def makeNewSpecies(structure, label='', reactive=True):
"""
Attempt to make a new species based on a chemical `structure`, which is a
:class:`Structure` object.
The proposed species is checked against the list of existing species; if the
species already exists, this function returns
the existing species. If the species does not exist, a :class:`Species`
object is created and returned after being appended to the global species
list.
"""
global speciesCounter
# # Recalculate atom types for proposed structure (hopefully not necessary)
# structure.simplifyAtomTypes()
# structure.updateAtomTypes()
# First check cache and return if species is found
for i, spec in enumerate(speciesCache):
if spec.isIsomorphic(structure):
speciesCache.pop(i)
speciesCache.insert(0, spec)
return spec
# Return an existing species if a match is found
for spec in speciesList:
if spec.isIsomorphic(structure):
speciesCache.insert(0, spec)
if len(speciesCache) > speciesCacheMaxSize: speciesCache.pop()
return spec
# Return None if the species has a forbidden structure
if thermo.forbiddenStructures is not None:
for lbl, struct in thermo.forbiddenStructures.iteritems():
if structure.isSubgraphIsomorphic(struct): return None
# Otherwise make a new species
if label == '':
# label = structure.getFormula()
# for atom in structure.atoms():
# if atom.hasFreeElectron(): label += 'J'
label = structure.toSMILES()
# Note in the log
spec = Species(speciesCounter+1, label, structure, reactive)
logging.verbose('Creating new species %s' % str(spec))
return processNewSpecies(spec)
def makeNewSpecies(structure, label='', reactive=True):
"""
Attempt to make a new species based on a chemical `structure`, which is a
:class:`Structure` object.
The proposed species is checked against the list of existing species; if the
species already exists, this function returns
the existing species. If the species does not exist, a :class:`Species`
object is created and returned after being appended to the global species
list.
"""
global speciesCounter
# # Recalculate atom types for proposed structure (hopefully not necessary)
# structure.simplifyAtomTypes()
# structure.updateAtomTypes()
# First check cache and return if species is found
for i, spec in enumerate(speciesCache):
if spec.isIsomorphic(structure):
speciesCache.pop(i)
speciesCache.insert(0, spec)
return spec
# Return an existing species if a match is found
for spec in speciesList:
if spec.isIsomorphic(structure):
speciesCache.insert(0, spec)
if len(speciesCache) > speciesCacheMaxSize: speciesCache.pop()
return spec
# Return None if the species has a forbidden structure
if thermo.forbiddenStructures is not None:
for lbl, struct in thermo.forbiddenStructures.iteritems():
if structure.isSubgraphIsomorphic(struct): return None
# Otherwise make a new species
if label == '':
# label = structure.getFormula()
# for atom in structure.atoms():
# if atom.hasFreeElectron(): label += 'J'
label = structure.toSMILES()
speciesCounter += 1
spec = Species(speciesCounter, label, structure, reactive)
speciesList.insert(0, spec)
spec.getResonanceIsomers()
if thermoDatabase is not None:
spec.getThermoData()
# Draw species
if settings.drawMolecules:
mol = pybel.Molecule(spec.toOBMol())
mol.draw(False, os.path.join(settings.outputDirectory, 'species/' + str(spec) + '.png'))
# Note in the log
logging.debug('Created new species ' + str(spec) )# + ': ' + spec.toInChI())
# Return the newly created species
speciesCache.insert(0, spec)
if len(speciesCache) > speciesCacheMaxSize: speciesCache.pop()
return spec
