JOELib
Encyclopedia
JOELib is a free software
chemical expert system
mainly used for converting chemical file format
s. Because of its strong relationship to informatics
, this program belongs more to the category cheminformatics
than to molecular modelling
. It is available for Windows
, Unix
and other systems supporting Java
. It is distributed under the GNU GPL.
is just the word JOELib in the Tengwar
script of J. R. R. Tolkien
. The letters are grouped as JO-E-Li-b. Vowel
s are usually grouped together with a consonant
, but two following vowels must be separated by a helper construct.
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
chemical expert system
Expert system
In artificial intelligence, an expert system is a computer system that emulates the decision-making ability of a human expert. Expert systems are designed to solve complex problems by reasoning about knowledge, like an expert, and not by following the procedure of a developer as is the case in...
mainly used for converting chemical file format
Chemical file format
This article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...
s. Because of its strong relationship to informatics
Informatics (academic field)
Informatics is the science of information, the practice of information processing, and the engineering of information systems. Informatics studies the structure, algorithms, behavior, and interactions of natural and artificial systems that store, process, access and communicate information...
, this program belongs more to the category cheminformatics
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
than to molecular modelling
Molecular modelling
Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...
. It is available for Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Unix
Unix
Unix is a multitasking, multi-user computer operating system originally developed in 1969 by a group of AT&T employees at Bell Labs, including Ken Thompson, Dennis Ritchie, Brian Kernighan, Douglas McIlroy, and Joe Ossanna...
and other systems supporting Java
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
. It is distributed under the GNU GPL.
Logo
The project logoLogo
A logo is a graphic mark or emblem commonly used by commercial enterprises, organizations and even individuals to aid and promote instant public recognition...
is just the word JOELib in the Tengwar
Tengwar
The Tengwar are an artificial script created by J. R. R. Tolkien. In his fictional universe of Middle-earth, the tengwar were invented by the Elf Fëanor, and used first to write the Elven tongues: Quenya, Telerin, and also Valarin. Later a great number of languages of Middle-earth were written...
script of J. R. R. Tolkien
J. R. R. Tolkien
John Ronald Reuel Tolkien, CBE was an English writer, poet, philologist, and university professor, best known as the author of the classic high fantasy works The Hobbit, The Lord of the Rings, and The Silmarillion.Tolkien was Rawlinson and Bosworth Professor of Anglo-Saxon at Pembroke College,...
. The letters are grouped as JO-E-Li-b. Vowel
Vowel
In phonetics, a vowel is a sound in spoken language, such as English ah! or oh! , pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis. This contrasts with consonants, such as English sh! , where there is a constriction or closure at some...
s are usually grouped together with a consonant
Consonant
In articulatory phonetics, a consonant is a speech sound that is articulated with complete or partial closure of the vocal tract. Examples are , pronounced with the lips; , pronounced with the front of the tongue; , pronounced with the back of the tongue; , pronounced in the throat; and ,...
, but two following vowels must be separated by a helper construct.
Major features
- Chemical expert system
- Query and substructure search (based on SMARTS (a SMILES extension)Simplified molecular input line entry specificationThe simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings...
) - Clique DetectionClique (graph theory)In the mathematical area of graph theory, a clique in an undirected graph is a subset of its vertices such that every two vertices in the subset are connected by an edge. Cliques are one of the basic concepts of graph theory and are used in many other mathematical problems and constructions on graphs...
- QSAR
- Data MiningData miningData mining , a relatively young and interdisciplinary field of computer science is the process of discovering new patterns from large data sets involving methods at the intersection of artificial intelligence, machine learning, statistics and database systems...
- Molecule MiningMolecule miningThis page describes mining for molecules. Since molecules may be represented by molecular graphs this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances...
(special case of Structured Data MiningStructured data miningStructure mining or structured data mining is the process of finding and extracting useful information from semi structured data sets. Graph mining is a special case of structured data mining.-Description:...
)
- Data Mining
- Feature/descriptor calculation
- Partition coefficientPartition coefficientIn chemistry and the pharmaceutical sciences, a partition- or distribution coefficient is the ratio of concentrations of a compound in the two phases of a mixture of two immiscible solvents at equilibrium. The terms "gas/liquid partition coefficient" and "air/water partition coefficient" are...
(log P) - Rule-of-five
- Partial charges
- Fingerprint calculation
- etc.
- Partition coefficient
- Chemical file formatChemical file formatThis article discusses some common molecular file formats, including usage and converting between them.-Distinguishing formats:Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format can be found by three...
s- MDL Molfile/SD format
- SMILESSimplified molecular input line entry specificationThe simplified molecular-input line-entry specification or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings...
- GAUSSIANGAUSSIANGaussian is a computational chemistry software program initially released in 1970 by John Pople and his research group at Carnegie-Mellon University as Gaussian 70. It has been continuously updated since then...
- Chemical Markup LanguageChemical Markup LanguageCML is an approach to managing molecular information using tools such as XML and Java. It was the first domain specific implementation based strictly on XML, first based on a DTD and later on XML Schema, the most robust and widely used system for precise information management in many areas...
- MOPACMOPACIn computational chemistry, MOPAC is a popular computer program designed to implement semi-empirical quantum chemistry algorithms, such as MINDO, MNDO, AM1, PM3, PM5, and . It was largely written in the group of Michael Dewar at University of Texas, Austin...
See also
- OpenBabelOpenBabelOpenBabel is free software, a chemical expert system mainly used for converting chemical file formats. 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, and Mac OS...
- C++ version of JOELib/OELibOELibOELib was an Open Source Cheminformatics library. Its actual GPLed C++ and Java successors are OpenBabel and JOELib. Its commercial successor is called OEChem.- External links :* *... - JmolJmolJmol is an open-source Java viewer for chemical structures in 3D,that does not require 3D acceleration plugins.Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g...
- Chemistry Development KitChemistry Development KitThe Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics. It is available for Windows, Unix, and Mac OS...
(CDK) - Software for molecular modeling
- Blue ObeliskBlue ObeliskBlue 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...
External links
- JOELib at SourceforgeSourceForgeSourceForge Enterprise Edition is a collaborative revision control and software development management system. It provides a front-end to a range of software development lifecycle services and integrates with a number of free software / open source software applications .While originally itself...
- Algorithm dictionary