Hi, I think the following behaviour is a bug but feel free to correct me. I have an SD file (attached) with two stereoisomers of alanine (built by openbabel from the smiles). I want to read it and write it's contents as isomeric smiles. I execute the following:
import rdkit
from rdkit import Chem
smiles_writer = Chem.SmilesWriter("ChiralTest.smi", includeHeader=False,
isomericSmiles=True)
suppl = Chem.SDMolSupplier("ChiralTest3D.sdf", sanitize=False)
for mol in suppl:
Chem.SanitizeMol(mol)
smiles_writer.write(mol)
smiles_writer.flush()
smiles_writer.close()
smiles_writer2 = Chem.SmilesWriter("ChiralTest2.smi", includeHeader=False,
isomericSmiles=True)
suppl2 = Chem.SDMolSupplier("ChiralTest3D.sdf", sanitize=True)
for mol in suppl2:
smiles_writer2.write(mol)
smiles_writer2.flush()
smiles_writer2.close()
The file ChiralTest.smi now contains:
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] L-alanine
[H]OC(=O)C([H])(N([H])[H])C([H])([H])[H] D-alanine
and ChiralTest2.smi contains:
C[C@H](N)C(=O)O L-alanine
C[C@@H](N)C(=O)O D-alanine
My question is why do I get different outputs depending on when
sanitization was performed?
Yours,
Toby Wright
--
InhibOx Ltd
ChiralTest3D.sdf
Description: Binary data
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