Methods for analyzing electron density maps in wwPDB
Project description
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:
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.
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