def add_thermodynamics(cursor):
from groups import GroupMissingTrainDataError, GroupDecompositionError
gc = GroupContribution(sqlite_name="gibbs.sqlite", html_name="pathologic")
gc.init()
cursor.execute("DROP TABLE IF EXISTS yeast_inchi2thermo")
cursor.execute(
"CREATE TABLE yeast_inchi2thermo (inchi TEXT, charge INT, nH INT, dG0_f REAL)"
)
cursor.execute("DROP INDEX IF EXISTS yeast_inchi2thermo_idx")
cursor.execute(
"CREATE INDEX yeast_inchi2thermo_idx ON yeast_inchi2thermo (inchi);")
inchi_list = []
for row in cursor.execute("SELECT distinct(inchi) " \
"FROM yeast_species2inchi WHERE inchi IS NOT NULL"):
inchi = row[0]
inchi_list.append(str(inchi))
for inchi in inchi_list:
try:
mol = Molecule.FromInChI(str(inchi))
pmap = gc.Mol2PseudoisomerMap(mol)
for ((z, nH), dG0) in pmap.iteritems():
cursor.execute(
"INSERT INTO yeast_inchi2thermo VALUES(?,?,?,?)",
[inchi, z, nH, dG0])
except (IOError, GroupMissingTrainDataError, GroupDecompositionError):
sys.stderr.write(
"Cannot convert the following InChI to a pybel Molecule")
def SetInChI(self, inchi):
if inchi == None:
self.inchi = None
self.mol = None
self.formula = None
self.mass = None
else:
self.inchi = inchi
self.mol = Molecule.FromInChI(inchi)
self.formula = self.mol.GetFormula()
self.mass = self.mol.GetExactMass()
def EstimateInChI(self, inchi):
mol = Molecule.FromInChI(inchi)
#mol.RemoveHydrogens()
decomposition = self.group_decomposer.Decompose(
mol, ignore_protonations=False, strict=True)
nH = decomposition.Hydrogens()
charge = decomposition.NetCharge()
nMg = decomposition.Magnesiums()
groupvec = decomposition.AsVector()
dG0, ker = self.EstimateGroupVector(groupvec)
return dG0, nH, charge, nMg, ker
def get_nH_and_charge(self):
if not self.mol and self.inchi:
self.mol = Molecule.FromInChI(self.inchi)
if self.mol:
return self.mol.GetHydrogensAndCharge()
# if there is no InChI assume that self.formula is correct and that
# it represents the number of H for the neutral species
atom_bag = self.get_atom_bag()
if not atom_bag:
return None
return atom_bag.get('H', 0), 0
def GetMolecule(self):
"""Gets a Molecule for this compound if possible.
Returns None if no molecular data is available.
"""
if self.mol:
return self.mol
if self.inchi:
self.mol = Molecule.FromInChI(self.inchi)
self.mol.SetTitle(self.name)
return self.mol
raise kegg_errors.KeggParseException(
"C%05d (%s) doesn't have an explicit molecular structure" %
(self.cid, self.name))
