Molecule editor
Encyclopedia
A molecule editor is a computer program
for creating and modifying representations of chemical structure
s.
Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical database
s. Three-dimensional molecule editors are 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 the user.
Molecule editors typically support reading and writing at least one file format
or line notation
. Examples of each include Molfile and SMILES
, respectively.
Files generated by molecule editors can be displayed by molecular graphics
tools.
Computer program
A computer program is a sequence of instructions written to perform a specified task with a computer. A computer requires programs to function, typically executing the program's instructions in a central processor. The program has an executable form that the computer can use directly to execute...
for creating and modifying representations of chemical structure
Chemical structure
A chemical structure includes molecular geometry, electronic structure and crystal structure of molecules. Molecular geometry refers to the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together. Molecular geometry can range from the very simple, such as...
s.
Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical database
Chemical database
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.- Chemical structures :...
s. Three-dimensional molecule editors are used to build molecular models, usually as part of 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...
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 the user.
Molecule editors typically support reading and writing at least one file format
File format
A file format is a particular way that information is encoded for storage in a computer file.Since a disk drive, or indeed any computer storage, can store only bits, the computer must have some way of converting information to 0s and 1s and vice-versa. There are different kinds of formats for...
or line notation
Line notation
Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature.Line notation is a word and symbol description of an electrochemical cell widely used in chemistry.-Chemistry:...
. Examples of each include Molfile and SMILES
Simplified molecular input line entry specification
The 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...
, respectively.
Files generated by molecule editors can be displayed by molecular graphics
Molecular graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
tools.
Standalone programs
| Program | Developer(s) | License | Platforms | Info |
|---|---|---|---|---|
| Accelrys Draw | Accelrys Accelrys Accelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Windows | freeware version available; includes name2structure and structure2name, InChI naming, and canonical SMILES |
| ACD/ChemSketch | ACD/Labs | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Windows | freeware version available |
| Ascalaph | GPL | Linux, Windows | freeware version available | |
| ArgusLab | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Windows | freeware | |
| Avogadro Avogadro (software) Avogadro is a molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas... |
OpenMolecules.net | GPL | Linux, Mac OS X, Windows | 3D molecule editor and visualizer |
| BALLView | BALL project team | GPL/LGPL GNU Lesser General Public License The GNU Lesser General Public License or LGPL is a free software license published by the Free Software Foundation . It was designed as a compromise between the strong-copyleft GNU General Public License or GPL and permissive licenses such as the BSD licenses and the MIT License... |
Linux, Mac OS X, Windows | viewer, editor and simulation tool |
| Bioclipse Bioclipse The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform... |
Example | EPL Eclipse Public License The Eclipse Public License is an open source software license used by the Eclipse Foundation for its software. It replaces the Common Public License and removes certain terms relating to litigations related to patents.... |
platform-independent | 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... . Eclipse RCP Rich Client Platform A rich client platform is software consisting of the following components:* A core , lifecycle manager* A standard bundling framework* A portable widget toolkit* File buffers, text handling, text editors... based |
| BKchem BKchem BKchem is a free 2D molecule editor written in Python by Beda Kosata. As such, it is largely platform-independent.-Major features:Drawing:* Bond by bond drawing* Straight and curved arrows* Radicals, lone pairs and charges... |
Beda Kosata | GPL | platform-independent | 2D molecule editor written in Python Python (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... |
| ChemDoodle | iChemLabs | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Linux, Mac OS X, Windows | |
| ChemDraw ChemDraw ChemDraw is a molecule editor developed by the cheminformatics company CambridgeSoft. ChemDraw is, along with Chem3D and ChemFinder, part of the ChemOffice suite of programs and is available for Macintosh and Microsoft Windows.-Features of ChemDraw 12.0:... |
CambridgeSoft | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Mac OS X, Windows | |
| ICEDIT | InfoChem | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
||
| ChemTool ChemTool Chemtool is free software program for drawing chemical structural formulas, written in C using GTK for Unix and Linux.-External links:*... |
Linux, Unix | 2D editor for chemical structural formulas, written in C using GTK | ||
| ChemWindow | Bio-Rad | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
available as part of the KnowItAll software environment; Freeware for academic research and teaching | |
| ICM-Chemist | MolSoft | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
available for Windows, Mac and Linux | Easy to use graphical user interface desktop chemistry editor |
| JChemPaint JChemPaint JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems... |
LGPL GNU Lesser General Public License The GNU Lesser General Public License or LGPL is a free software license published by the Free Software Foundation . It was designed as a compromise between the strong-copyleft GNU General Public License or GPL and permissive licenses such as the BSD licenses and the MIT License... |
platform-independent | 2D structural formula editor written in 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... |
|
| KnowItAll | Bio-Rad | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Freeware for academic research and teaching | |
| MarvinSketch/View | ChemAxon Chemaxon ChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions (see terms). Chemical editor and viewer, desktop version (Java Beans) |
|
| MarvinSpace | ChemAxon Chemaxon ChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions (see terms). 3D macromolecular visualization and ligand editing, desktop version (Java Beans) |
|
| MedChem Designer | Simulations Plus Simulations Plus Simulations Plus, Inc. develops absorption, distribution, metabolism, excretion, and toxicity modeling and simulation software for the pharmaceutical and biotechnology industries... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Windows | freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... - includes free S+logP, S+logD(7.4), TPSA, PEOE sigma charges, HBD, HBA, and Rule of 5 calculations. |
| Mobile Molecular DataSheet | Molecular Materials Informatics | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Runs on BlackBerry smartphones | |
| molsKetch | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
multiplatform editor, based on Qt4 Qt (toolkit) Qt is a cross-platform application framework that is widely used for developing application software with a graphical user interface , and also used for developing non-GUI programs such as command-line tools and consoles for servers... |
||
| ODYSSEY | Wavefunction, Inc. | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Mac OS X, Windows | |
| SketchEl | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
platform-independent | multiplatform editor, 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... , available on SourceForge |
|
| Smormo-Ed | BSD licenses BSD licenses BSD licenses are a family of permissive free software licenses. The original license was used for the Berkeley Software Distribution , a Unix-like operating system after which it is named.... |
Linux, Windows | ||
| SPARTAN Spartan (software) SPARTAN is a molecular modeling and computational chemistry application from . It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree-Fock models, and thermochemical recipes including T1.... |
Wavefunction, Inc. | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Linux, Mac OS X, Windows | |
| StruMM3D (Str3Di32) | Exorga, Inc. | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Windows | |
| XDrawChem XDrawChem XDrawChem 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... |
GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
Linux, Mac OS X, Windows | based on OpenBabel OpenBabel OpenBabel 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... |
|
| Zem | Example | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
Linux, Mac OS X, Windows | based on OpenBabel OpenBabel OpenBabel 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... |
Applets
| Applet | Developer(s) | License | Info |
|---|---|---|---|
| Accelrys JDraw | Accelrys Accelrys Accelrys is a software company headquartered in the US, with representation in Europe and Japan. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.Accelrys started in 2001... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions for non-profit use (see JDraw) |
| JChemPaint JChemPaint JChemPaint is an editor and viewer for chemical structures in 2D.It is free and open source software, written in Java and so it runs on Windows, Mac OS X, Linux and Unix systems... |
LGPL GNU Lesser General Public License The GNU Lesser General Public License or LGPL is a free software license published by the Free Software Foundation . It was designed as a compromise between the strong-copyleft GNU General Public License or GPL and permissive licenses such as the BSD licenses and the MIT License... |
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... . Both editor and viewer applets. |
|
| JME Molecular Editor | Peter Ertl | available from Molinspiration. Freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... for noncommercial use. |
|
| MarvinSketch | ChemAxon Chemaxon ChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions (see terms). Chemical editor applet implementation |
| MarvinSpace | ChemAxon Chemaxon ChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research... |
proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions (see terms). 3D macromolecular visualization and ligand editing |
| SDA ACD/Structure Drawing Applet | ACD/Labs | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
commercial and freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... versions |
| ChemWriter | Metamolecular | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
Version 1 requires Java Plugin. Version 2 requires no browser plugins. |
| SketchEl | GPL GNU General Public License The GNU General Public License is the most widely used free software license, originally written by Richard Stallman for the GNU Project.... |
available on SourceForge | |
| Chemis3D | Didier Collomb | proprietary Proprietary software Proprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary... |
available on Mol3D |
| FlaME Flash Molecular Editor | Pavel Dallakian, Norbert Haider | available on FlaME. Freeware Freeware Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the... for non-commercial use. |
Online editors
- ChemDoodle Web Components HTML5 chemistry web components including viewers, animations, interactive components and editors by iChemLabs. Pure Javascript code using Canvas and WebGL graphics. Free and open source under the GPL v3.0 license.
- ChemWriter by Metamolecular. Written in pure JavaScript. Runs on Internet Explorer 6-9 and modern standards-compliant browsers. Touch interface supported on iPad.
- jsMolEditor, the world's first molecule structure editor in Javascript. Runs in most web browsers, no plugin or virtual machine is required. Free and open source under the LGPL v3.0 license.
- Ketcher Written in pure Javascript, using SVG/VML via Raphaël.js. Supports all major desktop browsers. Open source initiative of GGA Software Services.
- Marvin molecule editor and viewer: proprietary softwareProprietary softwareProprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary...
from ChemAxonChemaxonChemAxon is a software company specializing in application programming interfaces and end user applications for cheminformatics and life science research...
. Supports all major formats and structure/query features. This 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...
implementation also includes unlimited structure based predictions for a range of properties (pKa, logD, name<>structure, etc.). - Molinspiration WebME molecule editor: proprietary softwareProprietary softwareProprietary software is computer software licensed under exclusive legal right of the copyright holder. The licensee is given the right to use the software under certain conditions, while restricted from other uses, such as modification, further distribution, or reverse engineering.Complementary...
, based on AjaxAjax (programming)Ajax is a group of interrelated web development methods used on the client-side to create asynchronous web applications...
technology which does not require Java. - PubChem online molecule editor, supports SMILES, SMARTSSmiles arbitrary target specificationSMiles ARbitrary Target Specification is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing....
and InChI as well as all common 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. - Molecular Editor and Image Sharer Molecular editor based on JChemPaint. Allows to store generated images on the server.
- OLN JSDraw by Scilligence Completely built on Javascript, running on all platforms, including Windows, Mac, Linux, iPad, iPhone, Android tablets and phones.
Mobile editors
- ChemDoodle Mobile: Free app for iOS and Android; integrated with ChemDoodle desktop.
- ChemJuice: iPhone app from IDBS.
- Mobile Molecular DataSheetMobile Molecular DataSheetThe Mobile Molecular DataSheet is is a mobile app which provides chemicalstructure diagram editing, molecular datasheet management and various other...
: BlackBerry app from Molecular Materials Informatics.
See also
- Molecular modellingMolecular modellingMolecular 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...
- Molecular graphicsMolecular graphicsMolecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
- Chemical databaseChemical databaseA chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data.- Chemical structures :...
s - PubChemPubChemPubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information , a component of the National Library of Medicine, which is part of the United States National Institutes of Health . PubChem can...
- ChemSpiderChemSpiderChemsSpider is a free chemical database, owned by the Royal Society of Chemistry.-Database:The database contains more than 26 million unique molecules from over 400 data sources including those listed below.* A-L: EPA DSSTox, U.S...
- Software for molecular mechanics modeling
- Molecular design softwareMolecular Design softwareMolecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.In contrast to the usual molecular modeling programs such as the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related...