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
def test_delete_items(self):
api.add_reaction(self.neti, 'AB', [0], [1])
with self.assertRaises(NodeNotFreeError):
api.delete_node(self.neti, 0)
with self.assertRaises(NodeNotFreeError):
api.delete_node(self.neti, 1)
api.delete_reaction(self.neti, 0)
api.delete_node(self.neti, 0)
api.delete_node(self.neti, 1)
api.delete_node(self.neti, 2)
self.assertEqual(list(), api.get_reactions(self.neti))
self.assertEqual(list(), api.get_nodes(self.neti))
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 test_add_alias(self):
size = Vec2(60, 60)
nodei = api.add_node(self.neti, id='Hookie', size=size)
api.add_alias(self.neti, nodei, size=size)
nodes = api.get_nodes(self.neti)
self.assertEqual(2, len(nodes))
original = NodeData(net_index=self.neti,
id='Hookie',
index=0,
original_index=-1,
size=size)
alias = NodeData(net_index=self.neti,
id='Hookie',
index=1,
original_index=0,
size=size)
self.assertEqual(original, nodes[0])
self.assertEqual(alias, nodes[1])
def test_add_basic(self):
node = Node('Charles', self.neti, pos=Vec2(50, 50), size=Vec2(50, 30))
api.add_node(
self.neti,
id=node.id,
position=node.position,
size=node.size,
fill_color=api._to_color(wx.RED), # HACK using API private methods
border_color=api._to_color(wx.BLUE),
border_width=2,
)
nodes = api.get_nodes(self.neti)
self.assertEqual(len(nodes), 1)
self.assertEqual(0, nodes[0].index)
expected = NodeData(id='Charles',
net_index=self.neti,
position=Vec2(50, 50),
size=Vec2(50, 30),
index=0)
self.assertEqual(expected, nodes[0])
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)
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 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 test_update_basic(self):
api.add_node(self.neti, id="Eric")
api.update_node(self.neti, 0, 'James')
nodes = api.get_nodes(self.neti)
self.assertEqual(len(nodes), 1)
self.assertEqual(nodes[0].id, 'James')