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Erroneous stereoisomer generating 2D sdf from SMILES (using gen2d). BUG in openbabel 2.3.0?

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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


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?

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4 answers


wdiwdi [ Editor ]

I call the Indigo cis/trans and tetrahedral stereochemistry support and raise them with

– allenes (odd and even, even with r4/r6/r8… rings in place of double bonds)
– square planar stereochemistry
– trans double bonds in macrocycles

Cactvs 2D layout depiction algorithms,

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