https://github.com/unixjunkie/omg
mirror of Open Molecule Generator from https://git.code.sf.net/p/openmg/code
https://github.com/unixjunkie/omg
chemical-formula exhaustive-search molecular-generation
Last synced: 6 months ago
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mirror of Open Molecule Generator from https://git.code.sf.net/p/openmg/code
- Host: GitHub
- URL: https://github.com/unixjunkie/omg
- Owner: UnixJunkie
- License: gpl-3.0
- Created: 2020-06-15T01:46:09.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-06-15T01:46:41.000Z (over 5 years ago)
- Last Synced: 2025-03-27T19:23:28.584Z (6 months ago)
- Topics: chemical-formula, exhaustive-search, molecular-generation
- Language: C
- Size: 23.7 MB
- Stars: 5
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.txt
- License: License-gpl-3.txt
Awesome Lists containing this project
README
OMG - Open Molecule Generator
Copyright 2011 The Netherland Metabolomics Center Team License: GPL v3, see
doc/License-gpl-3.txt
1. Introduction
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You are currently reading the README file for the OMG Project. This project is
hosted under http://sourceforge.net/p/openmg
OMG is an open-source tool for the generation of chemical structures, implemented
in the programming language Java(tm). The library is published under terms of the
standard The GNU General Public License (GPL) v3. This has implications on what
you can do with sources and binaries of the OMG library.
For details, please refer to the file LICENSE, which is provided with this
distribution.
PLEASE NOTE: OMG is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
2. System Requirements
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OMG.jar runs in the following OS;
- Ubuntu 32 bits
- Ubuntu 64 bits
- Mac OS X 64 bits
3. Using OMG tool
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In order to use the OMG tool in your program, you need to run the jar file via
command line and provide some arguments.
-ec: elemental composition of the molecules to be generated.
-o: SDF file where to store the molecules.
-fr: SDF file containing prescribed one or multiple substructures. In the case
of multiple substructures, they have to be non-overlapping.
Here there some examples of how to run OMG using the command line:
- Generating molecules
-- Generate molecules for the elemental composition C6H6
java -jar OMG.jar -ec C6H6
-- Generate molecules for the elemental composition C6H6 and store them in
-- out_C6H6.sdf
java -jar OMG.jar -ec C6H6 -o out_C6H6.sdf
- Generating molecules with prescribed substructure(s)
-- Generate molecules for the elemental composition C2H5NO2 (glycine) using the
-- prescribed substructure in fragment_CO2.sdf
java -jar OMG.jar -ec C2H5NO2 -fr fragment_CO2.sdf
4. Source Code
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You can download the source code at
http://sourceforge.net/p/openmg
5. Help
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If you need help don't hesitate to contact us (jpeironcely@gmail.com)
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Enjoy! Comments and feedback are appreciated!
Julio E. Peironcely
jpeironcely@gmail.com
Leiden, Netherlands
http://juliopeironcely.com