OpenBabel
Encyclopedia
OpenBabel is free software
, a chemical expert system
mainly used for converting chemical file format
s. 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
. It is distributed under the GNU GPL.
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."
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 library called "OBabel."
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...
, a 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. Due to the 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 Mac OS
Mac OS
Mac OS is a series of graphical user interface-based operating systems developed by Apple Inc. for their Macintosh line of computer systems. The Macintosh user experience is credited with popularizing the graphical user interface...
. It is distributed under the GNU GPL.
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
OpenBabel and JOELibJOELib
JOELib is a free software chemical expert system mainly used for converting chemical file formats. 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...
were derived from the OELib
OELib
OELib 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 :* *...
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...
library. In turn, OELib
OELib
OELib 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 :* *...
was based on ideas in the original chemistry program Babel and an unreleased object-oriented library called "OBabel."
Major features
- chemical expert system
- interconversion of many 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 - substructure search (based on SMARTSSimplified 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...
) - fingerprint calculation
- wrappers for PythonPython (programming language)Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
, PerlPerlPerl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally 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 and become widely popular...
, JavaJava (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...
, RubyRuby (programming language)Ruby is a dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. Ruby originated in Japan during the mid-1990s and was first developed and designed by Yukihiro "Matz" Matsumoto...
, C#/MonoMono (software)Mono, pronounced , is a free and open source project led by Xamarin to create an Ecma standard compliant .NET-compatible set of tools including, among others, a C# compiler and a Common Language Runtime....
See also
- AvogadroAvogadro (software)Avogadro is a molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas...
- molecular builder and editor based on OpenBabel - GhemicalGhemicalGhemical is a computational chemistry software package written in C++ and released under the GNU GPL. The program has GUI based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools...
- molecular mechanicsMolecular mechanicsMolecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...
program based on OpenBabel - JOELibJOELibJOELib is a free software chemical expert system mainly used for converting chemical file formats. 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 version of OpenBabel/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 :* *... - XDrawChemXDrawChemXDrawChem is a free software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS. It is distributed under the GNU GPL.- Major features :* Fixed length and fixed angle drawing* Automatic alignment of figures...
- 2D drawing program based on OpenBabel - 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
- OpenBabel Home Page
- E-BABEL interactive version of the OpenBabel at Virtual Computational Chemistry Laboratory
- Geoff Hutchison, the lead developer of the project, was interviewed on the podcast chemCast Episode 003
- Design flaws in OELib