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Molecule editor

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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
3D Molecules Edit&Drill Virtualnye Prostranstva LLC proprietary iOS commercial and freeware versions. 3D modeling tool and viewer for chemistry education in schools, colleges and universities.
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
Amira Visage Imaging
Zuse Institute Berlin		 proprietary Windows, Mac OS X, Linux 14 day trial version available
Ascalaph Agile Molecule GPL Linux, Windows freeware
ArgusLab proprietary Windows freeware
Avogadro Avogadro project team 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
Deneb AtelGraphics proprietary Linux,Windows Trial version available. Easy to use graphical user interface desktop for SIESTA, VASP, QE, etc., packages.
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 Windows Freeware for academic research and teaching
MarvinSketch/View ChemAxon proprietary platform-independent commercial and freeware versions (see terms). Chemical editor and viewer, desktop version (Java Beans)
MarvinSpace ChemAxon proprietary platform-independent 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
[[SCIGRESS]] [1] proprietary Linux, Windows
SPARTAN Wavefunction, Inc. proprietary Linux, Mac OS X, Windows
StruMM3D 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.).
  • Marvin for JavaScript: The JavaScript version of the MarvinSketch. This is a new release (released in 6.0 version in May 2013) so it offers somewhat less features as the Java based version at present.
  • chemicalize.org ChemAxon's free website that offers a lot of search types and the Java based MarvinSketch implemented.
  • 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.
  • JSME Free JavaScript equivalent of the Java applet JME from Peter Ertl. Runs on all major browsers including IE6, iPhone, iPad and Android touch devices. Support drag and drop on HTML5 compatible desktop browsers for importing and exporting MOL and RXN files.

Mobile editors

Notes and 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.

See also

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