Metadata-Version: 2.1
Name: bio-pyvol
Version: 1.6.7
Summary: a PyMOL plugin and python package for visualization, comparison, and volume calculation of protein drug-binding sites
Home-page: https://github.com/schlessingerlab/pyvol
Author: Ryan H.B. Smith
Author-email: ryan.smith@icahn.mssm.edu
License: MIT
Description: ---
        title: 'PyVOL: Protein Pocket Visualization, Segmentation, and Characterization'
        ---
        
        ![image](https://img.shields.io/pypi/v/bio_pyvol.svg)
        
        ![image](https://img.shields.io/pypi/l/bio_pyvol.svg)
        
        Overview
        ========
        
        PyVOL is a python library packaged into a [PyMOL](https://pymol.org/2/)
        GUI for identifying protein binding pockets, partitioning them into
        sub-pockets, and calculating their volumes. PyVOL can be run as a PyMOL
        plugin through its GUI or the PyMOL prompt, as an imported python
        library, or as a command-line program. Visualization of results is
        exclusively supported through PyMOL though exported surfaces are
        compatible with standard 3D geometry visualization programs. The project
        is hosted on github by the Schlessinger Lab. Please access the
        repository to view code or submit bugs. The package has been most
        extensively tested with PyMOL 2.3+ running Python 3.7. Support for all
        python versions 2.7+ is intended but not as thoroughly tested. Support
        for PyMOL 1.7.4+ without the GUI is under development. Unfortunately,
        PyVOL can not currently run on MacOS Catalina due to its restrictions on
        running 32-bit executables. The Mac-compatible MSMS executable is not
        yet available in a 64-bit form.
        
        Quick Installation into PyMOL 2.0+
        ==================================
        
        PyVOL can be installed into any python environment, but installing
        directly into PyMOL 2.0+ is easiest. Download the
        basic GUI installer &lt;https://github.com/schlessingerlab/pyvol/blob/master/installers/pyvol-installer.zip&gt;
        and then use the PyMOL plugin manager to install that file:
        Plugins --&gt; Plugin Manager --&gt; Install New Plugin --&gt; Install from local file --&gt;
        Choose file...
        
        This installs the PyVOL GUI. Select
        Plugins --&gt; PyVOL --&gt; Settings --&gt; Install PyVOL from PyPI to
        fetch PyVOL and any missing dependencies. Once PyVOL has been installed,
        the location of MSMS must be added to the path. In the MSMS Settings
        panel, common locations for the executable can be searched. Once an
        executable has been identified and is displayed, Change MSMS Path can be
        clicked to make that executable visible to the back-end. The GUI should
        then display that it can find MSMS. For academic users and non-academic
        users with the Schrodinger incentive PyMOL distribution, installation is
        now complete. For all others install:MSMS Installation.
        
        Example Basic Run
        =================
        
        A simple calculation using the PyMOL prompt is to load a protein of
        interest and then run the pocket command. This is an example for the
        Sorafenib-bound structure of BRAF:
        
        ``` {.sourceCode .python}
        fetch '1UWH'
        pocket "1UWH and chain B"
        ```
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
