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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] |
Warren Lyford DeLano
Warren Lyford DeLano (June 21, 1972 – November 3, 2009) was a bioinformatician and an advocate for the increased adoption of open source practices in the sciences, and especially drug discovery, where advances which save time and resources can also potentially save lives. Biography Born in Philadelphia on June 21, 1972, DeLano was educated at Yale University, where he helped produce campus humor magazine ''The Yale Record''. In 2000, he launched the PyMOL open-source molecular viewer in an attempt to demonstrate the practical impact open source might have on discovery of new medicines. Since then, PyMOL has been widely adopted for molecular structure visualization within the pharmaceutical industry and at public sector research institutions. In 2003, DeLano founded DeLano Scientific LLC to commercialize PyMOL and conduct an experiment in the "laboratory of the market" regarding the commercial viability of an open source software company. His hypothesis was that open source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python License
The Python License is a deprecated permissive computer software license created by the Corporation for National Research Initiatives (CNRI). It was used for versions 1.6 and 2.0 of the Python programming language, both released in the year 2000. The Python License is similar to the BSD License and, while it is a free software license, its wording in some versions meant that it was incompatible with the GNU General Public License (GPL) used by a great deal of free software including the Linux kernel. For this reason CNRI retired the license in 2001, and the license of current releases is the Python Software Foundation License. Origin Python was created by Guido van Rossum and the initial copyright was held by his employer, the Centrum Wiskunde & Informatica (CWI). During this time Python was distributed under a GPL-compatible variant of the Historical Permission Notice and Disclaimer license. CNRI obtained ownership of Python when Van Rossum became employed there, and after ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PyQt
PyQt is a Python binding of the cross-platform GUI toolkit Qt, implemented as a Python plug-in. PyQt is free software developed by the British firm Riverbank Computing. It is available under similar terms to Qt versions older than 4.5; this means a variety of licenses including GNU General Public License (GPL) and commercial license, but not the GNU Lesser General Public License (LGPL). PyQt supports Microsoft Windows as well as various kinds of UNIX, including Linux and macOS. PyQt implements around 440 classes and over 6,000 functions and methods including: * a substantial set of GUI widgets * classes for accessing SQL databases (ODBC, MySQL, PostgreSQL, Oracle, SQLite) * QScintilla, Scintilla-based rich text editor widget * data aware widgets that are automatically populated from a database * an XML parser * SVG support * classes for embedding ActiveX controls on Windows (only in commercial version) To automatically generate these bindings, Phil Thompson developed t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Aqua (user Interface)
Aqua is the graphical user interface, design language and Theme (computing), visual theme of Apple Inc.'s macOS and iOS operating systems. It was originally based on the theme of water, with droplet-like components and a liberal use of reflection effects and translucency. Its goal is to "incorporate color, depth, translucence, and complex textures into a visually appealing interface" in macOS applications. At its introduction, Steve Jobs noted that "... it's liquid, one of the design goals was when you saw it you wanted to lick it". Aqua was first introduced at the 2000 Macworld Conference & Expo in San Francisco. Its first appearance in a commercial product was in the July 2000 release of iMovie 2, followed by Mac OS X 10.0 the following year. Aqua is the successor to Appearance Manager, Platinum, which was used in Mac OS 8, Mac OS 9, and developer releases of Rhapsody (operating system), Rhapsody (including macOS Server, Mac OS X Server 1.2). The appearance of Aqua has changed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Widget (GUI)
A graphical widget (also graphical control element or control) in a graphical user interface is an element of interaction, such as a button or a scroll bar. Controls are software components that a computer user interacts with through direct manipulation to read or edit information about an application. User interface libraries such as Windows Presentation Foundation, Qt (software), Qt, GTK, and Cocoa (API), Cocoa, contain a collection of controls and the logic to render these. Each widget facilitates a specific type of user-computer interaction, and appears as a visible part of the application's GUI as defined by the theme and rendered by the rendering engine. The theme makes all widgets adhere to a unified aesthetic design and creates a sense of overall cohesion. Some widgets support interaction with the user, for example labels, Button (computing), buttons, and Checkbox, check boxes. Others act as Container (abstract data type)#Graphic containers, containers that group the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tk (software)
Tk is a cross-platform widget toolkit that provides a library of basic elements of GUI widgets for building a graphical user interface (GUI) in many programming languages. It is free and open-source software released under a BSD-style software license. Tk provides many widgets commonly needed to develop desktop applications, such as button, menu, canvas, text, frame, label, etc. Tk has been ported to run on most flavors of Linux, macOS, Unix, and Microsoft Windows. Like Tcl, Tk supports Unicode within the Basic Multilingual Plane, but it has not yet been extended to handle the current extended full Unicode (e.g., UTF-16 from UCS-2 that Tk supports). Tk was designed to be extended, and a wide range of extensions are available that offer new widgets or other capabilities. Since Tcl/Tk 8, it offers "native look and feel" (for instance, menus and buttons are displayed in the manner of "native" software for any given platform). Highlights of version 8.5 include a new theming engine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Poisson–Boltzmann Equation
The Poisson–Boltzmann equation describes the distribution of the electric potential in solution in the direction normal to a charged surface. This distribution is important to determine how the electrostatic interactions will affect the molecules in solution. It is expressed as a differential equation of the electric potential \psi, which depends on the solvent permitivity \varepsilon, the solution temperature T, and the mean concentration of each ion species c_i^0: :\nabla^2 \psi = - \frac \sum_i c_i^0 q_i \exp \left( \frac \right) The Poisson–Boltzmann equation is derived via mean-field assumptions. From the Poisson–Boltzmann equation many other equations have been derived with a number of different assumptions. Origins Background and derivation The Poisson–Boltzmann equation describes a model proposed independently by Louis Georges Gouy and David Leonard Chapman in 1910 and 1913, respectively. In the Gouy-Chapman model, a charged solid comes into contact with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FreeGLUT
freeglut is an open-source alternative to the OpenGL Utility Toolkit (GLUT) library. GLUT (and hence freeglut) allows the user to create and manage windows containing OpenGL contexts on a wide range of platforms and also read the mouse, keyboard and joystick functions. freeglut is intended to be a full replacement for GLUT, and has only a few differences. Since GLUT has gone into stagnation, freeglut is in development to improve the toolkit. It is released under the MIT License. History freeglut was originally written by Paweł W. Olszta with contributions from Andreas Umbach and Steve Baker. Since Paweł ceased working in 3D graphics, he passed the baton to Steve Baker. The current maintainers of freeglut are John F. Fay, John Tsiombikas, and Diederick C. Niehorster. Paweł started freeglut development on December 1, 1999. The project is now virtually a 100 % replacement for the original GLUT with only a few departures (such as the abandonment of SGI-specific features such as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenGL Extension Wrangler Library
OpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. The API is typically used to interact with a graphics processing unit (GPU), to achieve hardware-accelerated rendering. Silicon Graphics, Inc. (SGI) began developing OpenGL in 1991 and released it on June 30, 1992. It is used for a variety of applications, including computer-aided design (CAD), video games, scientific visualization, virtual reality, and flight simulation. Since 2006, OpenGL has been managed by the non-profit technology consortium Khronos Group. Design The OpenGL specification describes an abstract application programming interface (API) for drawing 2D and 3D graphics. It is designed to be implemented mostly or entirely using hardware acceleration such as a GPU, although it is possible for the API to be implemented entirely in software running on a CPU. The API is defined as a set of functions which may be cal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital computers in the mid-20th century. Early programs were written in the machine language specific to the hardware. The introduction of high-level programming languages in 1958 allowed for more human-readable instructions, making software development easier and more portable across different computer architectures. Software in a programming language is run through a compiler or Interpreter (computing), interpreter to execution (computing), execute on the architecture's hardware. Over time, software has become complex, owing to developments in Computer network, networking, operating systems, and databases. Software can generally be categorized into two main types: # operating systems, which manage hardware resources and provide services for applicat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Biology
Structural biology deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In the 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography, nuclear magnetic resonance, and Electron microscope, electron microscopy. Through the discovery of X-ray, X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, Nuclear magnetic resonance spectroscopy, NMR spectroscopy allowed information about protein structure and dynamic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source Model
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentralized software development model that encourages open collaboration. A main principle of open source software development is peer production, with products such as source code, blueprints, and documentation freely available to the public. The open source movement in software began as a response to the limitations of proprietary code. The model is used for projects such as in open source appropriate technology, and open source drug discovery. Open source promotes universal access via an open-source or free license to a product's design or blueprint, and universal redistribution of that design or blueprint. Before the phrase ''open source'' became widely adopted, developers and producers used a variety of other terms, such as ''free software'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
