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

pytest-pudb

Pytest PuDB debugger integration

biopandas

Working with molecular structures in pandas DataFrames

pdb-tools

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

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

pyjess

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

rmsd

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

madbg

A fully-featured remote and preemptive debugger for python

pypdb

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

cpdb-protein

Cython implementation of PDB -> DataFrame parsing

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

pdbecif

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

chatdbg

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

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

pdb2reaction

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

pdbe-mmcif-validator

Validate mmCIF/CIF files against the PDBx/mmCIF dictionary or any CIF dictionary

pdbe-arpeggio

Arpeggio calculates interatomic contacts based on the rules defined in CREDO.

pdbrust

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

pdbplus

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

enzymm

EnzyMM - Enzyme Motif Miner - Geometric matching of catalytic motifs in protein structures.

molecularnodes

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