Pytest-xprocess is an experimental py.test plugin for managing processes across test runs.

This package provides a pytest plugin for generating NUnit3 test result XML output

tidyall makes a lot of code tidiers and validators available from a single unified interface. You can run tidyall on a single file or on an entire project hierarchy, and configure which tidiers/validators are applied to which files. tidyall will back up files beforehand, and for efficiency will only consider files that have changed since they were last processed.

Note that if you see some missing tidier or validator modules error, you can let tidyall load them after install them. For example, one can run guix shell perl-perl-tidy perl in advance to load Perl::Tidy.

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.

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.

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

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

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.

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

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

MoleQueue is a system-tray resident desktop application for abstracting, managing, and coordinating the execution of tasks both locally and on remote computational resources. Users can set up local and remote queues that describe where the task will be executed. Each queue can have programs, with templates to facilitate the execution of the program. Input files can be staged, and output files collected using a standard interface.

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

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

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

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 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 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.

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.

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.

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

libcint is a C library (also with a Fortran API) to evaluate one- and two-electron integrals for GTOs.