Pdb Python Packages

pdbr

pdb + Rich library

remote-pdb

Remote vanilla PDB (over TCP sockets).

pdbp

pdbp (Pdb+): A drop-in replacement for pdb and pdbpp. To replace "pdb", add "import pdbp" to an "__init__.py" file.

pdbeccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

mdtraj

An open library for the analysis of molecular dynamics trajectories

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

biopandas

Working with molecular structures in pandas DataFrames

pytest-pudb

Pytest PuDB debugger integration

hbat

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

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

rmsd

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

pyjess

Cython bindings and Python interface to Jess, a 3D template matching software for protein structures. Now 10x faster!

pdbe-mmcif-validator

Real-time VSCode extension and standalone Python script for validating mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary.

tcren

Predicting TCR:pMHC binding from structural data

pdbrust

A Rust library for parsing PDB (Protein Data Bank) files

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

molecularnodes

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

pdbecif

A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"

cristma

CrIStMa — Crystallographic Infrastructure for Structures and Materials. Beta · Python 3.11+ · NumPy-only scientific library.

pypdb

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

proxide

High-performance protein I/O and physics bridging for JAX, with a Rust backend for structure parsing and force-field parameterization

pdb2reaction

End-to-end Reaction-Path Modeling from PDB Structures Using Machine-Learning Interatomic Potentials

chatdbg

ChatDBG - AI-assisted debugging. Uses AI to answer 'why'