Isomer generator

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Isomer generator

xh s
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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Re: Isomer generator

rafel israels
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

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 <[hidden email]> 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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Re: Isomer generator

Jean-Marc Nuzillard
Dear all,

The "C2N2O1 with cyanide" problem puzzled me...
The pyLSD (free) software -- http://eos.univ-reims.fr/LSD/JmnSoft/PyLSD/ -- was not designed
at all to solve this kind of problem but I gave it a try...

Here is a commented pyLSD input file for this problem (the lines of stars excluded):
*************************
; C2 N2 O1 isomers with a cyanide group
; anything between a semicolon and the end of the line is a comment

; gross formula
FORM "C 2 N 2 O 1"

; one-piece structure
PIEC 1

; syntax of non-H atom status description: MULT index element hybridization number-of-attached-H-atoms [opt. Charge]
; hybridization is 1, 2 or 3 for sp, sp2, sp3 atoms. Alternative possible values are listed between parenthesis.
; atoms indexed 1 and 3, below, are the C and N of the cyanide group, they are both sp atoms.
; the number of H attached to each non-H atom is 0 because the gross formula has 0 H.

; atom status
MULT 1 C 1 0
MULT 2 C (1 2 3) 0
MULT 3 N 1 0
MULT 4 N (1 2 3) 0
MULT 5 O (2 3) 0

; the cyanide bond
BOND 1 3

*************************

I got the three solutions reported by Rafel in about 0.15 s
with my old Linux box.
Most probably performance will drop when dealing with more complex molecules.
Other NMR-oriented structure generators can probably do the same, or better.

All the best,

Jean-Marc


Le 25/01/2017 à 11:47, Rafel Israels a écrit :
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

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 <[hidden email]> 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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-- 
Jean-Marc Nuzillard
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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