{"id":19339527,"url":"https://github.com/becksteinlab/mdpow-molconfgen","last_synced_at":"2025-07-31T11:38:22.037Z","repository":{"id":200779936,"uuid":"656509901","full_name":"Becksteinlab/mdpow-molconfgen","owner":"Becksteinlab","description":"torsional sampler","archived":false,"fork":false,"pushed_at":"2025-07-11T01:03:19.000Z","size":3518,"stargazers_count":0,"open_issues_count":3,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-11T05:31:03.582Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-06-21T05:11:57.000Z","updated_at":"2025-07-11T00:57:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"5e38ac7d-f82c-489b-a844-41e432c2d5cd","html_url":"https://github.com/Becksteinlab/mdpow-molconfgen","commit_stats":null,"previous_names":["becksteinlab/mdpow-molconfgen"],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/Becksteinlab/mdpow-molconfgen","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fmdpow-molconfgen","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fmdpow-molconfgen/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fmdpow-molconfgen/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fmdpow-molconfgen/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/mdpow-molconfgen/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2Fmdpow-molconfgen/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":268031110,"owners_count":24184457,"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","status":"online","status_checked_at":"2025-07-31T02:00:08.723Z","response_time":66,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-10T03:22:42.747Z","updated_at":"2025-07-31T11:38:22.027Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mdpow-molconfgen #\n\n[//]: # (Badges)\n\n| **Latest release** | [![Last release tag](https://img.shields.io/github/release-pre/becksteinlab/mdpow-molconfgen.svg)](https://github.com/becksteinlab/mdpow-molconfgen/releases) ![GitHub commits since latest release (by date) for a branch](https://img.shields.io/github/commits-since/becksteinlab/mdpow-molconfgen/latest)  [![Documentation Status](https://readthedocs.org/projects/mdpow-molconfgen/badge/?version=latest)](https://mdpow-molconfgen.readthedocs.io/en/latest/?badge=latest)|\n| :------ | :------- |\n| **Status** | [![GH Actions Status](https://github.com/becksteinlab/mdpow-molconfgen/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/becksteinlab/mdpow-molconfgen/actions?query=branch%3Amain+workflow%3Agh-ci) [![codecov](https://codecov.io/gh/becksteinlab/mdpow-molconfgen/branch/main/graph/badge.svg)](https://codecov.io/gh/becksteinlab/mdpow-molconfgen/branch/main) |\n| **Community** | [![License: GPL v2](https://img.shields.io/badge/License-GPLv2-blue.svg)](https://www.gnu.org/licenses/gpl-2.0)  [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16\u0026logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)|\n\nGeneration of conformers of small molecules.\n\n## Background ##\n\n1. find all N major torsions\n2. generate all conformers by rotating all torsions in increments\n   delta for a total of (2π/delta)^N conformers\n3. write to a trajectory\n4. evaluate the force field energy with `gmx mdrun -rerun`. \n5. find minima in the N-dimensional energy landscape\n\n### Implementation notes ###\n\n1. Load molecules with MDAnalysis.\n2. Convert to RDKit molecule.\n3. Perform torsion drive with [rdkit.Chem.rdMolTransforms](https://www.rdkit.org/docs/source/rdkit.Chem.rdMolTransforms.html)\n\n\n### Initial testing systems ###\nFrom the [COW dataset](https://github.com/Becksteinlab/cow-dataset): \n\n- V36-methylacetate : 1 dihedral\n- V46-2-methyl-1-nitrobenzene : steric hindrance\n- V39-butylacetate : 4 dihedrals\n\n## First steps\n\n### Community\n\nmdpow-molconfgen is bound by a [Code of Conduct](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/CODE_OF_CONDUCT.md).\n\n### Installation\n\nTo build mdpow-molconfgen from source,\nwe highly recommend using virtual environments.\nIf possible, we strongly recommend that you use \n[mamba](https://mamba.readthedocs.io/en/latest/index.html) as your package manager.\nBelow we provide instructions both for `mamba` and\nfor `pip`.\n\nNote that for some functionality you also need a working [GROMACS](https://www.gromacs.org) installation.\n\n#### With pip from PyPi\n\nYou can directly install the [mdpow-molconfgen package](https://pypi.org/project/mdpow-molconfgen/) PyPi package with\n```\npip install mdpow-molconfgen\n```\nThis will install all dependencies (except GROMACS).\n\n#### With mamba from source\n\nEnsure that you have [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installed.\n\nCreate a virtual environment and activate it:\n\n```\nmamba create --name mdpow-molconfgen\nmamba activate mdpow-molconfgen\n```\n\nInstall the development and documentation dependencies:\n\n```\nmamba env update --name mdpow-molconfgen --file devtools/conda-envs/test_env.yaml\nmamba env update --name mdpow-molconfgen --file docs/requirements.yaml\n```\n\nBuild this package from source:\n\n```\npip install -e .\n```\n\nIf you want to update your dependencies (which can be risky!), run:\n\n```\nmamba update --all\n```\n\nAnd when you are finished, you can exit the virtual environment with:\n\n```\nmamba deactivate\n```\n\n#### With pip from source\n\nTo build the package from source, run:\n\n```\npip install -e .\n```\n\nIf you want to create a development environment, install\nthe dependencies required for tests and docs with:\n\n```\npip install -e \".[test,doc]\"\n```\n\n### Copyright\n\nThe mdpow-molconfgen source code is hosted at https://github.com/becksteinlab/mdpow-molconfgen\nand is available under the GNU General Public License, version 2 (see the file [LICENSE](https://github.com/becksteinlab/mdpow-molconfgen/blob/main/LICENSE)).\n\nCopyright (c) 2023, Oliver Beckstein\n\n\n#### Acknowledgements\n \nProject based on the \n[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.\nPlease cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using mdpow-molconfgen in published work.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fmdpow-molconfgen","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fmdpow-molconfgen","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fmdpow-molconfgen/lists"}