{"id":17255166,"url":"https://github.com/unixjunkie/omg","last_synced_at":"2025-04-14T05:40:51.795Z","repository":{"id":144782535,"uuid":"272317236","full_name":"UnixJunkie/OMG","owner":"UnixJunkie","description":"mirror of Open Molecule Generator from https://git.code.sf.net/p/openmg/code","archived":false,"fork":false,"pushed_at":"2020-06-15T01:46:41.000Z","size":24809,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-27T19:23:28.584Z","etag":null,"topics":["chemical-formula","exhaustive-search","molecular-generation"],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.png","metadata":{"files":{"readme":"README.txt","changelog":null,"contributing":null,"funding":null,"license":"License-gpl-3.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-06-15T01:46:09.000Z","updated_at":"2022-07-15T18:39:56.000Z","dependencies_parsed_at":null,"dependency_job_id":"630f3569-31a6-4573-9423-a7c4ea40c6a1","html_url":"https://github.com/UnixJunkie/OMG","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FOMG","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FOMG/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FOMG/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FOMG/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/OMG/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248830416,"owners_count":21168271,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chemical-formula","exhaustive-search","molecular-generation"],"created_at":"2024-10-15T07:10:51.413Z","updated_at":"2025-04-14T05:40:51.776Z","avatar_url":"https://github.com/UnixJunkie.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"OMG - Open Molecule Generator\r\n \r\nCopyright 2011 The Netherland Metabolomics Center Team License: GPL v3, see\r\ndoc/License-gpl-3.txt\r\n\r\n1. Introduction\r\n----------------------------------------------------------------------------------\r\nYou are currently reading the README file for the OMG Project. This project is\r\nhosted under http://sourceforge.net/p/openmg\r\n\r\nOMG is an open-source tool for the generation of chemical structures, implemented \r\nin the programming language Java(tm). The library is published under terms of the \r\nstandard The GNU General Public License (GPL) v3. This has implications on what \r\nyou can do with sources and binaries of the OMG library. \r\nFor details, please refer to the file LICENSE, which is provided with this \r\ndistribution.\r\n\r\nPLEASE NOTE: OMG is distributed in the hope that it will be useful, but WITHOUT\r\nANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR \r\nA PARTICULAR PURPOSE.\r\n\r\n\r\n2. System Requirements\r\n----------------------------------------------------------------------------------\r\nOMG.jar runs in the following OS;\r\n- Ubuntu 32 bits\r\n- Ubuntu 64 bits\r\n- Mac OS X 64 bits\r\n\r\n\r\n3. Using OMG tool\r\n----------------------------------------------------------------------------------\r\nIn order to use the OMG tool in your program, you need to run the jar file via \r\ncommand line and provide some arguments. \r\n\r\n-ec:  elemental composition of the molecules to be generated.\r\n-o:   SDF file where to store the molecules.  \r\n-fr:  SDF file containing prescribed one or multiple substructures. In the case\r\n\t  of multiple substructures, they have to be non-overlapping. \r\n\r\nHere there some examples of how to run OMG using the command line: \r\n\r\n- Generating molecules\r\n-- Generate molecules for the elemental composition C6H6\r\njava -jar OMG.jar -ec C6H6\r\n\r\n-- Generate molecules for the elemental composition C6H6 and store them in \r\n-- out_C6H6.sdf\r\njava -jar OMG.jar -ec C6H6 -o out_C6H6.sdf\r\n\r\n- Generating molecules with prescribed substructure(s)\r\n-- Generate molecules for the elemental composition C2H5NO2 (glycine) using the \r\n-- prescribed substructure in fragment_CO2.sdf\r\njava -jar OMG.jar -ec C2H5NO2 -fr fragment_CO2.sdf\r\n\r\n\r\n\r\n4. Source Code\r\n----------------------------------------------------------------------------------\r\nYou can download the source code at\r\nhttp://sourceforge.net/p/openmg\r\n\r\n\r\n5. Help\r\n----------------------------------------------------------------------------------\r\nIf you need help don't hesitate to contact us (jpeironcely@gmail.com)\r\n\r\n----------------------------------------------------------------------------------\r\nEnjoy!  Comments and feedback are appreciated!\r\n\r\nJulio E. Peironcely\r\njpeironcely@gmail.com\r\nLeiden, Netherlands\r\nhttp://juliopeironcely.com\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fomg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fomg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fomg/lists"}