Dear Xianghai,
to my knowledge the only available tool is OMG, which is based on CDK, not
obabel. It is described in the following publication and can be downloaded
for free:
OMG: Open Molecule Generator (2012) Peironcely et al. Journal of
Cheminformatics
<https://jcheminf.springeropen.com/articles/10.1186/1758-2946-4-21>
OMG generates isomers for a given formula, but doesnt allow to specify
further filters and also doesnt seem to handle hydrogens explicitly. It can
be combined with Babel though, e.g. the following commands produce the 3
out of 50 isomers of C2N2O1 that contain a cyanide group:
% java -jar OMG.jar -ec C2N2O1 -o omg.out.sdf
NNCCO
C2N2O1
molecules 50
Duration: 678 miliseconds
%./obabel omg.out.sdf -O filtered.smi -sC#N
3 molecules converted
%more filtered.smi
N1=C(C#N)O1
N#COC#N
N#CN=C=O
%
OMG is a good starting point, but we found it to be insufficient for our
purposes, which is why we developed a new concept that we are submitting
for publication.
regards,
Rafel
On Wed, Jan 25, 2017 at 1:38 AM, xh s <sxh....@gmail.com> wrote:
> Hi,
>
> I recently started coding with the OpenBabel library. I am looking for a
> isomer generator program that generates isomers of a certain molecule with
> user-defined rules. Is there such a thing in OpenBabel? If not, how should
> I go about writing this program?
>
> Thank you,
> Xianghai
>
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