haddocking/pdb-tools

Working with molecular structures in pandas DataFrames

Reduce - tool for adding and correcting hydrogens in PDB files

MoleculeKit: Your favorite molecule manipulation kit

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

macromolecular crystallography library and utilities

A Julia package to read, write and manipulate macromolecular structures

A Python platform for Structural Bioinformatics

mmCIF Core Access Library

Parameter/topology editor and molecular simulator