Structural Bioinformatics Python Packages

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

diff-biophys

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

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..

buildamol

A fragment-based molecular assembly toolkit

py-packman

Python package built around protein structure and dynamics. OpenBabel-inspired objects.

protein-design-tools

A library of tools for protein design

dlpdb

collect statistics from the entire PDB library

frustration-gpu

Pure-PyTorch reimplementation of LAMMPS-AWSEM frustration analysis (Wolynes-lab AWSEM Hamiltonian + Ferreiro frustration index), GPU-accelerated.

old-pdb

Convert between PDB and CIF formats

intermap

Accelerated Detection of Interaction Fingerprints on Large-Scale Molecular Ensembles

zmpy3d

ZMPY3D NumPy version

go2pdb

Extract PDB entries annotated with specific GO codes

zmpy3d-tf

ZMPY3D Tensorflow version

zmpy3d-cp

Python implementation of 3D Zernike moments with CuPy

zmpy3d-pt

Python implementation of 3D Zernike moments with PyTorch

biobuild

A fragment-based molecular assembly toolkit