def _hydrogenize(block, hydro):
mol = Chem.MolFromMolBlock(block, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
res = Chem.AddHs(mol, addCoords=True) if hydro else Chem.RemoveHs(
mol, sanitize=False)
return MolToMarvin(Chem.MolToMolBlock(res))
def _clean(mrv, dim=2):
block = MarvinToMol(mrv)
mol = Chem.MolFromMolBlock(block)
if not mol:
print "No mol for block:\n %s" % block
return mrv
AllChem.Compute2DCoords(mol, bondLength=0.8)
if dim == 3:
mol = _2D23D(mol, True)
mol = Chem.RemoveHs(mol)
return MolToMarvin(Chem.MolToMolBlock(mol))
def _clean(mrv, dim=2):
block = MarvinToMol(mrv)
mol = Chem.MolFromMolBlock(block, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
if not mol:
print "No mol for block:\n %s" % block
return mrv
AllChem.Compute2DCoords(mol, bondLength=0.8)
if dim == 3:
mol = _2D23D(mol, True)
mol = Chem.RemoveHs(mol)
return MolToMarvin(Chem.MolToMolBlock(mol))
def _molExport(structure, **kwargs):
input_f = kwargs.get('input', None)
output_f = kwargs.get('output', None)
if not input_f:
mol = _autoDetect(str(structure))
elif input_f == 'mrv':
mol = Chem.MolFromMolBlock(MarvinToMol(structure), sanitize=False)
elif input_f == 'smiles':
mol = Chem.MolFromSmiles(str(structure), sanitize=False)
elif input_f == 'inchi':
mol = Chem.MolFromInchi(str(structure))
else:
mol = Chem.MolFromMolBlock(structure, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
if not mol.GetNumConformers() or mol.GetConformer().Is3D():
AllChem.Compute2DCoords(mol, bondLength=0.8)
if output_f == 'smiles':
out_structure = Chem.MolToSmiles(mol)
elif output_f == 'inchi':
out_structure = Chem.MolToInchi(mol)
elif output_f == 'inchikey':
out_structure = Chem.InchiToInchiKey(Chem.MolToInchi(mol))
elif output_f == 'mol':
out_structure = Chem.MolToMolBlock(mol)
elif output_f == 'sdf':
out_structure = Chem.MolToMolBlock(mol) + '\n$$$$\n'
elif output_f == 'mrv':
out_structure = MolToMarvin(Chem.MolToMolBlock(mol))
return {
"structure": out_structure,
"format": output_f,
"contentUrl": "",
"contentBaseUrl": ""
}
def _hydrogenize(block, hydro):
mol = Chem.MolFromMolBlock(block)
res = Chem.AddHs(mol, addCoords=True) if hydro else Chem.RemoveHs(mol)
return MolToMarvin(Chem.MolToMolBlock(res))