Metadata-Version: 1.1
Name: pdb_eda
Version: 1.1.0
Summary: Methods for analyzing electron density maps in wwPDB
Home-page: https://github.com/MoseleyBioinformaticsLab/pdb_eda
Author: Sen Yao
Author-email: yaosen1313@gmail.com
License: Modified Clear BSD License
Description: pdb-eda
        ==========
        
        .. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/pdb_eda/master/doc/_static/images/pdb_eda_logo.png
           :width: 50%
           :align: center
           :target: https://pdb-eda.readthedocs.io/
        
        Description
        -----------
        The `pdb_eda` package provides a simple Python tool for parsing and analyzing electron density maps data
        available from the world wide Protein Data Bank (PDB_).
        
        The `pdb_eda` package currently provides facilities that can:
            * Parse .ccp4 format file into their object representation.
            * Parse .pdb format file to get information that complimentary to the Bio.PDB module in BioPython_ package.
            * Analyze the electron density maps on atom/residue/chain level and
              interpret the electron densities in terms of number of electrons.
        
        Full API documentation, user guide, and tutorial can be found on readthedocs_
        
        Installation
        ------------
        `pdb_eda` runs under Python 3.4+ and is available through python3-pip.
        Install via pip or clone the git repo and install the following dependencies and you are ready to go!
        
        Install on Linux, Mac OS X
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
           python3 -m pip install pdb_eda
        
        GitHub Package installation
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Make sure you have git_ installed:
        
        .. code:: bash
        
           git clone https://github.com/MoseleyBioinformaticsLab/pdb_eda.git
        
        Dependencies
        ~~~~~~~~~~~~
        
        `pdb_eda` requires the following Python libraries:
        
           * Biopython_ for creating and analyzing the `pdb_eda` atom objects.
           * pandas_ for calculating aggregated results.
           * numpy_ and scipy_ for mathmatical calculations.
           * docopt_ for better command line interface.
           * jsonpickle_ for formatted and reusable output.
        
        To install dependencies manually:
        
        .. code:: bash
        
           pip3 install biopython
           pip3 install pandas
           pip3 install numpy
           pip3 install scipy
           pip3 install docopt
           pip3 install jsonpickle
        
        
        Basic usage
        -----------
        The `pdb_eda` package can be used in several ways:
        
           * As a library for accessing and manipulating data in PDB or CCP4 format files.
        
              * Create the `pdb_eda.densityAnalysis.fromPDBid` generator function that will generate
                (yield) single `pdb_eda.densityAnalysis` instance at a time.
        
              * Process each `pdb_eda.densityAnalysis` instance:
        
                 * Generate symmetry atoms.
                 * Generate red (negative density) or green (positive density) blob lists.
                 * Process PDB structures to aggregate cloud.
                 * Calculate atom blob list and statistics.
        
           * As a command-line tool:
        
              * Calculate statistics of a single PDB structure.
              * Calculate aggregated statistics of multiple PDB structures.
        
        
        
        
        .. _readthedocs: https://pdb-eda.readthedocs.io/en/latest/
        .. _PDB: https://www.wwpdb.org/
        .. _BioPython: https://biopython.org/
        .. _git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git/
        .. _pandas: http://pandas.pydata.org/
        .. _numpy: http://www.numpy.org/
        .. _scipy: https://scipy.org/scipylib/index.html
        .. _docopt: http://docopt.org/
        .. _jsonpickle: https://github.com/jsonpickle/jsonpickle
        
Keywords: PDB,electron densiy map
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
