{"id":21864731,"url":"https://github.com/redesignscience/cvpack","last_synced_at":"2025-10-04T21:47:21.779Z","repository":{"id":65460220,"uuid":"592512221","full_name":"RedesignScience/cvpack","owner":"RedesignScience","description":"Useful Collective Variables for OpenMM","archived":false,"fork":false,"pushed_at":"2024-05-09T16:14:29.000Z","size":7009,"stargazers_count":11,"open_issues_count":2,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-10-30T12:51:30.102Z","etag":null,"topics":["collective-variables","enhanced-sampling","metadynamics","molecular-dynamics","openmm"],"latest_commit_sha":null,"homepage":"https://redesignscience.github.io/cvpack/latest","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/RedesignScience.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/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":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-01-23T22:08:18.000Z","updated_at":"2024-09-11T20:39:45.000Z","dependencies_parsed_at":"2023-12-07T01:53:05.511Z","dependency_job_id":"43c0eb1b-bd23-4a55-a736-7636bbf669fe","html_url":"https://github.com/RedesignScience/cvpack","commit_stats":null,"previous_names":[],"tags_count":25,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RedesignScience%2Fcvpack","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RedesignScience%2Fcvpack/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RedesignScience%2Fcvpack/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/RedesignScience%2Fcvpack/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/RedesignScience","download_url":"https://codeload.github.com/RedesignScience/cvpack/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":226857045,"owners_count":17693016,"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":["collective-variables","enhanced-sampling","metadynamics","molecular-dynamics","openmm"],"created_at":"2024-11-28T04:11:29.383Z","updated_at":"2025-10-04T21:47:16.738Z","avatar_url":"https://github.com/RedesignScience.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Collective Variable Package\n===========================\n\n[//]: # (Badges)\n[![GitHub Actions Build Status](https://github.com/RedesignScience/cvpack/workflows/Linux/badge.svg)](https://github.com/RedesignScience/cvpack/actions?query=workflow%3ALinux)\n[![GitHub Actions Build Status](https://github.com/RedesignScience/cvpack/workflows/MacOS/badge.svg)](https://github.com/RedesignScience/cvpack/actions?query=workflow%3AMacOS)\n[![GitHub Actions Build Status](https://github.com/RedesignScience/cvpack/workflows/Windows/badge.svg)](https://github.com/RedesignScience/cvpack/actions?query=workflow%3AWindows)\n[![GitHub Actions Build Status](https://github.com/RedesignScience/cvpack/workflows/Linter/badge.svg)](https://github.com/RedesignScience/cvpack/actions?query=workflow%3ALinter)\n[![Documentation Status](https://github.com/RedesignScience/cvpack/workflows/Docs/badge.svg)](https://redesignscience.github.io/cvpack/development)\n[![Coverage Report](https://redesignscience.github.io/cvpack/development/coverage/coverage.svg)](https://redesignscience.github.io/cvpack/development/coverage)\n\n[![Conda version](https://img.shields.io/conda/v/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)\n[![Conda platforms](https://img.shields.io/conda/pn/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)\n[![Conda downloads](https://img.shields.io/conda/dn/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)\n[![PyPI version](https://img.shields.io/pypi/v/cvpack.svg)](https://pypi.org/project/cvpack)\n[![PyPI version](https://img.shields.io/pypi/pyversions/cvpack.svg)](https://pypi.org/project/cvpack)\n[![PyPI version](https://img.shields.io/pypi/dm/cvpack.svg)](https://pypi.org/project/cvpack)\n\n[![License](https://img.shields.io/badge/License-MIT-yellowgreen.svg?style=flat)](https://github.com/RedesignScience/cvpack/blob/main/LICENSE.md)\n[![Twitter](https://badgen.net/badge/About/RedesignScience)](https://www.redesignscience.com)\n\nOverview\n--------\n\nCollective variables (CVs) are functions of the coordinates of a molecular system and provide a\nmeans to project its conformational state onto a lower-dimensional space. By stimulating the\ndynamics of a judiciously chosen set of CVs, one can obtain an enhanced sampling of the\nconfiguration space, including regions that are otherwise difficult to access. The system's\nfree energy as a function of these CVs can be used to characterize the relative stability of\ndifferent states and to identify pathways connecting them.\n\nCVPack is a Python package that provides pre-defined CVs for the powerful molecular dynamics engine\n[OpenMM]. All these CVs are subclasses of OpenMM's [Force] class and, as such, can be directly added\nto a [CustomCVForce] or used to define a [BiasVariable] for [Metadynamics].\n\nCollective Variables\n--------------------\n\nThe CVs implemented in CVPack are listed in the table below.\n\n| Collective Variable     | Description                                                      |\n|-------------------------|------------------------------------------------------------------|\n| [Angle]                 | angle formed by three atoms                                      |\n| [Atomic Function]       | a user-defined function of the coordinates of a group of atoms   |\n| [Attraction Strength]   | strength of the attraction between two groups of atoms           |\n| [Centroid Function]     | a user-defined function of the centroids of groups of atoms      |\n| [Composite RMSD]        | multibody RMSD with concerted-rotation alignment                 |\n| [Distance]              | distance between two atoms                                       |\n| [Helix angle content]   | alpha-helix angle content of a sequence of residues              |\n| [Helix H-bond content]  | alpha-helix hydrogen-bond content of a sequence of residues      |\n| [Helix RMSD content]    | alpha-helix RMSD content of a sequence of residues               |\n| [Helix torsion content] | alpha-helix Ramachandran content of a sequence of residues       |\n| [Meta CV]               | a function of other collective variables                         |\n| [Number of contacts]    | number of contacts between two groups of atoms                   |\n| [OpenMM Force wrapper]  | converts an OpenMM Force object into a CVPack CV                 |\n| [Path in CV space]      | progress along (or deviation from) a path in CV space            |\n| [Path in RMSD space]    | progress along (or deviation from) a path in RMSD space          |\n| [Radius of gyration]    | radius of gyration of a group of atoms                           |\n| [(Radius of gyration)^2]| square of the radius of gyration of a group of atoms             |\n| [Residue coordination]  | number of contacts between two disjoint groups of residues       |\n| [RMSD]                  | root-mean-square deviation with respect to a reference structure |\n| [Sheet RMSD content]    | beta-sheet RMSD content of a sequence of residues                |\n| [Shortest Distance]     | shortest distance between two groups of atoms                    |\n| [Torsion]               | torsion angle formed by four atoms                               |\n| [Torsion similarity]    | degree of similarity between pairs of torsion angles             |\n\nInstallation and Usage\n----------------------\n\nCVPack is available as a conda package on the\n[mdtools](https://anaconda.org/mdtools/cvpack) channel. To install it, run:\n\n```bash\n    conda install -c conda-forge -c mdtools cvpack\n```\n\nOr:\n\n```bash\n    mamba install -c mdtools cvpack\n```\n\nTo use CVPack in your own Python script or Jupyter notebook, simply import it as follows:\n\n```python\n    import cvpack\n```\n\nDocumentation\n-------------\n\nDocumentation for the latest CVPack version is available on [Github Pages](https://redesignscience.github.io/cvpack/latest).\n\nCopyright\n---------\n\n\nCopyright (c) 2023-2024 [C. Abreu](https://github.com/craabreu) \u0026 [Redesign Science](https://www.redesignscience.com)\n\n\nAcknowledgments\n---------------\n\nInitial project based on the [CMS Cookiecutter] version 1.1.\n\n[BiasVariable]:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html\n[CMS Cookiecutter]:   https://github.com/molssi/cookiecutter-cms\n[CustomCVForce]:      http://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html\n[Force]:              http://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html\n[Metadynamics]:       http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html\n[OpenMM]:             http://openmm.org\n\n[Angle]:                  https://redesignscience.github.io/cvpack/latest/api/Angle.html\n[Atomic Function]:        https://redesignscience.github.io/cvpack/latest/api/AtomicFunction.html\n[Attraction Strength]:    https://redesignscience.github.io/cvpack/latest/api/AttractionStrength.html\n[Centroid Function]:      https://redesignscience.github.io/cvpack/latest/api/CentroidFunction.html\n[Composite RMSD]:         https://redesignscience.github.io/cvpack/latest/api/CompositeRMSD.html\n[Distance]:               https://redesignscience.github.io/cvpack/latest/api/Distance.html\n[Helix angle content]:    https://redesignscience.github.io/cvpack/latest/api/HelixAngleContent.html\n[Helix H-bond content]:   https://redesignscience.github.io/cvpack/latest/api/HelixHBondContent.html\n[Helix RMSD content]:     https://redesignscience.github.io/cvpack/latest/api/HelixRMSDContent.html\n[Helix torsion content]:  https://redesignscience.github.io/cvpack/latest/api/HelixTorsionContent.html\n[Meta CV]:                https://redesignscience.github.io/cvpack/latest/api/MetaCollectiveVariable.html\n[Number of contacts]:     https://redesignscience.github.io/cvpack/latest/api/NumberOfContacts.html\n[OpenMM Force wrapper]:   https://redesignscience.github.io/cvpack/latest/api/OpenMMForceWrapper.html\n[Path in CV space]:       https://redesignscience.github.io/cvpack/latest/api/PathInCVSpace.html\n[Path in RMSD space]:     https://redesignscience.github.io/cvpack/latest/api/PathInRMSDSpace.html\n[Radius of gyration]:     https://redesignscience.github.io/cvpack/latest/api/RadiusOfGyration.html\n[(Radius of gyration)^2]: https://redesignscience.github.io/cvpack/latest/api/RadiusOfGyrationSq.html\n[Residue coordination]:   https://redesignscience.github.io/cvpack/latest/api/ResidueCoordination.html\n[RMSD]:                   https://redesignscience.github.io/cvpack/latest/api/RMSD.html\n[Sheet RMSD content]:     https://redesignscience.github.io/cvpack/latest/api/SheetRMSDContent.html\n[Shortest Distance]:      https://redesignscience.github.io/cvpack/latest/api/ShortestDistance.html\n[Torsion]:                https://redesignscience.github.io/cvpack/latest/api/Torsion.html\n[Torsion similarity]:     https://redesignscience.github.io/cvpack/latest/api/TorsionSimilarity.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fredesignscience%2Fcvpack","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fredesignscience%2Fcvpack","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fredesignscience%2Fcvpack/lists"}