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.

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.

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.

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.

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

qcint is an optimized version of libcint, a C library (also with a Fortran API) to evaluate one- and two-electron integrals for Gaussian type functions.

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.

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

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

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.

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

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.

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

The stex package extends LaTeX with a handful of commands for including Scheme code (or pretty much any other kind of code, as long as you don't plan to use the Scheme-specific transcript support) in a document. It provides the programs scheme-prep and html-prep to convert stex documents to LaTeX and HTML, respectively, plus makefile templates, style files, and other resources. The stex system is used to typeset The Scheme Programming Language and the Chez Scheme User's Guix, among other documents.

This package provides a portable and efficient R[4567]RS implementation of regular expressions, supporting both POSIX syntax with various (irregular) PCRE extensions, as well as SCSH's SRE syntax, with various aliases for commonly used patterns.

Chez Scheme is a self-hosting compiler: building it requires ``boot files'' containing the Scheme-implemented portions compiled for the current platform. (Chez can then cross-compile boot files for all other supported platforms.)

The Racket package cs-bootstrap (part of the main Racket Git repository) implements enough of a Chez Scheme simulation to load the Chez Scheme compiler purely from source into Racket and apply the compiler to itself, thus bootstrapping Chez Scheme. Bootstrapping takes about 10 times as long as using an existing Chez Scheme, but cs-bootstrap supports Racket 7.1 and later, including the Racket BC variant.

This is the precise pre-release version of Chez Scheme from a specific Racket release. It is used to build Racket and to bootstrap the released version of Chez Scheme.

Chez Scheme is a self-hosting compiler: building it requires ``boot files'' containing the Scheme-implemented portions compiled for the current platform. (Chez can then cross-compile bootfiles for all other supported platforms.)

This package provides boot files for the released version of Chez Scheme bootstrapped by chez-scheme-for-racket. Chez Scheme 9.5.4 or any later version can be used for bootstrapping. Guix ultimately uses the Racket package cs-bootstrap to bootstrap its initial version of Chez Scheme.

The stex package extends LaTeX with a handful of commands for including Scheme code (or pretty much any other kind of code, as long as you don't plan to use the Scheme-specific transcript support) in a document. It provides the programs scheme-prep and html-prep to convert stex documents to LaTeX and HTML, respectively, plus makefile templates, style files, and other resources. The stex system is used to typeset The Scheme Programming Language and the Chez Scheme User's Guix, among other documents.

The Nanopass framework is an embedded domain-specific language for writing compilers composed of several simple passes that operate over well-defined intermediate languages. The goal of this organization is both to simplify the understanding of each pass, because it is responsible for a single task, and to simplify the addition of new passes anywhere in the compiler. Nanopass reduces the boilerplate required to create compilers, making them easier to understand and maintain.

Chez-sockets is an extensible sockets library for Chez Scheme.

This package provides a set of MIT/GNU Scheme compatibility libraries for Chez Scheme. The main goal was to provide the functionality required to port the program Scmutils to Chez Scheme.

This package provides a superset of the popular Scheme match package by Andrew Wright, written in fully portable syntax-rules and thus preserving hygiene.