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 a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is 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 a user.
Molecule editors typically support reading and writing at least one file format or line notation. Examples of each include Molfile and simplified molecular input line entry specification (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 drawing almost any chemical structure including organics, organometallics, polymers, and Markush structures. freeware version available | |
| Amira (software) | Visage Imaging Zuse Institute Berlin |
Proprietary | Windows, macOS, Linux | 14-day trial version available | |
| Ascalaph Designer | Agile Molecule | GNU GPL | Linux, Windows | freeware | |
| ArgusLab | Mark Thompson (author) | Proprietary | Windows | freeware | |
| Avogadro | Avogadro project team | GNU GPL | Linux, macOS, Windows | 3D molecule editor, visualizer | |
| BALLView | BALL project team | GNU GPL-LGPL | Linux, macOS, Windows | viewer, editor, simulation tool | |
| Bioclipse | Bioclipse Developers | EPL | cross-platform | Java, Eclipse Rich Client Platform (RCP) based | |
| BKChem | Beda Kosata | GNU GPL | cross-platform | 2D molecule editor written in Python | |
| ChemDoodle | iChemLabs | Proprietary | Linux, macOS, Windows | Complete chemical publishing system for drawing chemical structures, reactions, spectra and more. Free trial available. | |
| ChemDraw | PerkinElmer | Proprietary | macOS, Windows | Edit chemical structures and reactions | |
| Deneb | AtelGraphics | Proprietary | Linux, Windows | Trial version available; easy to use graphical user interface desktop for packages SIESTA, VASP, QE, etc. | |
| Elemental (software) | Dotmatics | Proprietary | Windows, iOS | freeware for PCs, iPhone, iPad | |
| ICEdit | InfoChem | Proprietary | Windows | Edit chemical structures and reactions | |
| Chemtool | GNU GPL | Linux, Unix | 2D editor for chemical structural formulas, written in C using GTK | ||
| ChemWindow | Wiley | Proprietary | Windows | available as part of the KnowItAll software environment; Freeware for academic research and teaching | |
| Gabedit | Abdulrahman Allouche | BSD | Linux, macOS, Windows | 3D molecule editor, visualizer | |
| ICM-Chemist | MolSoft | Proprietary | Windows, macOS, Linux | Easy to use graphical user interface desktop chemistry editor | |
| JChemPaint | GNU LGPL | cross-platform | 2D structural formula editor written in Java | ||
| HyperChem | Hypercube, Inc. | Proprietary | Windows | 3D molecule editor, visualizer | |
| KnowItAll | Wiley | Proprietary | Windows | Includes ChemWindow Freeware for academic research and teaching | |
| lhendraw | Lennard Wasserthal | GNU GPL | Linux | chemdraw cdx/cdxml compatible FOSS clone, search function | |
| MAPS (molecular software) | Scienomics | Proprietary | cross-platform | 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 | cross-platform | commercial and freeware versions. Chemical editor and viewer, desktop version (Java Beans) | |
| MarvinSpace | ChemAxon | Proprietary | cross-platform | commercial and freeware versions. 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. | |
| Molecular Operating Environment (MOE) | Chemical Computing Group | Proprietary | Windows, Linux, Mac; SVL programming language | Platform for molecular modelling / drug discovery applications, with 3D molecular sketching and editing, 2D depiction, and 2D to 3D conversion. | |
| molsKetch | GNU GPL | cross-platform | multiplatform editor, based on Qt4 | ||
| MOLTEMPLATE | BSD 3-clause | Linux, macOS, Windows | General text-based molecule builder for LAMMPS | ||
| ODYSSEY | Wavefunction, Inc. | Proprietary | macOS, Windows | ||
| SAMSON | Inria | Proprietary | Windows, Linux, macOS | Software platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON) | |
| SketchEl | GNU GPL | cross-platform | editor, Java, available on SourceForge | ||
| Smormo-Ed | BSD | Linux, Windows, available on SourceForge | |||
| Spartan | Wavefunction, Inc. | Proprietary | Linux, macOS, Windows | ||
| StruMM3D | Exorga, Inc. | Proprietary | Windows | ||
| Vimol | ISC | BSD, Linux, macOS, Windows | Powerful, with vim-like interface | ||
| XDrawChem | GNU GPL | Linux, macOS, Windows | based on OpenBabel | ||
| Zem (software) | Example | GNU GPL | Linux, macOS, Windows | based on OpenBabel |
Java Applets
| Applet | Developer(s) | License | Info | |
|---|---|---|---|---|
| Accelrys JDraw | Accelrys | Proprietary | commercial and freeware versions for nonprofit use | |
| ICEdit | InfoChem | Proprietary | Edit chemical structures and reactions | |
| JChemPaint | GNU LGPL | Editor and viewer applets | ||
| JME Molecule Editor | Peter Ertl | Proprietary | freeware available from Molinspiration; Freeware for noncommercial use | |
| MarvinSketch | ChemAxon | Proprietary | commercial and freeware versions. Chemical editor applet implementation | |
| MarvinSpace | ChemAxon | Proprietary | commercial and freeware versions. 3D macromolecular visualization and ligand editing | |
| SDA ACD/Structure Drawing Applet | ACD/Labs | Proprietary | commercial and freeware versions | |
| ChemWriter | Metamolecular | Proprietary | Version 1 needs Java plug-in, version 2 needs no browser plug-ins | |
| SketchEl | GNU GPL, available on SourceForge | |||
| Chemis3D | Didier Collomb | Proprietary | ||
| MolEdit | MolSoft | Proprietary | HTML5 editor allows drawing 2D chemical structure inside a web browser's page; needs no plug-ins (like Java); works in any modern HTML5 compatible browser with JavaScript enabled, including mobile platforms; lightweight, intuitive | |
| FlaME: Flash Molecular Editor | Pavel Dallakian, Norbert Haider | Freeware for noncommercial 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 | Draw organic structures and reaction schemes in SVG, available online and as AngularJS module; open-source (MIT) |
| ChemDoodle Web Components | iChemLabs | Yes | Yes | Yes | Yes | Yes | Unknown | HTML5 chemistry web components including viewers, animations, interactive components and editors; uses Canvas and WebGL graphics. Free and open source under GPL v3.0 license |
| ChemDraw JS | PerkinElmer | No | Yes | Unknown | Unknown | Unknown | Unknown | The JavaScript version of ChemDraw |
| ChemWriter 3 | Metamolecular | No | Yes | Yes | Unknown | Unknown | Unknown | |
| Elemental (software) | Dotmatics | Yes | Yes | Yes | Yes | Yes | Unknown | proprietary software |
| ICEdit | InfoChem | No | Yes | Yes | Yes | Yes | Yes | Edit chemical structures and reactions |
| Ketcher | [h[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; has somewhat less features than Java-based version at present |
| Molinspiration WebME molecule editor | Yes | Yes | Unknown | Unknown | Unknown | Unknown | proprietary software | |
| JSDraw | Scilligence | Yes | Yes | Yes | Yes | Yes | Unknown | |
| JSME | Peter Ertl | Yes | Yes | Yes | Yes | Yes | Unknown | Supports drag and drop on HTML5 compatible desktop browsers to import and export MOL and RXN files. The editor can generate SMILES and InChI. |
| VectorMol | Sciformation | Unknown | Yes | Unknown | Unknown | Yes | Unknown | Written using SVG/VML via Raphaël.js; supports drag and drop on HTML5 compatible desktop browsers to import MOL and RXN files. Integrated structure optimizers. License is CC-BY-NC-SA |
| WebMolKit | Molecular Materials Informatics | No | Yes | No | No | No | No | Also core library for SketchEl2. License is GPL. |
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, edit chemical structures and reactions |
| LAI4D | Lai4d Systems | Free light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type. |
| MolEdit | MolSoft | HTML5 editor allows drawing 2D chemical structure inside a web browser's page; needs no plug-ins (like Java); works in any modern HTML5 compatible browser with JavaScript enabled, including mobile platforms; lightweight, intuitive |
| 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 | Based on JChemPaint; allows storing generated images on a server | |
| PubChem online molecule editor | supports SMILES, SMARTS, InChI, and 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 | Freeware, 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 (software) | Dotmatics | Yes | Yes | Yes | No | Freeware |
| 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 | Freeware |
See also
Notes and references
- ^ Kenny, Peter W.; Sadowski, Jens (2005). "Structure Modification in Chemical Databases". Chemoinformatics in Drug Discovery. Methods and Principles in Medicinal Chemistry. pp. 271–285. doi:10.1002/3527603743.ch11. ISBN 9783527307531.
- ^ Lewell, Xiao Qing; Judd, Duncan B.; Watson, Stephen P.; Hann, Michael M. (1998). "RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry". Journal of Chemical Information and Computer Sciences. 38 (3): 511–522. doi:10.1021/ci970429i. PMID 9611787.
- ^ Vieth, Michal; Siegel, Miles G.; Higgs, Richard E.; Watson, Ian A.; Robertson, Daniel H.; Savin, Kenneth A.; Durst, Gregory L.; Hipskind, Philip A. (2004). "Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs". Journal of Medicinal Chemistry. 47: 224–232. doi:10.1021/jm030267j. PMID 14695836.