Benchmarks for comparing 3D structure file parser performance in Biopython

This repository contains Python 3.x code for comparing the file parsing performance of the PDB and PDBx/mmCIF (https://www.wwpdb.org/documentation/file-format) file formats with the new MacroMolecular Transmission Format (MMTF, http://mmtf.rcsb.org) using the following Biopython parsers: MMCIFParser, FastMMCIFParser, PDBParser, and MMTFParser. The results of these benchmarks are described in the paper: MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures (2017) bioRxiv 122689, https://doi.org/10.1101/122689.

This repository also contains benchmark datasets: sample_1000.csv is a set of 1000 randomly selected PDB structures, sample_25.csv, sample_50.csv, sample_75.csv contain 100 structures each around the 25, 50 and 75 percentile of the PDB size distribution: Q25 (2,309-2,313 atoms), Q50 (4,054-4,063 atoms), Q75 (7,862-7,885 atoms), sample_3j3q.csv contains the largest structure in the PDB.

Outputs and locations

The Python script will download and parse all proteins from each csv files, and return the download time in downdload_benchmark_results.csv, and the parsing time parsing_benchmark_results.csv. Downloaded structures will be saved into /pdb, /cif or /mmtf folder depending on their file type.

Version requirements

This script requires Python 3.x. You can download the latest Python versions from:

https://www.python.org/downloads/

or

https://www.continuum.io/downloads

Installing required python packages

The Python script in this repository requires a few packages, including biopython and wget. These packages can be installed through pip:

pip install biopython 
pip install wget 
pip install gzip

How to run the program

To run the benchmark, you have to get the lastest source code from git, then excute your Python file in terminal or command line:

$ git clone https://github.com/altaite/mmtf-python-benchmark.git
$ python benchmark_mmtf_python.py