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Samson
SAMSON (Software for Adaptive Modeling and Simulation Of Nanosystems) is a computer software platform for molecular design being developed bOneAngstromand previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA). SAMSON has a modular architecture that makes it suitable for different domains of nanoscience, including material science, life science, and drug design. SAMSON Elements SAMSON Elements are modules for SAMSON, developed with the SAMSON software development kit (SDK). SAMSON Elements help users perform tasks in SAMSON, including building new models, performing calculations, running interactive or offline simulations, and visualizing and interpreting results. SAMSON Elements may contain different class types, including for example: * ''Apps'' – generic classes with a graphical user interface that extend the functions of SAMSON * ''Editors'' – classes that receive user interaction events to provide editing functi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Qt (software)
Qt ( pronounced "cute") is a cross-platform application development framework for creating graphical user interfaces as well as Cross-platform software, cross-platform applications that run on various software and hardware platforms such as Linux, Windows, macOS, Android (operating system), Android or embedded systems with little or no change in the underlying codebase while still being a native application with native capabilities and speed. Qt is currently being developed by The Qt Company, a publicly listed company, and the Qt Project under open-source governance, involving individual developers and organizations working to advance Qt. Qt is available under both commercial licenses and open-source GNU General Public License, GPL 2.0, GPL 3.0, and GNU Lesser General Public License, LGPL 3.0 licenses. Purposes and abilities Qt is used for developing graphical user interfaces (GUIs) and multi-platform application software, applications that run on all major Desktop computer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jmol
Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. It can hence be embedded in web pages to display interactive 3D models of molecules and other structures without the need for any software apart from the web browser (''it does not use Java''). Both Jmol and JSmol render an interactive 3D representation of a molecule or other structure that may be used as a teaching tool, or for research, in several fields, e.g. chemistry, biochemistry, materials science, crystallography, symmetry or nanotechnology. Software Jmol is written in the programming language Java, so it can run on different operating systems: Windows, macOS, Linux, and Unix, as long as they have Java installed. It is free and open-source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry Software
A computation is any type of arithmetic or non-arithmetic calculation that is well-defined. Common examples of computation are mathematical equation solving and the execution of computer algorithms. Mechanical or electronic devices (or, historically, people) that perform computations are known as ''computers''. Computer science is an academic field that involves the study of computation. Introduction The notion that mathematical statements should be 'well-defined' had been argued by mathematicians since at least the 1600s, but agreement on a suitable definition proved elusive. A candidate definition was proposed independently by several mathematicians in the 1930s. The best-known variant was formalised by the mathematician Alan Turing, who defined a well-defined statement or calculation as any statement that could be expressed in terms of the initialisation parameters of a Turing machine. Other (mathematically equivalent) definitions include Alonzo Church's '' lambda-definabil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), 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 (software), RenderMan, Tachyon (software), Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python (programming language), 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. History VMD has been developed under the aegis of principal investigator Klaus Schulten in th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCSF Chimera
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). Chimera is no longer actively developed and is superseded by UCSF ChimeraX. General structure analysis * automatic identification of atom * hydrogen addition and partial charge assignment * high-quality hydrogen bond, contact, and clash detection * measurements: distances, angles, surface area, volume * calculation of cent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RasMol
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). History It was originally developed by Roger Sayle in the early 1990s. Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their cost, were less accessible to scholars. RasMol continues to be important for research in structural biology, and has become important in education. RasMol has a complex licensing version history. Starting with the version 2.7 series, RasMol source code is dual-licensed under a GNU General Public License (GPL), or custom license ''RASLIC''. Starting with version 2.7.5, a GPL is the only license valid for binary distributions. RasMol include ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PyMol
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 (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrödinger, LLC.), 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. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The ''Py'' part of the software's name refe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molekel
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. Molekel uses VTK and Qwt and therefore as well Qt. Major features * Visu ...[...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Design Software
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software ''directly'' supports the aspects related to constructing molecular models, including: * Molecular graphics * interactive molecular drawing and conformational editing * building polymeric molecules, crystals, and solvated systems * partial charges development * geometry optimization * support for the different aspects of force field development Comparison of software covering the major aspects of molecular design Notes and references See also {{columns-list, colwidth=30em, * Molecule editor *Molecular modelling * Molecular modeling on GPUs * Protein design *Drug design * Force field (chemistry) * Comparison of force field implementations * Comparison of nucleic acid simulation software *Comparison of softw ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molden
Molden is a general molecular and electronic structure processing program. Major features * Reads output from the ab initio packages GAMESS (US), Gaussian, MOLPRO, PySCF and from semi-empirical packages such as MOPAC, and supports a number of other formats. * Displays molecular orbitals or electron density Electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typical ... as contour plots or 3D grid plots and output to a number of graphical formats. * Animates reaction paths and molecular vibrations. * A Z-matrix editor. Molden program has been tested on different platforms, namely Linux, Windows NT, Windows95, Windows2000, WindowsXP, MacOSX, Silicon Graphics IRIX, Sun SunOS and Solaris. Ambfor, the main force field module of Molden, is an external program that can be initialized from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gabedit
Gabedit is a graphical user interface to GAMESS (US), Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, ORCA and Q-Chem computational chemistry packages. Major features * Builds molecules by atom, ring, group, amino acid and nucleoside. * Creates an input file for computational chemistry packages. * Reads output from the ab initio packages, and supports a number of other formats. * Displays molecular orbitals or electron density as contour plots or 3D grid plots and output to a number of graphical formats. * Animates molecular vibrations, contours, isosurfaces and rotation. See also * List of molecular graphics systems * PC GAMESS * ORCA * Quantum chemistry computer programs Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Most include the Hartree–Fock (HF) and some post-Hartree–Fock methods. They may also include density functional theory (DFT) ... * SAMSON External links Gabedit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microsoft Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sectors of the computing industry – Windows (unqualified) for a consumer or corporate workstation, Windows Server for a Server (computing), server and Windows IoT for an embedded system. Windows is sold as either a consumer retail product or licensed to Original equipment manufacturer, third-party hardware manufacturers who sell products Software bundles, bundled with Windows. The first version of Windows, Windows 1.0, was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). The name "Windows" is a reference to the windowing system in GUIs. The 1990 release of Windows 3.0 catapulted its market success and led to various other product families ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
