" + str(j)
reference.setId(ref_id)
reference.setStoichiometry(1.)
reference.setConstant(False)
# create the Layout
#
# set the LayoutPkgNamespaces for Level 3 Version1 Layout Version 1
#
layoutns = LayoutPkgNamespaces(3, 1, 1)
renderns = RenderPkgNamespaces(3, 1, 1)
#
# Get a LayoutModelPlugin object plugged in the model object.
#
# The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
# thus the value needs to be casted for the corresponding derived class.
#
mplugin = model.getPlugin("layout")
# rPlugin = model.getPlugin("render")
# if rPlugin is None:
# print("there is no render outside layout.")
# lolPlugin = mplugin.getListOfLayouts().getPlugin("render")
# if lolPlugin is None:
# print("there is no render info inside layout.")
if mplugin is None:
# print(
# "[Fatal Error] Layout Extension Level " + layoutns.getLevel() + " Version " + layoutns.getVersion() + " package version " + layoutns.getPackageVersion() + " is not registered.")
# sys.exit(1)
wx.MessageBox("There is no layout information.", "Message",
wx.OK | wx.ICON_INFORMATION)
#
# Creates a Layout object via LayoutModelPlugin object.
#
layout = mplugin.createLayout()
layout.setId("Layout_1")
layout.setDimensions(Dimensions(layoutns, 800.0, 800.0))
# random network (40+800x, 40+800y)
#create the CompartmentGlyph and SpeciesGlyphs
if numCompartments != 0:
for i in range(numCompartments):
comp_id = allcompartments[i].id
compartmentGlyph = layout.createCompartmentGlyph()
compG_id = "CompG_" + comp_id
compartmentGlyph.setId(compG_id)
compartmentGlyph.setCompartmentId(comp_id)
bb_id = "bb_" + comp_id
pos_x = allcompartments[i].position.x
pos_y = allcompartments[i].position.y
width = allcompartments[i].size.x
height = allcompartments[i].size.y
compartmentGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
for j in range(len(allcompartments[i].nodes)):
spec_id = allNodes[allcompartments[i].nodes[j]].id
speciesGlyph = layout.createSpeciesGlyph()
specG_id = "SpecG_" + spec_id
speciesGlyph.setId(specG_id)
speciesGlyph.setSpeciesId(spec_id)
bb_id = "bb_" + spec_id
pos_x = allNodes[
allcompartments[i].nodes[j]].position.x
pos_y = allNodes[
allcompartments[i].nodes[j]].position.y
width = allNodes[allcompartments[i].nodes[j]].size.x
height = allNodes[allcompartments[i].nodes[j]].size.y
speciesGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph = layout.createTextGlyph()
textG_id = "TextG_" + spec_id
textGlyph.setId(textG_id)
bb_id = "bb_spec_text_" + spec_id
textGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph.setOriginOfTextId(specG_id)
textGlyph.setGraphicalObjectId(specG_id)
else: #there is no compartment
for i in range(numNodes):
spec_id = allNodes[i].id
speciesGlyph = layout.createSpeciesGlyph()
specG_id = "SpecG_" + spec_id
speciesGlyph.setId(specG_id)
speciesGlyph.setSpeciesId(spec_id)
bb_id = "bb_" + spec_id
pos_x = allNodes[i].position.x
pos_y = allNodes[i].position.y
width = allNodes[i].size.x
height = allNodes[i].size.y
speciesGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph = layout.createTextGlyph()
textG_id = "TextG_" + spec_id
textGlyph.setId(textG_id)
bb_id = "bb_spec_text_" + spec_id
textGlyph.setBoundingBox(
BoundingBox(layoutns, bb_id, pos_x, pos_y, width,
height))
textGlyph.setOriginOfTextId(specG_id)
textGlyph.setGraphicalObjectId(specG_id)
# create the ReactionGlyphs and SpeciesReferenceGlyphs
for i in range(numReactions):
reaction_id = allReactions[i].id
reactionGlyph = layout.createReactionGlyph()
reactionG_id = "RectionG_" + reaction_id
reactionGlyph.setId(reactionG_id)
reactionGlyph.setReactionId(reaction_id)
reactionCurve = reactionGlyph.getCurve()
ls = reactionCurve.createLineSegment()
centroid = api.compute_centroid(0, allReactions[i].sources,
allReactions[i].targets)
ls.setStart(Point(layoutns, centroid.x, centroid.y))
ls.setEnd(Point(layoutns, centroid.x, centroid.y))
rct = [] # id list of the rcts
prd = []
rct_num = len(allReactions[i].sources)
prd_num = len(allReactions[i].targets)
for j in range(rct_num):
rct.append(allNodes[allReactions[i].sources[j]].id)
for j in range(prd_num):
prd.append(allNodes[allReactions[i].targets[j]].id)
for j in range(rct_num):
ref_id = "SpecRef_" + reaction_id + "_rct" + str(j)
speciesReferenceGlyph = reactionGlyph.createSpeciesReferenceGlyph(
)
specsRefG_id = "SpecRefG_" + reaction_id + "_rct" + str(j)
specG_id = "SpecG_" + rct[j]
speciesReferenceGlyph.setId(specsRefG_id)
speciesReferenceGlyph.setSpeciesGlyphId(specG_id)
speciesReferenceGlyph.setSpeciesReferenceId(ref_id)
speciesReferenceGlyph.setRole(SPECIES_ROLE_UNDEFINED)
speciesReferenceCurve = speciesReferenceGlyph.getCurve()
cb = speciesReferenceCurve.createCubicBezier()
#cb = speciesReferenceCurve.createLineSegment()
cb.setStart(Point(layoutns, centroid.x, centroid.y))
handles = api.default_handle_positions(
netIn, allReactions[i].index)
pos_x = handles[1 + j].x
pos_y = handles[1 + j].y
cb.setBasePoint1(Point(layoutns, pos_x, pos_y))
cb.setBasePoint2(Point(layoutns, pos_x, pos_y))
pos_x = allNodes[allReactions[i].sources[j]].position.x
pos_y = allNodes[allReactions[i].sources[j]].position.y
width = allNodes[allReactions[i].sources[j]].size.x
height = allNodes[allReactions[i].sources[j]].size.y
cb.setEnd(
Point(layoutns, pos_x + 0.5 * width,
pos_y - 0.5 * height))
for j in range(prd_num):
ref_id = "SpecRef_" + reaction_id + "_prd" + str(j)
speciesReferenceGlyph = reactionGlyph.createSpeciesReferenceGlyph(
)
specsRefG_id = "SpecRefG_" + reaction_id + "_prd" + str(j)
specG_id = "SpecG_" + prd[j]
speciesReferenceGlyph.setId(specsRefG_id)
speciesReferenceGlyph.setSpeciesGlyphId(specG_id)
speciesReferenceGlyph.setSpeciesReferenceId(ref_id)
speciesReferenceGlyph.setRole(SPECIES_ROLE_UNDEFINED)
speciesReferenceCurve = speciesReferenceGlyph.getCurve()
cb = speciesReferenceCurve.createCubicBezier()
#cb = speciesReferenceCurve.createLineSegment()
cb.setStart(Point(layoutns, centroid.x, centroid.y))
handles = api.default_handle_positions(
netIn, allReactions[i].index)
pos_x = handles[1 + j].x
pos_y = handles[1 + j].y
cb.setBasePoint1(Point(layoutns, pos_x, pos_y))
cb.setBasePoint2(Point(layoutns, pos_x, pos_y))
pos_x = allNodes[allReactions[i].targets[j]].position.x
pos_y = allNodes[allReactions[i].targets[j]].position.y
width = allNodes[allReactions[i].targets[j]].size.x
height = allNodes[allReactions[i].targets[j]].size.y
cb.setEnd(
Point(layoutns, pos_x + 0.5 * width,
pos_y - 0.5 * height))
sbmlStr_layout = writeSBMLToString(
document) #sbmlStr is w/o layout info
#self.SBMLText.SetValue(sbmlStr_layout)
doc = readSBMLFromString(sbmlStr_layout)
model_layout = doc.getModel()
mplugin = model_layout.getPlugin("layout")
# add render information to the first layout
layout = mplugin.getLayout(0)
rPlugin = layout.getPlugin("render")
uri = RenderExtension.getXmlnsL2() if doc.getLevel(
) == 2 else RenderExtension.getXmlnsL3V1V1()
# enable render package
doc.enablePackage(uri, "render", True)
doc.setPackageRequired("render", False)
rPlugin = layout.getPlugin("render")
rInfo = rPlugin.createLocalRenderInformation()
rInfo.setId("info")
rInfo.setName("Render Information")
rInfo.setProgramName("RenderInformation")
rInfo.setProgramVersion("1.0")
# add some colors
if numCompartments != 0:
fill_color = allcompartments[0].fill_color
border_color = allcompartments[0].border_color
comp_border_width = allcompartments[0].border_width
fill_color_str = '#%02x%02x%02x' % (fill_color.r, fill_color.g,
fill_color.b)
border_color_str = '#%02x%02x%02x' % (
border_color.r, border_color.g, border_color.b)
else:
comp_border_width = 2.
fill_color_str = '#9ea9ff'
border_color_str = '#001dff'
#nodeData does not have fill_color,border_color,border_width
node = allNodes[0]
# spec_fill_color = node.fill_color
# spec_border_color = node.border_color
# spec_border_width = node.border_width
# spec_fill_color_str = '#%02x%02x%02x' % (spec_fill_color.r,spec_fill_color.g,spec_fill_color.b)
# spec_border_color_str = '#%02x%02x%02x' % (spec_border_color.r,spec_border_color.g,spec_border_color.b)
spec_fill_color_str = '#ffcc99'
spec_border_color_str = '#ff6c09'
spec_border_width = 2.
if numReactions != 0:
reaction_fill_color = allReactions[0].fill_color
reaction_fill_color_str = '#%02x%02x%02x' % (
reaction_fill_color.r, reaction_fill_color.g,
reaction_fill_color.b)
reaction_line_thickness = allReactions[i].line_thickness
#add some colors
color = rInfo.createColorDefinition()
color.setId("black")
color.setColorValue("#000000")
color = rInfo.createColorDefinition()
color.setId("comp_fill_color")
color.setColorValue(fill_color_str)
color = rInfo.createColorDefinition()
color.setId("comp_border_color")
color.setColorValue(border_color_str)
color = rInfo.createColorDefinition()
color.setId("spec_fill_color")
color.setColorValue(spec_fill_color_str)
color = rInfo.createColorDefinition()
color.setId("spec_border_color")
color.setColorValue(spec_border_color_str)
if numReactions != 0:
color = rInfo.createColorDefinition()
color.setId("reaction_fill_color")
color.setColorValue(reaction_fill_color_str)
# add a list of styles
style = rInfo.createStyle("compStyle")
style.getGroup().setFillColor("comp_fill_color")
style.getGroup().setStroke("comp_border_color")
style.getGroup().setStrokeWidth(comp_border_width)
style.addType("COMPARTMENTGLYPH")
rectangle = style.getGroup().createRectangle()
rectangle.setCoordinatesAndSize(RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 100),
RelAbsVector(0, 100))
style = rInfo.createStyle("specStyle")
style.getGroup().setFillColor("spec_fill_color")
style.getGroup().setStroke("spec_border_color")
style.getGroup().setStrokeWidth(spec_border_width)
style.addType("SPECIESGLYPH")
rectangle = style.getGroup().createRectangle()
rectangle.setCoordinatesAndSize(RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 0),
RelAbsVector(0, 100),
RelAbsVector(0, 100))
style = rInfo.createStyle("textStyle")
style.getGroup().setStroke("black")
style.getGroup().setStrokeWidth(1.)
style.addType("TEXTGLYPH")
if numReactions != 0:
style = rInfo.createStyle("reactionStyle")
style.getGroup().setStroke("reaction_fill_color")
style.getGroup().setStrokeWidth(reaction_line_thickness)
style.addType("REACTIONGLYPH SPECIESREFERENCEGLYPH")
sbmlStr_layout_render = writeSBMLToString(doc)
self.SBMLText.SetValue(sbmlStr_layout_render)
def Save(self, evt):
"""
Handler for the "Save" button.
Save the SBML string to a file.
"""
self.dirname = "" #set directory name to blank
dlg = wx.FileDialog(self.window,
"Save As",
self.dirname,
wildcard="SBML files (*.xml)|*.xml",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
# Grab the content to be saved
itcontains = self.SBMLText.GetValue()
# Open the file for write, write, close
self.filename = dlg.GetFilename()
self.dirname = dlg.GetDirectory()
filehandle = open(os.path.join(self.dirname, self.filename), 'w')
filehandle.write(itcontains)
filehandle.close()
# Get rid of the dialog to keep things tidy
dlg.Destroy()
The color of all selected nodes and reactions are set to the picked color.
Version 0.01: Author: Gary Geng (2020)
"""
# pylint: disable=maybe-no-member
import wx
from typing import List
from rkplugin.plugins import CommandPlugin, PluginMetadata, WindowedPlugin
from rkplugin import api
metadata = PluginMetadata(
name='ColorSelected',
author='Gary Geng',
version='0.0.1',
short_desc='Pick a color, and set everything selected to that color.',
long_desc=
'The color of all selected nodes and reactions are set to the picked color.'
)
class ColorSelected(WindowedPlugin):
def __init__(self):
"""
Initialize the ColorSelected with no values for a Windowed Plugin.
Args:
self
"""
super().__init__(metadata)
The fill and border color of all nodes are set to a random color.
Version 0.01: Author: Gary Geng (2020)
"""
# pylint: disable=maybe-no-member
import wx
import random
from rkplugin.plugins import CommandPlugin, PluginMetadata
from rkplugin import api
metadata = PluginMetadata(
name='Disco',
author='Gary Geng',
version='0.0.1',
short_desc='Set all nodes to a random color.',
long_desc=
'The fill and border color of all nodes are set to a random color.')
class Disco(CommandPlugin):
def __init__(self):
"""
Initialize the ColorSelected with no values for a Command Plugin.
Args:
self
"""
super().__init__(metadata)