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cansarigol
pdbr

pdb + Rich library

6.5M 352 15
ionelmc
remote-pdb

Remote vanilla PDB (over TCP sockets).

978K 302 29
mdmintz
pdbp

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

822K 113 6
PDBeurope
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

198K 79 12
wronglink
pytest-pudb

Pytest PuDB debugger integration

108K 62 14
rasbt
biopandas

Working with molecular structures in pandas DataFrames

35K 751 117
haddocking
pdb-tools

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

28K 451 121
abhishektiwari
hbat

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

23K 9 2
althonos
pyjess

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

21K 10 0
charnley
rmsd

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

19K 572 122
kmaork
madbg

A fully-featured remote and preemptive debugger for python

19K 305 8
williamgilpin
pypdb

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

5K 335 76
pharmai
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

4K 676 141
a-r-j
cpdb-protein

Cython implementation of PDB -> DataFrame parsing

4K 34 1
PDBeurope
pdbecif

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

3K 38 4
plasma-umass
chatdbg

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

3K 1K 90
PDBeurope
pdbe-arpeggio

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

2K 126 23
mmagnus
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

2K 186 48
t-0hmura
pdb2reaction

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

2K 10 2
PDBeurope
pdbe-mmcif-validator

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

2K 10 3
HFooladi
pdbrust

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

1K 18 2
mdmintz
pdbplus

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

1K 113 6
rayhackett
enzymm

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

1K 39 2
t-0hmura
mlmm-toolkit

mlmm - ML/MM toolkit for enzyme reaction analysis

1K 15 4
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