Metadata-Version: 2.1
Name: prody-rhapsody
Version: 0.9.7
Summary: Python program, based on ProDy, for pathogenicity prediction
    of human missense variants.
Home-page: https://github.com/prody/rhapsody
Author: Luca Ponzoni
Author-email: lponzoni@pitt.edu
License: GPL
Project-URL: Bug Reports, https://github.com/prody/rhapsody/issues
Project-URL: Source, https://github.com/prody/rhapsody/
Keywords: SAV missense variant protein dynamics
Platform: Windows
Platform: MacOS X
Platform: POSIX
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.6, <4
Description-Content-Type: text/markdown
Requires-Dist: requests
Requires-Dist: tqdm
Requires-Dist: numpy
Requires-Dist: scikit-learn
Requires-Dist: matplotlib
Requires-Dist: biopython
Requires-Dist: pyparsing
Requires-Dist: prody
Provides-Extra: docs
Requires-Dist: sphinx (>=1.4) ; extra == 'docs'
Requires-Dist: sphinx-theme ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'

[![Build Status](https://travis-ci.com/prody/rhapsody.svg?branch=master)](https://travis-ci.com/prody/rhapsody)
[![PyPI](https://img.shields.io/pypi/v/prody-rhapsody.svg)](https://pypi.org/project/prody-rhapsody/)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/prody-rhapsody.svg)](http://rhapsody.csb.pitt.edu/download.php)
[![Documentation Status](https://readthedocs.org/projects/rhapsody/badge/?version=latest)](https://rhapsody.readthedocs.io/en/latest/?badge=latest)

# Rhapsody
Python program, based on ProDy, for pathogenicity prediction of human
missense variants.

## Install latest published version using pip
Rhapsody is published on [PyPI](https://pypi.org/). To install Rhapsody,
please use pip in the terminal:
```console
$ pip install -U prody-rhapsody
```
It might be necessary to manually install the DSSP program, for instance
by typing on Linux:
```console
$ sudo apt install dssp
```

## Install from source
Rhapsody is written in pure Python so no local compilation is needed.

To install all needed dependencies, we strongly suggest to use Conda and create
a new environment with:
```console
$ conda create -n rhapsody python=3 numpy scikit-learn requests pyparsing matplotlib biopython
$ conda activate rhapsody
$ pip install prody
$ conda install -c salilab dssp
```

After cloning/forking the Rhapsody repository, you can permanently add the
repository path to the conda environment with:
```console
$ conda develop path/to/local/repository
```

If not using Conda, you can manually install all dependencies and then add
the repository location to the `PYTHONPATH` environmental variable. For
example, on Linux simply add the following line to your `~/.bashrc`:
```console
export PYTHONPATH="path/to/local/repository/:$PYTHONPATH"
```

If you are running on Windows, please follow this
[tutorial](https://stackoverflow.com/a/4855685).

## Running initial setup

After installation, please run:
```console
import rhapsody as rd
rd.initialSetup()
```


