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SMILES
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 program ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SMILES
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 program ... [...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 ) * ''fil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
David Weininger
David Weininger (August 5, 1952 – November 2, 2016) was an American cheminformatician and entrepreneur. He was most notable for inventing the chemical line notations for structures (SMILES), substructures (SMARTS) and reactions (SMIRKS). He also founded Daylight Chemical Information Systems, Inc. Education and career Weininger studied at University of Rochester, first at the Eastman School of Music, then switched to chemistry. After graduation, he worked for General Electric in Canada, where he worked on water management. He then attended University of Wisconsin–Madison, where he graduated with a PhD in environmental engineering in 1978. His PhD project involves the study of Polychlorinated biphenyls in Lake Michigan at the University of Wisconsin–Madison. He developed a computational model using data from the United States Environmental Protection Agency (EPA) using computer graphics algorithms, by then still a nascent field. Upon graduation, he was hired by the EPA dir ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Chemical Identifier
The International Chemical Identifier (InChI or ) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by the International Union of Pure and Applied Chemistry (IUPAC) and National Institute of Standards and Technology (NIST) from 2000 to 2005, the format and algorithms are non-proprietary. Since May 2009, it has been developed by the InChI Trust, a nonprofit charity from the United Kingdom which works to implement and promote the use of InChI. The identifiers describe chemical substances in terms of ''layers'' of information — the atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information. Not all layers have to be provided; for instance, the tautomer layer can be omitted if that type of information is not relevant to the particular a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Blue Obelisk
Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obelisk, among which, in alphabetical order, Avogadro, Bioclipse, cclib, Chemistry Development Kit, GaussSum, JChemPaint, JOELib, Kalzium, Openbabel, OpenSMILES, and UsefulChem. The project has handed out personal awards for achievements in promoting Open Data, Open Source and Open Standards. Among those who received a Blue Obelisk Award are: *Christoph Steinbeck (2006) *Geoff Hutchinson (2006) *Bob Hanson (2006), *Egon Willighagen (2007) * Jean-Claude Bradley (2007) *Ola Spjuth (2007) *Noel O'Boyle (2010) *Rajarshi Guha (2010) * Cameron Neylon (2010) *Alex Wade (2010) *Nina Jeliazkova (2010) * Henry Rzepa (2011) *Dan Zaharevitz (2011) *Sam Adams (2011) *Jens Thomas (2011) *Marcus Hanwell (2011) *Roger Sayle (2011) *the Environmenta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ethanol
Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an alcohol with the chemical formula . Its formula can be also written as or (an ethyl group linked to a hydroxyl group). Ethanol is a volatile, flammable, colorless liquid with a characteristic wine-like odor and pungent taste. It is a psychoactive recreational drug, the active ingredient in alcoholic drinks. Ethanol is naturally produced by the fermentation process of sugars by yeasts or via petrochemical processes such as ethylene hydration. It has medical applications as an antiseptic and disinfectant. It is used as a chemical solvent and in the synthesis of organic compounds, and as a fuel source. Ethanol also can be dehydrated to make ethylene, an important chemical feedstock. As of 2006, world production of ethanol was , coming mostly from Brazil and the U.S. Etymology ''Ethanol'' is the systematic name defined by the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Union Of Pure And Applied Chemistry
The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is a member of the International Science Council (ISC). IUPAC is registered in Zürich, Switzerland, and the administrative office, known as the "IUPAC Secretariat", is in Research Triangle Park, North Carolina, United States. This administrative office is headed by IUPAC's executive director, currently Lynn Soby. IUPAC was established in 1919 as the successor of the International Congress of Applied Chemistry for the advancement of chemistry. Its members, the National Adhering Organizations, can be national chemistry societies, national academies of sciences, or other bodies representing chemists. There are fifty-four National Adhering Organizations and three Associate National Adhering Organizations. IUPAC's Inter-divisional Committee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemistry Development Kit
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0. History The CDK was created by Christoph Steinbeck, Egon Willighagen and Dan Gezelter, then developers of Jmol and JChemPaint, to provide a common code base, on 27–29 September 2000 at the University of Notre Dame. The first source code release was made on 11 May 2011. Since then more than 100 people have contributed to the project, leading to a rich set of functions, as given below. Between 2004 and 2007, ''CDK News'' was the project's newsletter of which all articles are available from a public archive. Due to an unsteady rate of contributions, the newsletter was put on hold. Later, unit testing, code quality checking, and Javadoc validation was introduced. Rajarshi Guha develop ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Editor
A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages. Database molecular editors such as Leatherface, RECAP, and Molecule Slicer allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by a user. Molecule editors typically support reading and writing at least one file format or line notation. Examples of each include Molfile and simplified molecular input line entry specification (SMILES), respectively. Files generated by m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Line Notation
Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature. Chemistry * Cell notation for representation of an electrochemical cell * Dyson / IUPAC (1944) * Hayward (1961) * International Chemical Identifier (InChI) * Wiswesser Line Notation (WLN) (1952) * Simplified molecular input line entry specification (SMILES) * Smiles arbitrary target specification (SMARTS) * SYBYL Line Notation (SLN) Mathematics * Mathematical markup language Music * GUIDO music notation Chess * Forsyth–Edwards Notation Forsyth–Edwards Notation (FEN) is a standard notation for describing a particular board position of a chess game. The purpose of FEN is to provide all the necessary information to restart a game from a particular position. FEN is based on a sy ... {{DEFAULTSORT:Line Notation Notation Chemical nomenclature Musical notation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dimension
In physics and mathematics, the dimension of a mathematical space (or object) is informally defined as the minimum number of coordinates needed to specify any point within it. Thus, a line has a dimension of one (1D) because only one coordinate is needed to specify a point on itfor example, the point at 5 on a number line. A surface, such as the boundary of a cylinder or sphere, has a dimension of two (2D) because two coordinates are needed to specify a point on itfor example, both a latitude and longitude are required to locate a point on the surface of a sphere. A two-dimensional Euclidean space is a two-dimensional space on the plane. The inside of a cube, a cylinder or a sphere is three-dimensional (3D) because three coordinates are needed to locate a point within these spaces. In classical mechanics, space and time are different categories and refer to absolute space and time. That conception of the world is a four-dimensional space but not the one that was ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
