def mol_to_dict(self, mol):
"""
Capture all the information from a SureChEMBL molecule into a dictionary
mol_to_dict( (Surechembl)self, (rdkit.Chem.Mol)mol) -> dict
"""
props = set(mol.GetPropNames())
d = {p.lower(): self.cast(mol.GetProp(p)) for p in props}
d["id"] = "https://www.surechembl.org/chemical/" + mol.GetProp("ID")
smiles = []
rdkit_mol = rdkit_standardize(mol)
rs = rdkit_smiles(rdkit_mol)
if rs is not None:
d["rdkit_smiles"] = rs
smiles.append(rs)
descs = rdkit_descriptors(rdkit_mol)
for name in descs:
d["rdkit_" + name.lower()] = descs[name]
if smiles:
d["smiles"] = list(set(smiles))
return d
def mol_to_dict(self, mol):
"""
Capture all the information from a PubChem molecule into a dictionary
mol_to_dict( (Pubchem)self, (rdkit.Chem.Mol)mol) -> dict
"""
props = set(mol.GetPropNames())
d = {p.lower(): self.cast(mol.GetProp(p)) for p in props}
d["id"] = "https://pubchem.ncbi.nlm.nih.gov/compound/" + mol.GetProp("PUBCHEM_COMPOUND_CID")
smiles = [mol.GetProp(p) for p in self.SMILES_PROPS if p in props]
smiles.append(rdkit_smiles(mol)) # Original SMILES
if smiles:
d["smiles"] = list(set(smiles))
synonyms = [mol.GetProp(p) for p in self.SYNONYM_PROPS if p in props]
if synonyms:
d["synonyms"] = list(set(synonyms))
if "pubchem_compound_canonicalized" in d:
canon = d["pubchem_compound_canonicalized"]
if canon == 1:
d["pubchem_compound_canonicalized"] = True
elif canon == 0:
d["pubchem_compound_canonicalized"] = False
else:
del d["pubchem_compound_canonicalized"]
rdkit_mol = rdkit_standardize(mol)
rs = rdkit_smiles(rdkit_mol)
if rs is not None:
d["rdkit_smiles"] = rs
smiles.append(rs)
descs = rdkit_descriptors(rdkit_mol)
for name in descs:
d["rdkit_" + name.lower()] = descs[name]
return d