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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] |
C Programming Language
''The C Programming Language'' (sometimes termed ''K&R'', after its authors' initials) is a computer programming book written by Brian Kernighan and Dennis Ritchie, the latter of whom originally designed and implemented the language, as well as co-designed the Unix operating system with which development of the language was closely intertwined. The book was central to the development and popularization of the C programming language and is still widely read and used today. Because the book was co-authored by the original language designer, and because the first edition of the book served for many years as the ''de facto'' standard for the language, the book was regarded by many to be the authoritative reference on C. History C was created by Dennis Ritchie at Bell Labs in the early 1970s as an augmented version of Ken Thompson's B. Another Bell Labs employee, Brian Kernighan, had written the first C tutorial, and he persuaded Ritchie to coauthor a book on the language. Ker ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free And Open-source Software
Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source code is openly shared so that people are encouraged to voluntarily improve the design of the software. This is in contrast to proprietary software, where the software is under restrictive copyright licensing and the source code is usually hidden from the users. FOSS maintains the software user's civil liberty rights (see the Four Essential Freedoms, below). Other benefits of using FOSS can include decreased software costs, increased security and stability (especially in regard to malware), protecting privacy, education, and giving users more control over their own hardware. Free and open-source operating systems such as Linux and descendants of BSD are widely utilized today, powering millions of servers, desktops, smartphones (e.g., ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
XDrawChem
XDrawChem is a free software program for drawing chemical structural formulas, available for Unix and macOS. It is distributed under the GNU GPL. In Microsoft Windows this program is called WinDrawChem. Major features * Fixed length and fixed angle drawing * Automatic alignment of figures * Detection of structures, text, and arrows, and their automatic placement * Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in a built-in library * Retrieval of structures from a network database based on CAS number, formula, or name * Retrieval of information on a molecule based on a drawing * Symbols such as partial charge and radicals * Reading MDL Molfiles, CML (Chemical Markup Language), ChemDraw binary format, ChemDraw XML text format * Writing MDL Molfiles, CML, ChemDraw XML text format * Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats. * Image export in Portable Network Gra ... [...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] |
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] |
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] |
C Sharp (programming Language)
C# (pronounced ) is a general-purpose, high-level multi-paradigm programming language. C# encompasses static typing, strong typing, lexically scoped, imperative, declarative, functional, generic, object-oriented (class-based), and component-oriented programming disciplines. The C# programming language was designed by Anders Hejlsberg from Microsoft in 2000 and was later approved as an international standard by Ecma (ECMA-334) in 2002 and ISO/IEC (ISO/IEC 23270) in 2003. Microsoft introduced C# along with .NET Framework and Visual Studio, both of which were closed-source. At the time, Microsoft had no open-source products. Four years later, in 2004, a free and open-source project called Mono began, providing a cross-platform compiler and runtime environment for the C# programming language. A decade later, Microsoft released Visual Studio Code (code editor), Roslyn (compiler), and the unified .NET platform (software framework), all of which support C# and are free, open ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ruby (programming Language)
Ruby is an interpreted, high-level, general-purpose programming language which supports multiple programming paradigms. It was designed with an emphasis on programming productivity and simplicity. In Ruby, everything is an object, including primitive data types. It was developed in the mid-1990s by Yukihiro "Matz" Matsumoto in Japan. Ruby is dynamically typed and uses garbage collection and just-in-time compilation. It supports multiple programming paradigms, including procedural, object-oriented, and functional programming. According to the creator, Ruby was influenced by Perl, Smalltalk, Eiffel, Ada, BASIC, Java and Lisp. History Early concept Matsumoto has said that Ruby was conceived in 1993. In a 1999 post to the ''ruby-talk'' mailing list, he describes some of his early ideas about the language: Matsumoto describes the design of Ruby as being like a simple Lisp language at its core, with an object system like that of Smalltalk, blocks inspired by higher-o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally developed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Perl
Perl is a family of two high-level, general-purpose, interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned "sister language", Perl 6, before the latter's name was officially changed to Raku in October 2019. Though Perl is not officially an acronym, there are various backronyms in use, including "Practical Extraction and Reporting Language". Perl was developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions. Raku, which began as a redesign of Perl 5 in 2000, eventually evolved into a separate language. Both languages continue to be developed independently by different development teams and liberally borrow ideas from each other. The Perl languages borrow features from other programming languages including C, sh, AWK, and sed; They provide text processing facilities without the arbitrary data-le ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simplified Molecular-input Line-entry System
The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. The original SMILES specification was initiated in the 1980s. It has since been modified and extended. In 2007, an open standard called OpenSMILES was developed in the open-source chemistry community. History The original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch (Pomona College) for supporting the work, and Arthur Weininger (Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in programmi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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