def from_mol(self) -> dict:
if self.get('extension') in ('mol', 'sdf', 'mdl'):
mol = Chem.MolFromMolBlock(self.get('block'),
sanitize=True,
removeHs=False,
strictParsing=True)
elif self.get('extension') in ('mol2', ):
mol = Chem.MolFromMol2Block(self.get('block'),
sanitize=True,
removeHs=False)
elif self.get('extension') in ('pdb', ):
mol = Chem.MolFromPDBBlock(self.get('block'),
sanitize=True,
removeHs=False,
proximityBonding=False)
else:
raise exc.HTTPClientError(
f"Format {self.get('extension')} not supported")
if self.get_bool('protons') is True:
mol = AllChem.AddHs(mol)
p = Params.from_mol(mol,
self.name,
generic=self.generic,
atomnames=self.atomnames)
return self.to_dict(p)
def from_pdb(self) -> dict:
smiles = self.get('smiles').strip()
block = self.get('block').strip()
if smiles != '':
p = Params.from_smiles_w_pdbblock(pdb_block=block,
smiles=smiles,
generic=self.generic,
name=self.name,
proximityBonding=False)
return self.to_dict(p)
else:
protein = Chem.MolFromPDBBlock(block,
removeHs=False,
proximityBonding=False)
mol = Chem.SplitMolByPDBResidues(protein,
whiteList=[self.name])[self.name]
AllChem.SanitizeMol(mol)
mol = AllChem.AddHs(mol)
p = Params.from_mol(mol,
self.name,
generic=self.generic,
atomnames=self.atomnames)
return self.to_dict(p)