def __init__(self, index=-1, label='', thermo=None, conformer=None,
molecule=None, transportData=None, molecularWeight=None,
energyTransferModel=None, reactive=True, props=None, aug_inchi=None,
symmetryNumber = -1, creationIteration = 0, explicitlyAllowed=False):
self.index = index
self.label = label
self.thermo = thermo
self.conformer = conformer
self.molecule = molecule or []
self.transportData = transportData
self.reactive = reactive
self.molecularWeight = molecularWeight
self.energyTransferModel = energyTransferModel
self.props = props or {}
self.aug_inchi = aug_inchi
self.symmetryNumber = symmetryNumber
self.isSolvent = False
self.creationIteration = creationIteration
self.explicitlyAllowed = explicitlyAllowed
# Check multiplicity of each molecule is the same
if molecule is not None and len(molecule)>1:
mult = molecule[0].multiplicity
for m in molecule[1:]:
if mult != m.multiplicity:
raise SpeciesError('Multiplicities of molecules in species {species} do not match.'.format(species=label))
def __init__(self,
index=-1,
label='',
thermo=None,
conformer=None,
molecule=None,
transport_data=None,
molecular_weight=None,
energy_transfer_model=None,
reactive=True,
props=None,
smiles='',
inchi='',
aug_inchi=None,
symmetry_number=-1,
creation_iteration=0,
explicitly_allowed=False):
self.index = index
self.label = label
self.thermo = thermo
self.conformer = conformer
self.molecule = molecule or []
self.transport_data = transport_data
self.reactive = reactive
self.molecular_weight = molecular_weight
self.energy_transfer_model = energy_transfer_model
self.props = props or {}
self.aug_inchi = aug_inchi
self.symmetry_number = symmetry_number
self.is_solvent = False
self.creation_iteration = creation_iteration
self.explicitly_allowed = explicitly_allowed
self._fingerprint = None
self._inchi = None
self._smiles = None
if inchi and smiles:
logging.warning(
'Both InChI and SMILES provided for Species instantiation, '
'using InChI and ignoring SMILES.')
if inchi:
self.molecule = [Molecule(inchi=inchi)]
self._inchi = inchi
elif smiles:
self.molecule = [Molecule(smiles=smiles)]
self._smiles = smiles
# Check multiplicity of each molecule is the same
if molecule is not None and len(molecule) > 1:
mult = molecule[0].multiplicity
for m in molecule[1:]:
if mult != m.multiplicity:
raise SpeciesError(
'Multiplicities of molecules in species {species} '
'do not match.'.format(species=label))
def __init__(self,
index=-1,
label='',
thermo=None,
conformer=None,
molecule=None,
transportData=None,
molecularWeight=None,
energyTransferModel=None,
reactive=True,
props=None,
SMILES='',
InChI='',
aug_inchi=None,
symmetryNumber=-1,
creationIteration=0,
explicitlyAllowed=False):
self.index = index
self.label = label
self.thermo = thermo
self.conformer = conformer
self.molecule = molecule or []
self.transportData = transportData
self.reactive = reactive
self.molecularWeight = molecularWeight
self.energyTransferModel = energyTransferModel
self.props = props or {}
self.aug_inchi = aug_inchi
self.symmetryNumber = symmetryNumber
self.isSolvent = False
self.creationIteration = creationIteration
self.explicitlyAllowed = explicitlyAllowed
self._fingerprint = None
self._inchi = None
self._smiles = None
if InChI and SMILES:
logging.warning(
'Both InChI and SMILES provided for Species instantiation, using InChI and ignoring SMILES.'
)
if InChI:
self.molecule = [Molecule(InChI=InChI)]
self._inchi = InChI
elif SMILES:
self.molecule = [Molecule(SMILES=SMILES)]
self._smiles = SMILES
# Check multiplicity of each molecule is the same
if molecule is not None and len(molecule) > 1:
mult = molecule[0].multiplicity
for m in molecule[1:]:
if mult != m.multiplicity:
raise SpeciesError(
'Multiplicities of molecules in species {species} do not match.'
.format(species=label))
def getPartitionFunction(self, T):
"""
Return the partition function for the transition state at the
specified temperature `T` in K.
"""
cython.declare(Q=cython.double)
if self.conformer is not None and len(self.conformer.modes) > 0:
Q = self.conformer.getPartitionFunction(T)
else:
raise SpeciesError('Unable to calculate partition function for transition state {0!r}: no statmech data available.'.format(self.label))
return Q