pdb-eda 2.7.1

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/domain levels and interpret the electron densities in terms of number of electrons by estimating a density-electron ratio.

Full API documentation, user guide, and tutorial can be found on readthedocs

Citation

Please cite the following papers when using pdb_eda:

Sen Yao and Hunter N.B. Moseley. “A chemical interpretation of protein electron density maps in the worldwide protein data bank” PLOS One 15, e0236894 (2020). https://doi.org/10.1371/journal.pone.0236894

Sen Yao and Hunter N.B. Moseley. “Finding high-quality metal ion-centric regions across the worldwide Protein Data Bank” Molecules 24, 3179 (2019). https://doi.org/10.3390/molecules24173179

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.

• Cython for cythonizing low-level utility functions to improve computational performance.

  • Requires gcc to be installed for the cythonization process.

• numpy and scipy for mathmatical calculations.

• docopt for better command line interface.

• jsonpickle for formatted and reusable output.

• PyCifRW for reading Cif formatted files.

  • Requires gcc to be installed for compiling components of the package.

• pymol for calculating crystal contacts. (This package is not required, except for this functionality).

To install dependencies manually:

pip3 install biopython
pip3 install cython
pip3 install numpy
pip3 install scipy
pip3 install docopt
pip3 install jsonpickle
pip3 install PyCifRW

Basic usage

The pdb_eda package can be used in several ways:

• As a library for accessing and manipulating data in PDB and CCP4 format files.

  • Use the ~pdb_eda.densityAnalysis.fromPDBid generator function that will generate (yield) a 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.

  • Calculate atom regional discrepancies and statistics.

  • Calculate residue regional discrepancies and statistics.

• As a command-line tool using the pdb_eda command (or “python3 -m pdb_eda”).

  • The command-line interface has multiple modes.

  • single - single-structure mode:

    • Convert electron density map CCP4 files into its equivalent JSON file format.

    • Aggregate electron density map by atom, residue, and domain, and return the results in either JSON or csv format.

    • Aggregate difference electron density map into green (positive) or red (negative) blobs, and return the object or statistics results in either JSON or csv format.

    • Aggregate difference electron density map for atom and residue specific regions and return results in either JSON or csv format.

    • Return traditional quality metrics and statistics for atoms and residues.

  • multiple - multiple-structure mode:

    • Analyze and return cumulative statistics for a given list of PDB IDs.

    • Filter list of PDB IDs by cumulative statistic criteria.

    • Check and redownload problematic PDB entries.

    • Run single structure mode with multicore processing.

    • Run crystal contacts mode with multicore processing.

  • contacts - crystal contacts mode:

    • Analyze and return atoms with crystal contacts.

    • This mode requires pymol to be installed.

  • generate - parameter generation mode: (rarely used mode)

    • Downloads PDB chemical component list and extracts information to create atom type parameters.

    • Analyzes list of PDB IDs for specific atom types.

    • Generates atom type parameter file and list of PDB IDs for their optimization.

  • optimize - parameter optimization mode: (rarely used mode)

    • Optimizes atom type radii and b-factor density correction slopes using a given list of PDB IDs.

CHANGELOG

Version 2.4.1: Added -O3 compile option to cythonization.

Version 2.3.2: Fixed logical and runtime errors in single density –atom-mask option. Improved cythonization further. Added –optimized-radii option to single density submode.

Version 2.2.1: Moved previous single density submode to cloud submode. Created new single density submode that has near parallel options to single difference submode. Added –atom-mask option to single density submode. Improved cythonization to gain additional computational performance. Performed a variety of bug fixes.

Version 2.1.1: Over 2200 lines of additional code has been written and most of the code base has been revised and refactored. Computationally intensive parts of the code have been cythonized to improve execution performance. Many variables and functions have been renamed to greatly improve readability and understanding of the code base, API, and CLI.

The application programming interface (API) has been greatly expanded and much of the functionality streamlined.

The command line interface has been greatly expanded and now includes single, multiple, contacts, generate, and optimize modes.

Optimize mode has a new penalty function being optimized that both minimizes differences in density-electron ratio estimates and maximizes electron cloud aggregation. The optimization is also roughly 10-fold faster than the previous generation of algorithm.

The atom types have been systematically generated from the wwPDB master chemical components file. Both amino acid and nucleic acid type parameters have been optimized. So both protein and nucleic acid PDB entries can be analyzed now.

License

A modified Clear BSD License

Copyright (c) 2019, Sen Yao, Hunter N.B. Moseley All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted (subject to the limitations in the disclaimer below) provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

• Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

• If the source code is used in a published work, then proper citation of the source code must be included with the published work.

NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY’S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.