{ "info": { "author": "P C Kroon", "author_email": "p.c.kroon@rug.nl", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry" ], "description": "# Martinize2 and vermouth: The ultimate resolution transformation tools\n\n[![Build Status](https://github.com/marrink-lab/vermouth-martinize/actions/workflows/run_tests.yml/badge.svg)](https://github.com/marrink-lab/vermouth-martinize/actions)\n[![codecov](https://codecov.io/gh/marrink-lab/vermouth-martinize/branch/master/graph/badge.svg)](https://codecov.io/gh/marrink-lab/vermouth-martinize)\n[![Documentation Status](https://readthedocs.org/projects/vermouth-martinize/badge/?version=latest)](https://vermouth-martinize.readthedocs.io/en/latest/?badge=latest)\n\n\nMartinize2 is a rewrite of [Martinize]. It is aimed at producing\ncoarse-grained structures and topologies from an atomistic structure. Martinize\nis primarily developed for the [Martini] coarse-grained force field and the\n[Gromacs] simulation engine. However the architecture of the program will\nallow us to support a broader range of force fields and simulation engines in\nthe future.\n\nVermouth (for VERsatile, MOdular, and Universal Tranformation Helper) is the\npython library that powers Martinize2. It allows to describe and apply\ntransformation on molecular structures and topologies using graph algorithms.\n\n## Disclaimer\n\nMartinize2 and Vermouth are under development. So far they have mostly been\ntested on Martini 2 and Martini 3. If you use Martinize 2 and Vermouth for any\nother force field be sure to carefully check the resulting topologies! \nBugs can occur. If you encounter an issue, please report it on\n. Carefully check your\n input and output files before using them; read the messages displayed by the\n program.\n\n## Installation\n\nMartinize2 and vermouth require python 3.6 or greater. They are distributed via [PyPi][pypi_vermouth], and can be\ninstalled using the `pip` command:\n \n pip install vermouth\n\nThis installs the last released version. You can update an existing installation by running `pip install -U vermouth`.\nIn some cases you may want to experiment with running the latest development version. You can install this version with\nthe following command: \n\n pip install git+https://github.com/marrink-lab/vermouth-martinize.git#vermouth\n\nNote that vermouth and Martinize2, in particular development versions, may contain bugs that cause it to produce\nincorrect topologies. Check the produced output carefully!\n\nThe behavior of the `pip` command can vary depending of the specificity of your\npython installation. See the [documentation on installing a python\npackage][pipdoc] to learn more.\n\n## Basic usage\n\nInstalling Martinize2 and vermouth with `pip` adds the `martinize2` program to\nthe research PATH. You can see the available option of the program by running:\n\n martinize2 -h\n\nAt the moment, martinize2 tries to reproduce the interface of the original\nMartinize. You can find explanations on how to use Martinize on the [Martini\ntutorials]; in most cases, replacing calls to `martinize.py` by calls to\n`martinize2` should produce similar results.\n\nThe documentation of the vermouth python library will come soon.\n\n## License\n\nMartinize2 and vermouth are distributed under the Apache 2.0 license.\n\n Copyright 2018 University of Groningen\n\n\tLicensed under the Apache License, Version 2.0 (the \"License\");\n\tyou may not use this file except in compliance with the License.\n\tYou may obtain a copy of the License at\n\n\t\thttp://www.apache.org/licenses/LICENSE-2.0\n\n\tUnless required by applicable law or agreed to in writing, software\n\tdistributed under the License is distributed on an \"AS IS\" BASIS,\n\tWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n\tSee the License for the specific language governing permissions and\n\tlimitations under the License.\n\nThe [full text of the license][license] is available in the source repository.\n\n## Contributions\n\nThe development of Martinize2 and vermouth is done on [github]. Contributions\nare welcome as [bug reports] and [pull requests]. Note however that the\ndecision of whether or not contributions can give authorship on the resulting\nacademic paper is left to our sole discretion.\n\n[Martinize]: https://github.com/Tsjerk/Martinize\n[Martini]: http://cgmartini.nl\n[Martini tutorials]: http://cgmartini.nl/index.php/tutorials-general-introduction-gmx5\n[Gromacs]: http://www.gromacs.org\n[pypi_vermouth]: https://pypi.org/project/vermouth/\n[pipdoc]: https://packaging.python.org/tutorials/installing-packages/#installing-packages\n[license]: https://github.com/marrink-lab/vermouth-martinize/blob/master/LICENSE\n[github]: https://github.com/marrink-lab/vermouth-martinize\n[bug reports]: https://github.com/marrink-lab/vermouth-martinize/issues\n[pull requests]: https://github.com/marrink-lab/vermouth-martinize/pulls\n\n\n\n", "description_content_type": "text/markdown; charset=UTF-8", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": 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