Protein Data Bank Python Packages

rcsb-api

Python interface for RCSB.org API services

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures https://hbat-web.abhishek-tiwari.com

graphein

Protein Graph Library

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

mmcif-gen

This application is designed to create mmcif files from facilities data.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

wwpdb-validation

Read wwPDB validation reports completely and correctly. All 36 per-residue and ~90 entry-level fields, plus the four traps that silently corrupt results.

diff-biophys

Differentiable biophysical modeling in JAX (SAXS, NMR, CD), with Jupyter Notebook examples.

mmtfpyspark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

pdbminebuilder

Build a Mine-schema database from PDB data. Load PDBj structural biology data into PostgreSQL with RDKit chemical search support.

pdb-objects

Object-oriented processing of PDB files in Python