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Status](https://readthedocs.org/projects/contact-map/badge/?version=latest)](http://contact-map.readthedocs.io/en/latest/?badge=latest)\n[![Unit tests](https://github.com/dwhswenson/contact_map/actions/workflows/unit-tests.yml/badge.svg?branch=master)](https://github.com/dwhswenson/contact_map/actions/workflows/unit-tests.yml)\n[![codecov](https://codecov.io/gh/dwhswenson/contact_map/branch/master/graph/badge.svg?token=4so8QmiC5W)](https://codecov.io/gh/dwhswenson/contact_map)\n[![PyPI](https://img.shields.io/pypi/v/contact-map.svg)](https://pypi.python.org/pypi/contact-map/)\n[![conda-forge](https://img.shields.io/conda/v/conda-forge/contact_map.svg)](https://github.com/conda-forge/contact_map-feedstock)\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dwhswenson/contact_map/master)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6)](https://www.codacy.com/app/dwhswenson/contact_map?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=dwhswenson/contact_map\u0026amp;utm_campaign=Badge_Grade)\n[![Maintainability](https://api.codeclimate.com/v1/badges/84768756d594176d8da6/maintainability)](https://codeclimate.com/github/dwhswenson/contact_map/maintainability)\n# Contact Map Explorer\n\nThis package provides tools for analyzing and exploring contacts\n(residue-residue and atom-atom) from a trajectory generated by molecular\ndynamics. It builds on the excellent tools provided by\n[MDTraj](http://mdtraj.org).\n\nContacts can be an important tool for defining (meta)stable states in\nprocesses involving biomolecules. For example, an analysis of contacts can\nbe particularly useful when defining bound states during a binding processes\nbetween proteins, DNA, and small molecules (such as potential drugs).\n\nThe contacts analyzed by Contact Map Explorer can be either intermolecular or\nintramolecular, and can be analyzed on a residue-residue basis or an atom-atom\nbasis.\n\nThis package makes it very easy to answer questions like:\n\n* What contacts are present in a trajectory?\n* Which contacts are most common in a trajectory?\n* What is the difference between the frequency of contacts in one trajectory\n  and another?  (Or with a specific frame, such as a PDB entry.)\n* For a particular residue-residue contact pair of interest, which atoms are\n  most frequently in contact?\n\nIt also facilitates visualization of the contact matrix, with colors\nrepresenting the fraction of trajectory time that the contact was present.\n\nFull documentation is at http://contact-map.readthedocs.io/.\n\nTry it out online: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dwhswenson/contact_map/master?filepath=%2Fexamples) (Note: the performance of the online servers can vary widely.)\n\n## Installation\n\nThe easiest way to install is with `conda`. Conda is a powerful package and\nenvironment management system. If you do not already have a highly\ncustomized Python environment, we recommend starting by installing `conda`,\neither in the [full anaconda\ndistribution](https://www.anaconda.com/download/) or the [smaller-footprint\nminiconda](https://conda.io/miniconda.html). This package is distributed\nthrough the [conda-forge](http://conda-forge.org) channel; install it with:\n\n```bash\nconda install -c conda-forge contact_map\n```\n\nIf you don't want to use `conda`, you can also use `pip` (via a more\ncomplicated process) or do a developer install. See the [installation\ndocumentation](http://contact-map.readthedocs.io/en/latest/installing.html)\nfor details.\n\n## Support and development\n\nContact Map Explorer is an open source project, released under the GNU LGPL,\nversion 2.1 or (at your option) any later version. Development takes place\nin public at https://github.com/dwhswenson/contact_map; your contributions\nwould be welcome!\n\nIf you have suggestions or bug reports, please [raise an issue on our GitHub\nissue page](https://github.com/dwhswenson/contact_map/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdwhswenson%2Fcontact_map","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdwhswenson%2Fcontact_map","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdwhswenson%2Fcontact_map/lists"}