| Repository | |
|---|---|
| Written in | C++ |
| Operating system | Windows, Linux |
| Available in | English |
| Type | Chemoinformatics |
| License | GPL 2.0 |
Molsketch is a molecule editor for 2D computer graphics published as free software. [1] It is written in C++ with the Qt toolkit for Microsoft Windows and Linux. [2]
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.
Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III. Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock, Post-Hartree–Fock electron correlation methods, and density functional theory. The program can compute energies, optimize molecular geometries, and compute vibrational frequencies. The major part of the program is written in C++, while Python API is also available, which allows users to perform complex computations or automate tasks easily.
Massively Parallel Quantum Chemistry (MPQC) is an ab initio computational chemistry software program. Three features distinguish it from other quantum chemistry programs such as Gaussian and GAMESS: it is open-source, has an object-oriented design, and is created from the beginning as a parallel processing program. It is available in Ubuntu and Debian.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB).
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license, and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats.
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry.
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
Gabedit is a graphical user interface to GAMESS (US), Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, ORCA and Q-Chem computational chemistry packages.
QuteMol is an open-source, interactive, molecular visualization system. QuteMol utilizes the current capabilities of modern GPUs through OpenGL shaders to offer an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
Molekel is a free software multiplatform molecular visualization program. It was originally developed at the University of Geneva by Peter F. Flükiger in the 1990s for Silicon Graphics Computers. In 1998, Stefan Portmann took over responsibility and released Version 3.0. Version 4.0 was a nearly platform independent version. Further developments lead to version 4.3, before Stefan Portmann moved on and ceased to develop the codes. In 2006, the Swiss National Supercomputing Centre (CSCS) restarted the project and version 5.0 was released on 21 December 2006.
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.
JChemPaint is computer software, a molecule editor and file viewer for chemical structures using 2D computer graphics. It is free and open-source software, released under a GNU Lesser General Public License (LGPL). It is written in Java and so can run on the operating systems Windows, macOS, Linux, and Unix. There is a standalone application (editor), and two varieties of applet that can be integrated into web pages.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
Python-based Simulations of Chemistry Framework (PySCF) is an ab initio computational chemistry program natively implemented in Python program language. The package aims to provide a simple, light-weight and efficient platform for quantum chemistry code developing and calculation. It provides various functions to do the Hartree–Fock, MP2, density functional theory, MCSCF, coupled cluster theory at non-relativistic level and 4-component relativistic Hartree–Fock theory. Although most functions are written in Python, the computation critical modules are intensively optimized in C. As a result, the package works as efficient as other C/Fortran-based quantum chemistry program. PySCF is developed by Qiming Sun. PySCF2.0 is the latest version of the program.
