{"id":34029867,"url":"https://github.com/timbernat/polymerist","last_synced_at":"2026-04-10T10:32:43.347Z","repository":{"id":187584778,"uuid":"677186683","full_name":"timbernat/polymerist","owner":"timbernat","description":"Polymer-Oriented LibrarY of Monomer-Expression Rules and In-silico Synthesis Tools","archived":false,"fork":false,"pushed_at":"2026-03-10T05:50:33.000Z","size":3026,"stargazers_count":8,"open_issues_count":15,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-03-10T13:58:10.111Z","etag":null,"topics":["molecular-dynamics","openforcefield","polymerscience"],"latest_commit_sha":null,"homepage":"","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/timbernat.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-08-11T00:39:06.000Z","updated_at":"2026-02-25T04:48:52.000Z","dependencies_parsed_at":"2023-08-11T08:20:45.728Z","dependency_job_id":"f4e95ebc-c1d8-4e47-90c5-956afd9c54a9","html_url":"https://github.com/timbernat/polymerist","commit_stats":null,"previous_names":["timbernat/polysaccharide2","timbernat/polymerist"],"tags_count":16,"template":false,"template_full_name":null,"purl":"pkg:github/timbernat/polymerist","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timbernat%2Fpolymerist","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timbernat%2Fpolymerist/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timbernat%2Fpolymerist/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timbernat%2Fpolymerist/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/timbernat","download_url":"https://codeload.github.com/timbernat/polymerist/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/timbernat%2Fpolymerist/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31638477,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-10T07:40:12.752Z","status":"ssl_error","status_checked_at":"2026-04-10T07:40:11.664Z","response_time":98,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["molecular-dynamics","openforcefield","polymerscience"],"created_at":"2025-12-13T17:56:11.094Z","updated_at":"2026-04-10T10:32:43.339Z","avatar_url":"https://github.com/timbernat.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Polymer-Oriented LibrarY of Monomer Expression Rules and In-silico Synthesis Tools\n==============================\n[//]: # (Badges)\n[![GitHub Actions Build Status](https://github.com/timbernat/polymerist/workflows/CI/badge.svg)](https://github.com/timbernat/polymerist/actions?query=workflow%3ACI)\n[![codecov](https://codecov.io/gh/timbernat/polymerist/main/graph/badge.svg)](https://codecov.io/gh/timbernat/polymerist/branch/main)\n\nA unified set of tools for setting up molecular dynamics simulations of general organic polymer systems. Based upon concepts introduced in [\"Parameterization of General Organic Polymers within the Open Force Field Framework\" (Davel, Connor M., Bernat, Timotej, Wagner, Jeffrey R., and Shirts, Michael R.)](https://pubs.acs.org/doi/10.1021/acs.jcim.3c01691)\n\n![abstract](docs/images/polymer_param_graphic_TOC.png)\n\n## Features\nIncludes functionality for:\n* Generating chemical information-rich monomer residue templates\n* Enumeration of all possible repeat units of a polymer ensemble given initial monomers and a target polymerization mechanism\n* Building of linear homopolymers and copolymers (both topologies and coordinates)\n* Solvating polymer systems\n* Packing of many polymer chains into melt-like boxes\n* Force-field parameterization within the [OpenFF](https://openforcefield.org/about/organization/) framework\n* Interfaces to semi-empirical and graph neural network-based atomic partial charge assignment\n* Reproducible simulation specification API\n* Interfaces to OpenMM for running serial simulations with different thermodynamic parameters\n* Much more!\n\n## Documentation\nComplete documentation for polymerist can be found on the [`polymerist` ReadTheDocs page](https://polymerist.readthedocs.io/en/latest/)\n  \n## Examples\nExamples of how to import and invoke the core features of `polymerist` can be found in the accompanying [polymerist_examples repository](https://github.com/timbernat/polymerist_examples).\n\n## Requirements\n### OS\n`polymerist` is compatible with Linux (recommended) and Mac machines capable of installing Python 3.11. Due to [lack of support from AmberTools](https://ambermd.org/InstWindows.php), direct installation on Windows machines is not supported; **however**, this can easily be circumvented by using the [Windows Subsystem for Linux (WSL2)](https://learn.microsoft.com/en-us/windows/wsl/install)\n\n### Python package manager\nBefore proceeding with installation, ensure you have some iteration of a Python package and environment management system installed on your machine. We recommend using `mamba`, installable via [Miniforge](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html). [Miniconda](https://docs.anaconda.com/free/miniconda/miniconda-install/) and other [Anaconda](https://www.anaconda.com/download) manager also work; however **if you opt to use `conda` over `mamba`, be prepared for a markedly slower and more tedious install process!**\n\n## Installation\nThe distribution for `polymerist` is hosted on [PyPI](https://pypi.org/project/polymerist/). For detailed instruction on how to install polymerist and other required toolkits, see [the installation docs](https://polymerist.readthedocs.io/en/docs/installation/index.html). Here we provide an abridged summary to get you going\n\n### Base install\nA fully-featured install in a safe virtual environment (named \"polymerist-env\", here) can be obtained by running the following terminal commands:\n#### Mamba install (basic)\n```bash\nmamba create -n polymerist-env python=3.11\nmamba activate polymerist-env\npip install polymerist\nmamba install -c conda-forge openff-toolkit mbuild openbabel \"packmol\u003c=20.15.1\"\n```\n\n#### Mamba install (extended)\nAn extended install with [Jupyter Notebook](https://jupyter.org/) support, molecular visualization capability, and chemical data querying capability can be obtained very similarly:\n```bash\nmamba create -n polymerist-env python=3.11\nmamba activate polymerist-env\npip install polymerist[interactive,chemdb]\nmamba install -c conda-forge openff-toolkit mbuild openbabel \"packmol\u003c=20.15.1\"\n```\n\n### Testing installation\nTo see if the installation was successful, one can run the following short set of commands which should yield the outputs shown:\n```python\nmamba activate polymerist-env; python\n\u003e\u003e\u003e import polymerist as ps\n\u003e\u003e\u003e print(ps.pascal(5))\n    1    \n   1 1   \n  1 2 1  \n 1 3 3 1 \n1 4 6 4 1\n```\n\n### Parameterization toolkits\nAssigning atomic partial charges using some flavor of [AM1-BCC](https://docs.eyesopen.com/toolkits/python/quacpactk/molchargetheory.html#am1bcc-charges) and enhanced conformer generation also requires installation of some supplementary toolkits. These can be installed as follows:\n```bash\nmamba activate polymerist-env\nmamba install -c openeye openeye-toolkits\nmamba install -c conda-forge espaloma_charge \"torchdata\u003c=0.9.0\"\nmamba install -c conda-forge openff-nagl \"torchdata\u003c=0.9.0\"\n```\n\n### Installing from source (optional)\n`polymerist` and all required dependencies can also be installed directly from the source code in this repository.\nTo install, execute the following set of terminal commands in whichever directory you'd like the installation to live on your local machine:\n```bash\ngit clone https://github.com/timbernat/polymerist\ncd polymerist\nmamba env create -n polymerist-env -f devtools/conda-envs/release-build.yml\nmamba activate polymerist-env\npip install .\n```\n\n### Developer installation (for advanced users only)\nThose developing for `polymerist` may like to have an editable local installation, in which they can make changes to the source code and test behavior changes in real-time. This type of installation proceeds as follows:\n```bash\ngit clone https://github.com/timbernat/polymerist\ncd polymerist\nmamba env create -n polymerist-dev -f devtools/conda-envs/dev-build.yml\nmamba activate polymerist-dev\npip install -e . --config-settings editable_mode=strict\n```\nThe `--config-settings editable_mode` flag in the final line allows this installation to \"play nicely\" with PyLance, making auto-completion and navigation to source code much easier for VSCode users. **It is optional, and can be removed if this compatibility is not desired**\n\n\n## Copyright\nCopyright (c) 2024, Timotej Bernat (timotej.bernat@colorado.edu)\n\n## Acknowledgements\nProject based on the \n[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftimbernat%2Fpolymerist","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftimbernat%2Fpolymerist","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftimbernat%2Fpolymerist/lists"}