I’m using babel 2.3 and I’m trying to generate an sdf file with 2D coordinates (using command —gen2d) from SMILES. This result in the erroneous stereoisomer.
For example, if you try to convert the trans-dibromoethene (represented equivalently from smiles Br/C=C/Br or Br\C=C\Br), from SMILES to sdf generating 2D coordinates with command:
babel —gen2D -ismi trans1.smi -osdf trans1.sdf
I OBTAIN the WRONG STEREOISOMER!
If we use the —gen3d parameter instead, generating 3D coordinates the stereoisomer produced is correct.
Anybody know if this a bug of version 2.3?
Noel O'Boyle [ Admin ]
Stereochemistry is not supported in generation of 2D structures. So, not so much a bug as a missing feature (I’m working on it though…stay tuned...now working in r4403).