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

Asked by about 2 years ago

Hi!
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?

4 answers

Noel O'Boyle [ Admin ] Mar 2, 2011 (Edited Mar 2, 2011)

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).

NN comments

When is the next version (2.3.1) of openbabel due then?

Mar 2, 2011

I don’t know.

Mar 2, 2011

green69 Mar 2, 2011

OK, I didn’t know that.
I think that feature would be so useful.
Many thanks!

NN comments

wdiwdi [ Editor ] Mar 4, 2011

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, www.xemistry.com/academic

NN comments

Dmitry Pavlov [ Editor ] Mar 2, 2011

A bit offtopic, but you can use indigo-depict utility to convert your structures:

indigo-depict file.smi file.sdf

It preserves cis-trans and tetrahedral stereochemistry.

NN comments

Welcome

Top 5 users

Recent badges

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