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 | 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 | Bioclipse Developers | 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 | free trial |
| ChemDraw | CambridgeSoft | proprietary | Mac OS X, Windows | Chemical structure and reaction editor |
| 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 | Windows | chemical structure and reaction editor (see ICEDIT) |
| 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 |
| lhendraw | Lennard Wasserthal | GPL | Linux | chemdraw cdx/cdxml compatible FOSS clone, search function |
| MAPS | Scienomics | proprietary | platform-independent | Build complex molecular (molecules, metal complexes, polymers...) and periodic (crystal, surface, interface, CNT, nanosystems...) systems, generate amorphous conformations. Read SMILES and 3D formats (pdb, xyz, cif...). |
| 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 | ||
| MOLTEMPLATE | 3-clause BSD | Linux, Mac OS X, Windows | General text-based molecule builder for LAMMPS | |
| 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
| Applet | Developer(s) | License | Info | |
|---|---|---|---|---|
| Accelrys JDraw | Accelrys | proprietary | commercial and freeware versions for non-profit use (see JDraw) | |
| ICEDIT | InfoChem | proprietary | Chemical structure and reaction editor (see ICEDIT) | |
| 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 | ||
| MolEdit | MolSoft | HTML5 Molecular Editor allows you to draw 2D chemical structure inside the web browser's page. It does not require any plug-ins (like Java) and works in any modern HTML5 compatible browser with Java Script enabled (including mobile platforms).
It is lightweight, intuitive and easy to use. | ||
| FlaME Flash Molecular Editor | Pavel Dallakian, Norbert Haider | Freeware for non-commercial use. |
JavaScript embeddable editors
| Program | Developer | Desktop Browser IE6,7,8 | Desktop Browser other | iPad | iPhone | Android | Windows Phone | |
|---|---|---|---|---|---|---|---|---|
| AngularDrawChem | Michał Malik | Unknown | Yes | No | No | No | Unknown |
open-source (MIT) editor for drawing organic structures and reaction schemes in SVG, available on-line and as an AngularJS module |
| ChemDoodle Web Components | iChemLabs | Unknown | Yes | Unknown | 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 | Unknown | |
| Elemental | Dotmatics | Yes | Yes | Yes | Yes | Yes | Unknown | |
| ICEDIT | InfoChem | No | Yes | Yes | Yes | Yes | Yes |
chemical structure and reaction editor (see ICEDIT) |
| Ketcher | GGA Software Services | Yes | Yes | Unknown | Unknown | Unknown | Unknown |
Written using SVG/VML via Raphaël.js. Open source initiative. |
| LAI4D | Lai4d Systems | No | Yes | Yes | Yes | Yes | Yes |
Free light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type. |
| Marvin JS | ChemAxon | No | Yes | Unknown | Unknown | Unknown | Unknown |
The JavaScript version of MarvinSketch. It offers somewhat less features than the Java-based version at present. |
| Molinspiration WebME molecule editor | Yes | Yes | Unknown | Unknown | Unknown | Unknown | ||
| OLN JSDraw | Scilligence | Yes | Yes | Yes | Yes | Yes | Unknown | |
| JSME | Peter Ertl | Yes | Yes | Yes | Yes | Yes | Unknown |
Support drag and drop on HTML5 compatible desktop browsers for importing and exporting MOL and RXN files. |
Online editors
| Program | Developer | Info |
|---|---|---|
| AngularDrawChem | Michał Malik | open-source (MIT) editor for drawing organic structures and reaction schemes in SVG, available on-line and as an AngularJS module |
| ICEDIT | InfoChem | free trial, chemical structure and reaction editor (see ICEDIT) |
| LAI4D | Lai4d Systems | Free light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type. |
| MolEdit | MolSoft | HTML5 Molecular Editor allows you to draw 2D chemical structure inside the web browser's page. It does not require any plug-ins (like Java) and works in any modern HTML5 compatible browser with Java Script enabled (including mobile platforms).
It is lightweight, intuitive and easy to use. |
| 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
| Program | Developer | iPad | iPhone | Android | BlackBerry | Info |
|---|---|---|---|---|---|---|
| ChemDoodle Mobile | iChemLabs | Yes | Yes | Yes | No | Free app. Integrated with ChemDoodle desktop. |
| ChemJuice | IDBS | Yes | Yes | No | No | |
| Chirys Draw | Integrated Chemistry Design | Yes | No | No | No | |
| Chirys Sketch | Integrated Chemistry Design | No | Yes | No | No | |
| Elemental | Dotmatics | Yes | Yes | Yes | No |
Free app. |
| ICEDIT | InfoChem | Unknown | Unknown | Yes | Unknown |
beta version available by InfoChem |
| 3D Molecules Edit & Test for iOS | Virtual Space | Yes | Yes | No | No | |
| 3D Molecules Editor for iOS | Virtual Space | Yes | Yes | No | No | |
| 3D Molecules View & Edit Lite for iOS | Virtual Space | Yes | Yes | No | No | Free app. |
Notes and references
- ↑ Kenny, P.W.; Sadowski, J. (2005) Structure modification in chemical databases Chemoinformatics in drug discovery (editor—Oprea, T.I.), 271-285 (Wiley).
- ↑ 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.
- ↑ 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
- 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
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