Analytical chemistry, cheminformatics, computational chemistry, crystallography, nanochemistry, nuclear chemistry ...

Chemharp :: An efficient IO library for chemistry file formats.
ChemSpiPy :: Python wrapper for the ChemSpider API. Documentation
pyquante2 :: PyQuante is a Quantum Chemistry suite written in Python, rewritten as PyQuante2 to clean up the old package.
Pymatgen :: is the Python materials analysis library powering the Materials Project. Source code.
- Paper : Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis
Pymol-script-repo :: Collected scripts for Pymol. Pymol wiki

Computational Chemistry

BioStructMap :: a Python package for integration of protein structure and sequence-based features. Publications: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223362/

Cantera : An open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes.
MDTraj : A modern, open library for the analysis of molecular dynamics trajectories.
PDBFixer :: An easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.

Open Source chemical kinetics library

chemreac :: Library for chemical kinetics in homogeneous or isotropically symmetric inhomogenous systems.
chemreac_anaconda :: Conda recipes for conda packages published under conda.anaconda.org/chemreac.
chemreac-benchmarks :: benchmarks for chemreac.

Molecular Chemistry

FRETUtils :: FRET simulation and distance reconstruction utilities written in Python. Website.
MDAnalysis :: An object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.
TEA :: Thermochemical Equilibrium Abundances (TEA), a code to calculate gaseous molecular abundances under thermochemical equilibrium conditions.

GSAS_Bayes :: Extension to the Rietveld package GSAS-II.
tomopy :: An open-sourced Python toolbox to perform tomographic data processing and image reconstruction tasks at the Advanced Photon Source. Documentation.