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Ghemical
Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+, GTK+2 and supports quantum mechanics, quantum mechanical and molecular mechanics, molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. Ghemical relies on external code to provide the quantum-mechanical calculations — MOPAC provides the semi-empirical MNDO, MINDO, Austin Model 1, AM1, and PM3 (chemistry), PM3 methods, and MPQC methods based on Hartree–Fock method, Hartree–Fock calculations. The chemical expert system is based on OpenBabel, which provides basis functionality like atom typing, rotamer generation and import/export of chemical file formats. See also * Open Babel — chemical expert system * XDrawChem — 2D drawing program, also based on Open Babel * Molecule editor * Avogadro (software) References External link ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ghemical 2
Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+, GTK+2 and supports quantum mechanics, quantum mechanical and molecular mechanics, molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. Ghemical relies on external code to provide the quantum-mechanical calculations — MOPAC provides the semi-empirical MNDO, MINDO, Austin Model 1, AM1, and PM3 (chemistry), PM3 methods, and MPQC methods based on Hartree–Fock method, Hartree–Fock calculations. The chemical expert system is based on OpenBabel, which provides basis functionality like atom typing, rotamer generation and import/export of chemical file formats. See also * Open Babel — chemical expert system * XDrawChem — 2D drawing program, also based on Open Babel * Molecule editor * Avogadro (software) References External link ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical File Format
A chemical file format is a type of data file which is used specifically to depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another. Distinguishing formats Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:(see ) * ''f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Avogadro (software)
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. Features * Molecule builder-editor for Windows, Linux, Unix, and macOS. * All source code is licensed under the GNU General Public License (GPL) version 2. * Supported languages include: Chinese, English, French, German, Italian, Russian, Spanish, and Polish. * Supports multi-threaded rendering and computation. * Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts. * OpenBabel import of files, input generation for multiple computational chemistry packages, X-ray crystallography, and biomolecule A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or develo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' representation in which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Babel
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. About Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0. The project's stated goal is: "Open Babel is a community-driven scientific project assisting both users and developers as a cross-platform program and library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data." History Open Babel and JOELib were derived from the OELib cheminformatics library. In turn, OELib was based on ideas in the original chemistry program Babel and an unreleased object-oriented programming library called ''OBabel''. Major features * chemical expert system * interconversion of many chemical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenBabel
Open Babel is computer software, a chemical expert system mainly used to interconvert chemical file formats. About Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0. The project's stated goal is: "Open Babel is a community-driven scientific project assisting both users and developers as a cross-platform program and library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data." History Open Babel and JOELib were derived from the OELib cheminformatics library. In turn, OELib was based on ideas in the original chemistry program Babel and an unreleased object-oriented programming library called ''OBabel''. Major features * chemical expert system * interconversion of many chemica ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Expert System
In artificial intelligence, an expert system is a computer system emulating the decision-making ability of a human expert. Expert systems are designed to solve complex problems by reasoning through bodies of knowledge, represented mainly as if–then rules rather than through conventional procedural code. The first expert systems were created in the 1970s and then proliferated in the 1980s. Expert systems were among the first truly successful forms of artificial intelligence (AI) software. An expert system is divided into two subsystems: the inference engine and the knowledge base. The knowledge base represents facts and rules. The inference engine applies the rules to the known facts to deduce new facts. Inference engines can also include explanation and debugging abilities. History Early development Soon after the dawn of modern computers in the late 1940s and early 1950s, researchers started realizing the immense potential these machines had for modern society. One of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Chemistry Software
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media personali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Software Programmed In C++
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media personal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry Software
Computation is any type of arithmetic or non-arithmetic calculation that follows a well-defined model (e.g., an algorithm). Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. An especially well-known discipline of the study of computation is computer science. Physical process of Computation Computation can be seen as a purely physical process occurring inside a closed physical system called a computer. Examples of such physical systems are digital computers, mechanical computers, quantum computers, DNA computers, molecular computers, microfluidics-based computers, analog computers, and wetware computers. This point of view has been adopted by the physics of computation, a branch of theoretical physics, as well as the field of natural computing. An even more radical point of view, pancomputationalism (inaudible word), is the postulate of digital physics that argues that the evolution of the universe is itself a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioclipse
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009, and a command line version in 2021. Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality. The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, and OpenTox were added. Bioclipse is developed as a collaboration between the Prot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GAMESS (US)
General Atomic and Molecular Electronic Structure System (GAMESS (US)) is computer software for computational chemistry program. The original code started on October 1, 1977 as a National Resources for Computations in Chemistry project. In 1981, the code base split into GAMESS (US) and GAMESS (UK) variants, which now differ significantly. GAMESS (US) is maintained by the members of the Gordon Research Group at Iowa State University. GAMESS (US) source code is available as source-available freeware, but is not open-source software, due to license restrictions. Abilities GAMESS (US) can perform several general computational chemistry calculations, including Hartree–Fock method, density functional theory (DFT), generalized valence bond (GVB), and multi-configurational self-consistent field (MCSCF). Correlation corrections after these SCF calculations can be estimated by configuration interaction (CI), second order Møller–Plesset perturbation theory (MP2), and coupled clust ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
