pdb-eda 1.0.1

Methods for analyzing electron density maps in wwPDB

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

python3 -m pip install pdb_eda

GitHub Package installation

Make sure you have git installed:

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:

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.