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[edit]

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 A chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. 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 Mark Thompson(author) 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.
Elemental Dotmatics proprietary Windows, iOS freeware for PCs, iPhone, iPad
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.
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 Exorga, Inc. proprietary Windows
Vimol BSD BSD, Linux, Mac OS X, Windows Powerful molecular building and trajectory visualization package with vi-like interface.
XDrawChem GPL Linux, Mac OS X, Windows based on OpenBabel
Zem Example GPL Linux, Mac OS X, Windows based on OpenBabel

Java Applets[edit]

Applet Developer(s) License Info
Accelrys JDraw Accelrys proprietary commercial and freeware versions for non-profit use (see JDraw)
JChemPaint LGPL 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
Chemis3D Didier Collomb proprietary
FlaME Flash Molecular Editor Pavel Dallakian, Norbert Haider Freeware for non-commercial use.

JavaScript embeddable editors[edit]

Program Developer Desktop Browser IE6,7,8 Desktop Browser other iPad iPhone Android Info
ChemDoodle Web Components iChemLabs Unknown Yes Unknown Unknown Unknown HTML5 chemistry web components including viewers, animations, interactive components and editors. Uses Canvas and WebGL graphics. Free and open source under the GPL v3.0 license.
ChemWriter 3 Metamolecular No Yes Yes Unknown Unknown
jsMolEditor Unknown Yes Unknown Unknown Unknown Free and open source under the LGPL v3.0 license.
Ketcher GGA Software Services Yes Yes Unknown Unknown Unknown Written using SVG/VML via Raphaël.js. Open source initiative.
Marvin for JavaScript ChemAxon No Yes Unknown Unknown Unknown 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 Unknown Yes Unknown Unknown Unknown ChemAxon's free website that offers a lot of search types and the Java based MarvinSketch implemented.
Molinspiration WebME molecule editor Yes Yes Unknown Unknown Unknown proprietary software
OLN JSDraw Scilligence Yes Yes Yes Yes Yes
JSME Peter Ertl Yes Yes Yes Yes Yes Support drag and drop on HTML5 compatible desktop browsers for importing and exporting MOL and RXN files.

Online editors[edit]

Program Developer Info
MolView Herman Bergwerf Free software. Built for desktops, tablets and smartphones. Integrates some online databases including PubChem, RCSB, the NCI/CADD Chemical Identifier Resolver and the Crystallography Open Database.
Marvin molecule editor and viewer ChemAxon proprietary software. 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.).
Molecular Editor and Image Sharer Molecular editor based on JChemPaint. Allows to store generated images on the server.
PubChem online molecule editor supports SMILES, SMARTS and InChI as well as all common chemical file formats.
MolEditor Ambinter Small chemical database edition, manipulation and export (Structure Data File SDF, SMILES...) - Free Software(GPL)

Mobile editor apps[edit]

Program Developer iPad iPhone Android BlackBerry Info
ChemDoodle Mobile iChemLabs Yes Yes Yes No Free app. Integrated with ChemDoodle desktop.
chemicalize.org for Android ChemAxon No No Yes No Free app of chemicalize.org page.
ChemJuice IDBS Yes Yes No No
Chirys Draw Integrated Chemistry Design Yes No No No
Chirys Sketch Integrated Chemistry Design No Yes No No
Mobile Molecular DataSheet Molecular Materials Informatics Yes Yes Yes Yes
3D Molecules Edit&Drill for iOS Virtualnye Prostranstva Yes Yes No No
3D Molecules Viewer and Editor Lite for iOS Virtualnye Prostranstva Yes Yes No No Free app.

Notes and references[edit]

  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[edit]

External links[edit]