{"id":19740088,"url":"https://github.com/efliks/molaristools","last_synced_at":"2025-04-30T05:32:48.456Z","repository":{"id":135104117,"uuid":"43472367","full_name":"efliks/MolarisTools","owner":"efliks","description":"Python scripts to facilitate working with Molaris-XG","archived":false,"fork":false,"pushed_at":"2021-07-03T09:37:11.000Z","size":1618,"stargazers_count":3,"open_issues_count":0,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-10-25T19:39:34.460Z","etag":null,"topics":["computational-chemistry","proteins","python"],"latest_commit_sha":null,"homepage":"","language":"Python","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/efliks.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-10-01T01:24:46.000Z","updated_at":"2023-10-25T19:39:34.461Z","dependencies_parsed_at":"2023-09-17T07:40:16.953Z","dependency_job_id":null,"html_url":"https://github.com/efliks/MolarisTools","commit_stats":null,"previous_names":["feliksm1/molaristools","skilefm/molaristools","efliks/molaristools","mikolajfeliks/molaristools"],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/efliks%2FMolarisTools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/efliks%2FMolarisTools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/efliks%2FMolarisTools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/efliks%2FMolarisTools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/efliks","download_url":"https://codeload.github.com/efliks/MolarisTools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224198850,"owners_count":17272179,"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":["computational-chemistry","proteins","python"],"created_at":"2024-11-12T01:19:26.769Z","updated_at":"2024-11-12T01:19:30.697Z","avatar_url":"https://github.com/efliks.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":":warning: **IMPORTANT NOTE** :warning:\n\n**This is a legacy library that is only compatible with Python 2.\nIt is kept here solely for historical reasons.**\n\n\n# MolarisTools\nA Python toolkit to facilitate working with Molaris-XG.\n\n\n_Key features:_\n  * QM/MM interface with electrostatic embedding to Gaussian, Mopac, GAMESS-US, ORCA, Q-Chem\n  * Parsing of Molaris files (input, log, gap, FVX, mol.in, evb.dat)\n  * Parsing of files from quantum chemical packages (Gaussian, Mopac, GAMESS-US, ORCA, Q-Chem)\n  * Parsing of geometry files (PDB, xyz, xyz trajectories)\n  * Reading and writing of Molaris libraries (amino-library, ENZYMIX \\\u0026 EVB parameters)\n  * Handling of amino-components (calculation of partial charges, generation of angles and dihedrals, topology operations, merging)\n  * Conversion between Molaris and CHARMM topology formats\n  * Generation of tables for input files with EVB atoms \\\u0026 bonds\n  * Automatic generation of amino-components from PDB files based on coordinates and distances\n  * Parsing of 1D \\\u0026 2D PES scans\n  * LRA calculations\n\n\n_Installation instructions:_\n\nMolarisTools is a stand-alone Python library and as such does not \nneed Molaris to be preinstalled. Nevertheless, a copy of Molaris can\nbe obtained from the [Warshel Group](http://laetro.usc.edu/software.html).\n\nTo install MolarisTools, clone the repository from GitHub (assuming that you have \ngit installed on your computer):\n\n```\ngit clone https://github.com/mfx9/MolarisTools.git\n```\n\nOr download and unpack the ZIP package from this website. In the next\nstep, adjust the PYTHONPATH variable so it points to the location\nof MolarisTools, for example (in Bash):\n\n```\nexport PYTHONPATH=${HOME}/MolarisTools:${PYTHONPATH}\n```\n\nAdd the above line to your ~/.profile or ~/.bashrc file.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fefliks%2Fmolaristools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fefliks%2Fmolaristools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fefliks%2Fmolaristools/lists"}