Using OpenBabel 2.3.1, on Ubuntu Linux 10.10 Using the attached *seemingly unsuspect and correct* sdf file - zzz.sdf.
Converting this file to smiles: $ obabel zzz.sdf -osmi -Ozzz.smi 2 molecules converted Gives us the expected and correct result: $ more zzz.smi C[C@@H](N)C(=O)O Ala1 C[C@H](N)C(=O)O Ala2 Adding hydrogens to the original sdf file: $ obabel zzz.sdf -osdf -OzzzH.sdf -h 2 molecules converted Now converting the H-added sdf file to smiles: $ obabel zzzH.sdf -osmi -OzzzH.smi 2 molecules converted STEREO INVERTED:: (!!!) $ more zzzH.smi C[C@H](N)C(=O)O Ala1 C[C@@H](N)C(=O)O Ala2 Any ideas why this happens? This is somewhat unexpected behaviour. - Jean-Paul Ebejer Early Stage Researcher
zzz.sdf
Description: Binary data
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