Metadata-Version: 2.1
Name: md-davis
Version: 0.3.0
Summary: A tool for comparative analysis of molecular dynamics simulations of proteins.
Home-page: https://github.com/djmaity/md-davis
Author: Dibyajyoti Maity
Author-email: djdibs@gmail.com
License: MIT license
Project-URL: Documentation, https://md-davis.readthedocs.io/
Project-URL: Changelog, https://md-davis.readthedocs.io/en/latest/changelog.html
Project-URL: Issue Tracker, https://github.com/djmaity/md-davis/issues
Keywords: analysis,data visualization,molecular dynamics,protein
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

MD DaVis
========

[![PyPI Package latest release][pypi-badge]][pypi-link]
[![Documentation Status][docs-badge]][docs-link]
[![PyPI Wheel][wheel-badge]][wheel-link]
[![Supported versions][python-badge]][python-link]
[![Commits since latest release][commits-badge]][commits-link]
[![MIT License][license-badge]][license-link]

Introduction
------------
MD DaVis is a tool for comparative analysis of molecular dynamics simulations of proteins.

Documentation: [https://md-davis.readthedocs.io](https://md-davis.readthedocs.io)

Features
--------
1. Free energy landscape
2. Residue properties plot
3. Surface electrostatics
4. Electric field dynamics
5. H-bond/Contact matrix

System Requirements
-------------------

* A 64-bit operating system
* A Python 3 installation with version ≥ 3.7

Installation
------------
The easiest installation method is with
[Anaconda](https://www.anaconda.com/products/individual) or
[Miniconda](https://docs.conda.io/en/latest/miniconda.html).
It is highly recommended to install MD DaVis in a virtual environment.
The [environment.yml](https://github.com/djmaity/md-davis/blob/master/environment.yml)
is provided to ease the process.
```
conda env create -f environment.yml -n md_davis_env
```
This automatically creates a conda environment called `md_davis_env` with all required dependencies.
Activate the environment and install MD DaVis in it using:
```
conda activate md_davis_env
pip install md-davis
```

For detailed installation instructions, see:
[https://md-davis.readthedocs.io/en/latest/install.html](https://md-davis.readthedocs.io/en/latest/install.html)

### Dependencies

The following dependencies will have to be obtained separately.
* [Delphi](http://compbio.clemson.edu/delphi)
* [MSMS](http://mgltools.scripps.edu/downloads#msms)
* [GROMACS](https://www.gromacs.org)

Usage
-----

If MD DaVis is installed in a virtual environment, it should be activated before using MD DaVis.
For example, to activate the virtual environment created with conda, use:
```
conda activate md_davis_env
```

The MD DaVis CLI can be called with:
```
md_davis
```

Author
------
Dibyajyoti Maity - [www.djmaity.com](http://www.djmaity.com)

<!--  --------------------------------------------------------------------- -->
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[pypi-link]: https://pypi.org/project/md-davis
[docs-badge]: https://readthedocs.org/projects/md-davis/badge/?version=latest
[docs-link]: https://md-davis.readthedocs.io/en/latest/
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[wheel-link]: https://pypi.org/project/md-davis
[python-badge]: https://img.shields.io/pypi/pyversions/md-davis.svg
[python-link]: https://pypi.org/project/md-davis
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[license-link]: https://github.com/djmaity/md-davis/blob/master/LICENSE


