def loadEntry(
self,
index,
label,
group,
statmech,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
if (group[0:3].upper() == 'OR{' or group[0:4].upper() == 'AND{'
or group[0:7].upper() == 'NOT OR{'
or group[0:8].upper() == 'NOT AND{'):
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
self.entries[label] = Entry(
index=index,
label=label,
item=item,
data=statmech,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
)
def loadEntry(
self,
index,
label,
molecule,
solute,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
try:
spc = Species().fromSMILES(molecule)
except:
logging.debug(
"Solute '{0}' does not have a valid SMILES '{1}'".format(
label, molecule))
try:
spc = Species().fromAdjacencyList(molecule)
except:
logging.error(
"Can't understand '{0}' in solute library '{1}'".format(
molecule, self.name))
raise
self.entries[label] = Entry(
index=index,
label=label,
item=spc,
data=solute,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
)
def loadEntry(self,
index,
label,
molecule,
solute,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
try:
mol = Molecule(SMILES=molecule)
except:
try:
mol = Molecule().fromAdjacencyList(molecule)
except:
logging.error("Can't understand '{0}' in solute library '{1}'".format(molecule,self.name))
raise
self.entries[label] = Entry(
index = index,
label = label,
item = mol,
data = solute,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def loadEntry(self,
index,
label,
molecule,
thermo,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
molecule = Molecule().fromAdjacencyList(molecule)
# Internal checks for adding entry to the thermo library
if label in self.entries.keys():
raise DatabaseError('Found a duplicate molecule with label {0} in the thermo library. Please correct your library.'.format(label))
for entry in self.entries.values():
if molecule.isIsomorphic(entry.item):
if molecule.multiplicity == entry.item.multiplicity:
raise DatabaseError('Adjacency list and multiplicity of {0} matches that of existing molecule {1} in thermo library. Please correct your library.'.format(label, entry.label))
self.entries[label] = Entry(
index = index,
label = label,
item = molecule,
data = thermo,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def loadEntry(
self,
index,
label,
solvent,
molecule=None,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
if molecule is not None:
if not isinstance(molecule, list):
molecule = [molecule]
spc_list = []
for mol in molecule:
spc0 = Species(label=label)
spc0.set_structure(mol)
spc_list.append(spc0)
else:
spc_list = None
self.entries[label] = Entry(
index=index,
label=label,
item=spc_list,
data=solvent,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
)
def loadEntry(self, index, label, molecule, thermo, reference=None, referenceType='', shortDesc='', longDesc=''):
entry = Entry(
index = index,
label = label,
item = Molecule().fromAdjacencyList(molecule),
data = thermo,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
self.entries[label] = entry
return entry
def getFrequencyGroups(self, molecule):
"""
Return the set of characteristic group frequencies corresponding to the
speficied `molecule`. This is done by searching the molecule for
certain functional groups for which characteristic frequencies are
known, and using those frequencies.
"""
frequencies = []
groupCount = {}
# This is an additional hardcoded functional group for C-H with C in a ring
# It is hardcoded because the adjacency list format isn't well-equipped
# to handle this sort of functional group
ringCH = Entry(
label='ringCH',
item=None,
data=GroupFrequencies([(2750., 3150., 1), (900., 1100., 1)]),
)
# Generate estimate of thermodynamics
for atom in molecule.atoms:
# Iterate over heavy (non-hydrogen) atoms
if atom.isHydrogen(): continue
if molecule.isAtomInCycle(atom):
# Atom is in cycle
# Add each C-H bond to the ringCH group
# This is hardcoding of functional groups!
if atom.isCarbon():
for atom2 in atom.edges:
if atom2.isHydrogen():
try:
groupCount[ringCH] += 1
except KeyError:
groupCount[ringCH] = 1
else:
# Atom is not in cycle, so find a group for it
node = self.__getNode(molecule, {'*': atom})
if node is not None:
try:
groupCount[node] += 1
except KeyError:
groupCount[node] = 1
return groupCount
def loadEntry(self,
index,
label,
solvent,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
self.entries[label] = Entry(
index = index,
label = label,
data = solvent,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def loadEntry(self,
index,
label,
molecule,
statmech,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
self.entries[label] = Entry(
index = index,
label = label,
item = Molecule().fromAdjacencyList(molecule),
data = statmech,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
