def matchNodeToStructure(self, node, structure, atoms):
"""
Return :data:`True` if the `structure` centered at `atom` matches the
structure at `node` in the dictionary. The structure at `node` should
have atoms with the appropriate labels because they are set on loading
and never change. However, the atoms in `structure` may not have the
correct labels, hence the `atoms` parameter. The `atoms` parameter may
include extra labels, and so we only require that every labeled atom in
the functional group represented by `node` has an equivalent labeled
atom in `structure`.
"""
group = self.dictionary[node]
if group.__class__ == str or group.__class__ == unicode:
if group.lower() == 'union':
match = False
for child in self.tree.children[node]:
if self.matchNodeToStructure(child, structure, atoms):
match = True
return match
else:
return False
else:
centers = group.getLabeledAtoms()
map12_0 = {}; map21_0 = {}
for label in centers.keys():
if label in centers and label in atoms:
center = centers[label]; atom = atoms[label]
# Make sure labels actually pointed to atoms
if center is None or atom is None:
return False
# Semantic check #1: atoms with same label are equivalent
elif not atom.equivalent(center):
return False
# Semantic check #2: labeled atoms that share bond in one
# also share equivalent bond in the other
for atom1, atom2 in map21_0.iteritems():
if group.hasBond(center, atom1) and structure.hasBond(atom, atom2):
bond1 = group.getBond(center, atom1)
bond2 = structure.getBond(atom, atom2)
if not bond1.equivalent(bond2):
return False
elif group.hasBond(center, atom1) or structure.hasBond(atom, atom2):
return False
# Passed semantic checks, so add to maps of already-matched
# atoms
map21_0[center] = atom; map12_0[atom] = center
else:
return False
return structure.isSubgraphIsomorphic(group, map12_0, map21_0)
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