def test_add_basic(self):
"""Simple tests for reactions."""
api.add_reaction(self.neti, 'AB', [0], [1])
reactions = api.get_reactions(self.neti)
self.assertEqual(1, len(reactions))
self.assertEqual(1, len(reactions[0].sources))
self.assertEqual(1, len(reactions[0].targets))
self.assertEqual(0, reactions[0].sources[0])
self.assertEqual(1, reactions[0].targets[0])
def test_reverse(self):
api.add_reaction(self.neti, 'AB', [0], [1])
self.assertTrue(api.is_reactant(self.neti, 0, 0))
self.assertFalse(api.is_reactant(self.neti, 1, 0))
self.assertFalse(api.is_product(self.neti, 0, 0))
self.assertTrue(api.is_product(self.neti, 1, 0))
self.assertFalse(api.is_reactant(self.neti, 2, 0))
self.assertFalse(api.is_product(self.neti, 2, 0))
api.add_reaction(self.neti, 'AC', [0], [2])
self.assertEqual(api.get_reactions_as_reactant(self.neti, 0), {0, 1})
self.assertEqual(api.get_reactions_as_product(self.neti, 0), set())
self.assertEqual(api.get_reactions_as_product(self.neti, 2), {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 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 test_simple_handles(self):
"""Simple tests for Bezier handles."""
api.add_reaction(self.neti, 'AB', [0], [1])
api.set_reaction_center_handle(0, 0, Vec2(-10, 30))
self.assertEqual(api.get_reaction_center_handle(0, 0), Vec2(-10, 30))
api.set_reaction_node_handle(0, 0, 0, True, Vec2(40, 50))
self.assertEqual(api.get_reaction_node_handle(0, 0, 0, True),
Vec2(40, 50))
with self.assertRaises(NodeIndexError):
api.get_reaction_node_handle(0, 0, 12, True)
# test for the case where node exists but not reactant/product
with self.assertRaises(ValueError):
api.get_reaction_node_handle(0, 0, 1, True)
with self.assertRaises(ValueError):
api.get_reaction_node_handle(0, 0, 0, False)
with self.assertRaises(ReactionIndexError):
api.get_reaction_node_handle(0, 2, 0, True)
def test_exceptional_reactions(self):
with self.assertRaises(ValueError):
api.add_reaction(self.neti, 'circular', [2], [2])
with self.assertRaises(ValueError):
api.add_reaction(self.neti, 'empty_reactants', [], [2])
with self.assertRaises(ValueError):
api.add_reaction(self.neti, 'empty_products', [2], [])
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 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])