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 two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical databases. Three-dimensional molecule editors are used to build molecular models, usually as part of molecular modelling software packages.

Database molecular editors such as Leatherface,^[1] RECAP^[2] and Molecule Slicer^[3] 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.

Standalone programs

Program	Developer(s)	License	Platforms	Info
Accelrys Draw	Accelrys	proprietary	Windows	freeware version available; includes name2structure and structure2name, InChI naming, and canonical SMILES
ACD/ChemSketch	ACD/Labs	proprietary	Windows	freeware version available
Ascalaph		GPL	Linux, Windows	freeware version available
ArgusLab		proprietary	Windows	freeware
Avogadro	OpenMolecules.net	GPL	Linux, Mac OS X, Windows	3D molecule editor and visualizer
BALLView	BALL project team	GPL/LGPL	Linux, Mac OS X, Windows	viewer, editor and simulation tool
Bioclipse	Example	EPL	platform-independent	Java. Eclipse RCP based
BKchem	Beda Kosata	GPL	platform-independent	2D molecule editor written in Python
ChemDoodle	iChemLabs	proprietary	Linux, Mac OS X, Windows
ChemDraw	CambridgeSoft	proprietary	Mac OS X, Windows
ICEDIT	InfoChem	proprietary
ChemTool			Linux, Unix	2D editor for chemical structural formulas, written in C using GTK
ChemWindow	Bio-Rad	proprietary		available as part of the KnowItAll software environment; Freeware for academic research and teaching
ICM-Chemist	MolSoft	proprietary	available for Windows, Mac and Linux	Easy to use graphical user interface desktop chemistry editor
JChemPaint		LGPL	platform-independent	2D structural formula editor written in Java
KnowItAll	Bio-Rad	proprietary		Freeware for academic research and teaching
MarvinSketch/View	ChemAxon	proprietary		commercial and freeware versions (see terms). Chemical editor and viewer, desktop version (Java Beans)
MarvinSpace	ChemAxon	proprietary		commercial and freeware versions (see terms). 3D macromolecular visualization and ligand editing, desktop version (Java Beans)
MedChem Designer	Simulations Plus	proprietary	Windows	freeware - 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		Runs on BlackBerry smartphones
molsKetch		GPL		multiplatform editor, based on Qt4
ODYSSEY	Wavefunction, Inc.	proprietary	Mac OS X, Windows
SketchEl		GPL	platform-independent	multiplatform editor, Java, available on SourceForge
Smormo-Ed		BSD licenses	Linux, Windows
SPARTAN	Wavefunction, Inc.	proprietary	Linux, Mac OS X, Windows
StruMM3D (Str3Di32)	Exorga, Inc.	proprietary	Windows
XDrawChem		GPL	Linux, Mac OS X, Windows	based on OpenBabel
Zem	Example	GPL	Linux, Mac OS X, Windows	based on OpenBabel

Applets

Applet	Developer(s)	License	Info
Accelrys JDraw	Accelrys	proprietary	commercial and freeware versions for non-profit use (see JDraw)
JChemPaint		LGPL	Java. Both editor and viewer applets.
JME Molecular Editor	Peter Ertl		available from Molinspiration. Freeware for noncommercial use.
MarvinSketch	ChemAxon	proprietary	commercial and freeware versions (see terms). Chemical editor applet implementation
MarvinSpace	ChemAxon	proprietary	commercial and freeware versions (see terms). 3D macromolecular visualization and ligand editing
SDA ACD/Structure Drawing Applet	ACD/Labs	proprietary	commercial and freeware versions
ChemWriter	Metamolecular	proprietary	Version 1 requires Java Plugin. Version 2 requires no browser plugins.
SketchEl		GPL	available on SourceForge
Chemis3D	Didier Collomb	proprietary	available on Mol3D
FlaME Flash Molecular Editor	Pavel Dallakian, Norbert Haider		available on FlaME. Freeware 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 software from ChemAxon. Supports all major formats and structure/query features. This Java implementation also includes unlimited structure based predictions for a range of properties (pKa, logD, name<>structure, etc.).
• Molinspiration WebME molecule editor: proprietary software, based on Ajax technology which does not require Java.
• PubChem online molecule editor, supports SMILES, SMARTS and InChI as well as all common chemical file formats.
• 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 DataSheet: BlackBerry app from Molecular Materials Informatics.

See also

• Molecular modelling
• Molecular graphics
• Chemical databases
• PubChem
• ChemSpider
• Software for molecular mechanics modeling
• Molecular design software

External links

• Molecular structure input on the web
• The Chemical Structure Editor: Bridging Chemistry and Cheminformatics
• Basic primitives for molecular diagram sketching

References

1. ^ Kenny, P.W.; Sadowski, J. (2005) Structure modification in chemical databases Chemoinformatics in drug discovery (editor—Oprea, T.I.), 271-285 (Wiley).
2. ^ Lewell, X.Q.; Judd, D.B; Watson, S.P.; Hann, M.M. (1998) RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry J. Chem. Inf. Comput. Sci. 38, 511-522.
3. ^ Vieth, M.; Siegel, M.G.; Higgs, R.E.; Watson, I.A.; Robertson, D.H.; Savin, K.A.; Durst, G.L.; Hipskind; P.A. (2004) Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs J. Med. Chem. 47, 224-232.