def reactionBasedAtomizationFile(xmlFile, outputDataFrame, options):
"""
get atomization metrics from a bng-xml file
"""
ratomizationDict = {}
try:
# console.bngl2xml('complex/output{0}.bngl'.format(element),timeout=10)
molecules, reactions, _ = readBNGXML.parseXML(xmlFile)
atomizedProcesses = 0
trueProcessesCounter = 0
for reaction in reactions:
if '0' in [str(x) for x in reaction[0].reactants] or '0' in \
[str(x) for x in reaction[0].products]:
continue
trueProcessesCounter += 1
# if len([x for x in action.action if x in ['Add','Delete']]) == 0:
# atomizedProcesses +=1
for action in reaction[0].actions:
if action.action in [
'AddBond', 'DeleteBond', 'StateChange',
'ChangeCompartment'
]:
atomizedProcesses += 1
break
#ato, nonato = stoichiometryAnalysis(rules)
#atomizedDistro.extend(ato)
#nonAtomizedDistro.extend(nonato)
score = atomizedProcesses * 1.0 / trueProcessesCounter if trueProcessesCounter != 0 else 0
#outputDataFrame = outputDataFrame.set_value(xmlFile,'score',score)
#outputDataFrame = outputDataFrame.set_value(xmlFile,'lenght',len(rules))
ccompression = len(molecules) * 1.0 / readBNGXML.getNumObservablesXML(
xmlFile) if readBNGXML.getNumObservablesXML(xmlFile) > 0 else 1
return xmlFile, score, len(reactions), ccompression
#ratomizationDict['score'] = score
#ratomizationDict['weight'] = weight
#ratomizationDict['length'] = len(rules)
except IOError:
print 'io', xmlFile
def reactionBasedAtomizationFile(xmlFile,outputDataFrame,options):
"""
get atomization metrics from a bng-xml file
"""
ratomizationDict = {}
try:
# console.bngl2xml('complex/output{0}.bngl'.format(element),timeout=10)
molecules, reactions, _ = readBNGXML.parseXML(xmlFile)
atomizedProcesses = 0
trueProcessesCounter = 0
for reaction in reactions:
if '0' in [str(x) for x in reaction[0].reactants] or '0' in \
[str(x) for x in reaction[0].products]:
continue
trueProcessesCounter += 1
# if len([x for x in action.action if x in ['Add','Delete']]) == 0:
# atomizedProcesses +=1
for action in reaction[0].actions:
if action.action in ['AddBond', 'DeleteBond', 'StateChange', 'ChangeCompartment']:
atomizedProcesses += 1
break
#ato, nonato = stoichiometryAnalysis(rules)
#atomizedDistro.extend(ato)
#nonAtomizedDistro.extend(nonato)
score = atomizedProcesses * 1.0 / trueProcessesCounter if trueProcessesCounter != 0 else 0
#outputDataFrame = outputDataFrame.set_value(xmlFile,'score',score)
#outputDataFrame = outputDataFrame.set_value(xmlFile,'lenght',len(rules))
ccompression = len(molecules)*1.0/readBNGXML.getNumObservablesXML(xmlFile) if readBNGXML.getNumObservablesXML(xmlFile) > 0 else 1
return xmlFile,score,len(reactions),ccompression
#ratomizationDict['score'] = score
#ratomizationDict['weight'] = weight
#ratomizationDict['length'] = len(rules)
except IOError:
print 'io',xmlFile
def spaceCoveredCDF():
spaceCoveredArray = []
atomizationDict = {}
with open("sortedD.dump", "rb") as f:
atomizationStats = pickle.load(f)
for element in atomizationStats:
try:
atomizationDict[element["index"]] = element["atomization"]
except:
continue
for element in range(1, 491):
try:
if element in atomizationDict and atomizationDict[element] > 0:
console.bngl2xml("complex/output{0}.bngl".format(element), timeout=10)
species, _, _ = readBNGXML.parseXML("output{0}.xml".format(element))
observablesLen = readBNGXML.getNumObservablesXML("output{0}.xml".format(element))
try:
spaceCoveredArray.append([atomizationDict[element], spaceCovered(species, observablesLen)])
print element, spaceCoveredArray[-1]
except CycleError:
spaceCoveredArray.append([atomizationDict[element], 0])
print element, -1
except (IOError, IndexError):
print
continue
with open("spaceCovered.dump", "wb") as f:
pickle.dump(spaceCoveredArray, f)
atomization, space = zip(*spaceCoveredArray)
heatmap, xedges, yedges = np.histogram2d(space, atomization, bins=8)
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]
plt.clf()
plt.imshow(heatmap, extent=extent)
plt.xlabel("space")
plt.ylabel("atomization")
plt.show()
plt.savefig("spaceCovered.png")
