This package provides a Python library intended for use in automated tests. One difficulty when testing software is that the code under test might need to read or write to files in the local file system. If the file system is not set up in just the right way, it might cause a spurious error during the test. The pyfakefs library provides a solution to problems like this by mocking file system interactions. In other words, it arranges for the code under test to interact with a fake file system instead of the real file system. The code under test requires no modification to work with pyfakefs.

coordgenlibs contains algorithms to generate 2D coordinates of molecules including macrocycles and metal complexes. It has an emphasis on quality rather than speed.

geomeTRIC is a Python library and program for geometry optimization of molecular structures, which works with different external quantum chemistry (and molecular mechanics) softwares.

maeparser is a parser for Schrodinger Maestro files.

This package is a wrapper around simple-dftd3 and dftd4 for use with pyscf.

GEMMI is a C++ library for macromolecular crystallography. It can be used for working with

1. macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),

2. refinement restraints (CIF files),

3. reflection data (MTZ and mmCIF formats),

4. data on a 3D grid (electron density maps, masks, MRC/CCP4 format)

5. crystallographic symmetry.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's a collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

TRAJNG (Trajectory next generation) is a program library for handling molecular dynamics (MD) trajectories. It can store coordinates, and optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.

The InChI (IUPAC International Chemical Identifier) algorithm turns chemical structures into machine-readable strings of information. InChIs are unique to the compound they describe and can encode absolute stereochemistry making chemicals and chemistry machine-readable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation.

YAeHMOP contains a program and library for performing extended Hückel calculations and analyzing the results.

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Spglib is a library for finding and handling crystal symmetries written in C. Spglib can be used to:

1. Find symmetry operations

2. Identify space-group type

3. Wyckoff position assignment

4. Refine crystal structure

5. Find a primitive cell

6. Search irreducible k-points

PyMOL is a capable molecular viewer and renderer. It can be used to prepare publication-quality figures, to share interactive results with your colleagues, or to generate pre-rendered animations.

RingDecomposerLib is a library for the calculation of unique ring families, relevant cycles, the smallest set of smallest rings and other ring topology descriptions.

This is a generic C++ library that can be used to rapidly align two small molecules in 3D space, with shape - and optionally color - Tanimoto scoring.

This extension to python-pyscf provides calculations of different electromagnetic properties for molecules and crystals.

FreeSASA is a command line tool and C-library for calculating SASAs. By default Lee & Richards' algorithm is used, but Shrake & Rupley's is also available. Both can be parameterized to arbitrary precision, and for high resolution versions of the algorithms, the calculations give identical results.

RDKit is a C++ and Python library for cheminformatics, which includes (among other things) the analysis and modification of molecules in 2D and 3D and descriptor generation for machine learning.

Avogadro 2 is an advanced molecule editor and visualizer designed for use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

This package contains a library and programs for canonicalization of SMILES and MOL files, molecular structure fingerprinting and rendering molecules.

libmsym is a C library dealing with point group symmetry in molecules.

PySCF (Python-based Simulations of Chemistry Framework) is a Python library for quantum chemistry calculations and method development. Most of the functionality is implemented in Python, while computationally critical parts are implemented in C.

XCFun is a library of exchange-correlation functionals with arbitrary-order derivatives for density functional theory.