task-file-io

A project (and object) for storing, manipulating, and converting molecular mechanics data.

Some useful RDKit functions

A Python library for structural cheminformatics

macromolecular crystallography library and utilities

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

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

The Chemistry Development Kit

Official git repository for Biopython (originally converted from CVS)

A comprehensive library for computational molecular biology

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

Annotated data.

Molecular Processing Made Easy.

Molecule Validation and Standardization

Tools (written in C using htslib) for manipulating next-generation sequencing data

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Parsers and algorithms for computational chemistry logfiles

Source code for molecular graphics program UCSF ChimeraX

bedtools - the swiss army knife for genome arithmetic

MoleculeKit: Your favorite molecule manipulation kit

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.