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):
raise DatabaseError('Adjacency list 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 getSolventStructure(self, solvent_name):
try:
solventStructure = self.libraries['solvent'].getSolventStructure(
solvent_name)
except:
raise DatabaseError(
'Solvent {0!r} not found in database'.format(solvent_name))
return solventStructure
def __addGroupThermoData(self, thermoData, database, molecule, atom):
"""
Determine the group additivity thermodynamic data for the atom `atom`
in the structure `structure`, and add it to the existing thermo data
`thermoData`.
"""
node0 = database.descendTree(molecule, atom, None)
if node0 is None:
raise KeyError('Node not found in database.')
# It's possible (and allowed) that items in the tree may not be in the
# library, in which case we need to fall up the tree until we find an
# ancestor that has an entry in the library
node = node0
while node.data is None and node is not None:
node = node.parent
if node is None:
raise DatabaseError(
'Unable to determine thermo parameters for {0}: no library entries for {1} or any of its ancestors.'
.format(molecule, node0))
data = node.data
comment = node.label
while isinstance(data, basestring) and data is not None:
for entry in database.entries.values():
if entry.label == data:
data = entry.data
comment = entry.label
break
data.comment = '{0}({1})'.format(database.label, comment)
# This code prints the hierarchy of the found node; useful for debugging
# result = ''
# while node is not None:
# result = ' -> ' + node.label + result
# node = node.parent
# print result[4:]
if thermoData is None:
return data
else:
return self.__addThermoData(thermoData, data)
def saveEntry(f, entry):
"""
Write a Pythonic string representation of the given `entry` in the solvation
database to the file object `f`.
"""
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Species):
if Molecule(SMILES=entry.item.molecule[0].toSMILES()).isIsomorphic(entry.item.molecule[0]):
# The SMILES representation accurately describes the molecule, so we can save it that way.
f.write(' molecule = "{0}",\n'.format(entry.item.molecule[0].toSMILES()))
else:
f.write(' molecule = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList(removeH=False))
f.write('""",\n')
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
elif entry.item is not None:
f.write(' group = "{0}",\n'.format(entry.item))
if isinstance(entry.data, SoluteData):
f.write(' solute = SoluteData(\n')
f.write(' S = {0!r},\n'.format(entry.data.S))
f.write(' B = {0!r},\n'.format(entry.data.B))
f.write(' E = {0!r},\n'.format(entry.data.E))
f.write(' L = {0!r},\n'.format(entry.data.L))
f.write(' A = {0!r},\n'.format(entry.data.A))
if entry.data.V is not None: f.write(' V = {0!r},\n'.format(entry.data.V))
f.write(' ),\n')
elif isinstance(entry.data, SolventData):
f.write(' solvent = SolventData(\n')
f.write(' s_g = {0!r},\n'.format(entry.data.s_g))
f.write(' b_g = {0!r},\n'.format(entry.data.b_g))
f.write(' e_g = {0!r},\n'.format(entry.data.e_g))
f.write(' l_g = {0!r},\n'.format(entry.data.l_g))
f.write(' a_g = {0!r},\n'.format(entry.data.a_g))
f.write(' c_g = {0!r},\n'.format(entry.data.c_g))
f.write(' s_h = {0!r},\n'.format(entry.data.s_h))
f.write(' b_h = {0!r},\n'.format(entry.data.b_h))
f.write(' e_h = {0!r},\n'.format(entry.data.e_h))
f.write(' l_h = {0!r},\n'.format(entry.data.l_h))
f.write(' a_h = {0!r},\n'.format(entry.data.a_h))
f.write(' c_h = {0!r},\n'.format(entry.data.c_h))
f.write(' A = {0!r},\n'.format(entry.data.A))
f.write(' B = {0!r},\n'.format(entry.data.B))
f.write(' C = {0!r},\n'.format(entry.data.C))
f.write(' D = {0!r},\n'.format(entry.data.D))
f.write(' E = {0!r},\n'.format(entry.data.E))
f.write(' alpha = {0!r},\n'.format(entry.data.alpha))
f.write(' beta = {0!r},\n'.format(entry.data.beta))
f.write(' eps = {0!r},\n'.format(entry.data.eps))
f.write(' ),\n')
elif entry.data is None:
f.write(' solute = None,\n')
else:
raise DatabaseError("Not sure how to save {0!r}".format(entry.data))
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
f.write(')\n\n')
def saveEntry(f, entry):
"""
Write a Pythonic string representation of the given `entry` in the transport
database to the file object `f`.
"""
f.write('entry(\n')
f.write(' index = {0:d},\n'.format(entry.index))
f.write(' label = "{0}",\n'.format(entry.label))
if isinstance(entry.item, Molecule):
f.write(' molecule = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList(removeH=False))
f.write('""",\n')
elif isinstance(entry.item, Group):
f.write(' group = \n')
f.write('"""\n')
f.write(entry.item.toAdjacencyList())
f.write('""",\n')
else:
f.write(' group = "{0}",\n'.format(entry.item))
if isinstance(entry.data, CriticalPointGroupContribution):
f.write(' transportGroup = CriticalPointGroupContribution(\n')
f.write(' Tc = {0!r},\n'.format(entry.data.Tc))
f.write(' Pc = {0!r},\n'.format(entry.data.Pc))
f.write(' Vc = {0!r},\n'.format(entry.data.Vc))
f.write(' Tb = {0!r},\n'.format(entry.data.Tb))
f.write(' structureIndex = {0!r},\n'.format(entry.data.structureIndex))
f.write(' ),\n')
elif entry.data is None:
f.write(' transportGroup = None,\n')
elif isinstance(entry.data, TransportData):
f.write(' transport = TransportData(\n')
f.write(' shapeIndex = {0!r},\n'.format(entry.data.shapeIndex))
f.write(' epsilon = {0!r},\n'.format(entry.data.epsilon))
f.write(' sigma = {0!r},\n'.format(entry.data.sigma))
f.write(' dipoleMoment = {0!r},\n'.format(entry.data.dipoleMoment))
f.write(' polarizability = {0!r},\n'.format(entry.data.polarizability))
f.write(' rotrelaxcollnum = {0!r},\n'.format(entry.data.rotrelaxcollnum))
f.write(' ),\n')
else:
raise DatabaseError("Not sure how to save {0!r}".format(entry.data))
f.write(' shortDesc = u"""')
try:
f.write(entry.shortDesc.encode('utf-8'))
except:
f.write(entry.shortDesc.strip().encode('ascii', 'ignore'))
f.write('""",\n')
if entry.longDesc:
f.write(' longDesc = \n')
f.write('u"""\n')
try:
f.write(entry.longDesc.strip().encode('utf-8') + "\n")
except:
f.write(entry.longDesc.strip().encode('ascii', 'ignore')+ "\n")
f.write('""",\n')
else:
f.write(' longDesc = u"""""",\n')
f.write(')\n\n')