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 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

Accelrys DrawAccelrysProprietaryWindowsfreeware version available; includes name2structure and structure2name, InChI naming, and canonical SMILES
ACD/ChemSketchACD/LabsProprietaryWindowsA 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
ProprietaryWindows, macOS, Linux14-day trial version available
Ascalaph DesignerAgile MoleculeGNU GPLLinux, Windowsfreeware
ArgusLabMark Thompson (author)ProprietaryWindowsfreeware
AvogadroAvogadro project teamGNU GPLLinux, macOS, Windows3D molecule editor, visualizer
BALLViewBALL project teamGNU GPL-LGPLLinux, macOS, Windowsviewer, editor, simulation tool
BioclipseBioclipse DevelopersEPLcross-platformJava, Eclipse Rich Client Platform (RCP) based
BKChemBeda KosataGNU GPLcross-platform2D molecule editor written in Python
ChemDoodleiChemLabsProprietaryLinux, macOS, WindowsComplete chemical publishing system for drawing chemical structures, reactions, spectra and more. Free trial available.
ChemDrawPerkinElmerProprietarymacOS, WindowsEdit chemical structures and reactions
DenebAtelGraphicsProprietaryLinux, WindowsTrial version available; easy to use graphical user interface desktop for packages SIESTA, VASP, QE, etc.
Elemental (software)DotmaticsProprietaryWindows, iOSfreeware for PCs, iPhone, iPad
ICEditInfoChemProprietaryWindowsEdit chemical structures and reactions
ChemtoolGNU GPLLinux, Unix2D editor for chemical structural formulas, written in C using GTK
ChemWindowBio-RadProprietaryavailable as part of the KnowItAll software environment; Freeware for academic research and teaching
GabeditAbdulrahman AlloucheBSDLinux, macOS, Windows3D molecule editor, visualizer
ICM-ChemistMolSoftProprietaryWindows, macOS, LinuxEasy to use graphical user interface desktop chemistry editor
JChemPaintGNU LGPLcross-platform2D structural formula editor written in Java
HyperChemHypercube, Inc.ProprietaryWindows3D molecule editor, visualizer
KnowItAllBio-RadProprietaryWindowsFreeware for academic research and teaching
lhendrawLennard WasserthalGNU GPLLinuxchemdraw cdx/cdxml compatible FOSS clone, search function
MAPS (molecular software)ScienomicsProprietarycross-platformBuild 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/ViewChemAxonProprietarycross-platformcommercial and freeware versions. Chemical editor and viewer, desktop version (Java Beans)
MarvinSpaceChemAxonProprietarycross-platformcommercial and freeware versions. 3D macromolecular visualization and ligand editing, desktop version (Java Beans)
MedChem DesignerSimulations PlusProprietaryWindowsfreeware – 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 GroupProprietaryWindows, Linux, Mac; SVL programming languagePlatform for molecular modelling / drug discovery applications, with 3D molecular sketching and editing, 2D depiction, and 2D to 3D conversion.
molsKetchGNU GPLcross-platformmultiplatform editor, based on Qt4
MOLTEMPLATEBSD 3-clauseLinux, macOS, Windows General text-based molecule builder for LAMMPS
ODYSSEYWavefunction, Inc.ProprietarymacOS, Windows
SAMSONInriaProprietaryWindows, Linux, macOSSoftware platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON)
SketchElGNU GPLcross-platformeditor, Java, available on SourceForge
Smormo-EdBSDLinux, Windows, available on SourceForge
SpartanWavefunction, Inc.ProprietaryLinux, macOS, Windows
StruMM3DExorga, Inc.ProprietaryWindows
VimolISCBSD, Linux, macOS, WindowsPowerful, with vim-like interface
XDrawChemGNU GPLLinux, macOS, Windowsbased on OpenBabel
Zem (software)ExampleGNU GPLLinux, macOS, Windowsbased on OpenBabel

Java Applets

Accelrys JDrawAccelrysProprietarycommercial and freeware versions for nonprofit use
ICEditInfoChemProprietaryEdit chemical structures and reactions
JChemPaintGNU LGPLEditor and viewer applets
JME Molecule EditorPeter ErtlProprietaryfreeware available from Molinspiration; Freeware for noncommercial use
MarvinSketchChemAxonProprietarycommercial and freeware versions. Chemical editor applet implementation
MarvinSpaceChemAxonProprietarycommercial and freeware versions. 3D macromolecular visualization and ligand editing
SDA ACD/Structure Drawing AppletACD/LabsProprietarycommercial and freeware versions
ChemWriterMetamolecularProprietaryVersion 1 needs Java plug-in, version 2 needs no browser plug-ins
SketchElGNU GPL, available on SourceForge
Chemis3DDidier CollombProprietary
MolEditMolSoftProprietaryHTML5 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 EditorPavel Dallakian, Norbert HaiderFreeware for noncommercial use

JavaScript embeddable editors

ProgramDeveloperDesktop Browser IE6-7-8Desktop Browser otheriPadiPhoneAndroidWindows Phone
AngularDrawChemMichał MalikUnknownYesNoNoNoUnknownDraw organic structures and reaction schemes in SVG, available online and as AngularJS module; open-source (MIT)
ChemDoodle Web ComponentsiChemLabsYesYesYesYesYesUnknownHTML5 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 JSPerkinElmerNoYesUnknownUnknownUnknownUnknownThe JavaScript version of ChemDraw
ChemWriter 3MetamolecularNoYesYesUnknownUnknownUnknown
Elemental (software)DotmaticsYesYesYesYesYesUnknownproprietary software
ICEditInfoChemNoYesYesYesYesYesEdit chemical structures and reactions
Ketcher[h[GGA Software Services]]YesYesUnknownUnknownUnknownUnknownWritten using SVG/VML via Raphaël.js. Open source initiative.
LAI4DLai4d SystemsNoYesYesYesYesYesFree light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type.
Marvin JSChemAxonNoYesUnknownUnknownUnknownUnknownThe JavaScript version of MarvinSketch; has somewhat less features than Java-based version at present
Molinspiration WebME molecule editorYesYesUnknownUnknownUnknownUnknownproprietary software
JSMEPeter ErtlYesYesYesYesYesUnknownSupports drag and drop on HTML5 compatible desktop browsers to import and export MOL and RXN files. The editor can generate SMILES and InChI.
VectorMol SciformationUnknownYesUnknownUnknownYesUnknown 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
WebMolKitMolecular Materials InformaticsNoYesNoNoNoNoAlso core library for SketchEl2. License is GPL.

Online editors

AngularDrawChemMichał Malikopen-source (MIT) editor for drawing organic structures and reaction schemes in SVG, available on-line and as an AngularJS module
ICEditInfoChem free trial, edit chemical structures and reactions
LAI4DLai4d SystemsFree light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type.
MolEditMolSoftHTML5 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
MolViewHerman BergwerfFree 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 viewerChemAxonproprietary 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 SharerBased on JChemPaint; allows storing generated images on a server
PubChem online molecule editorsupports SMILES, SMARTS, InChI, and all common chemical file formats.
MolEditor | AmbinterSmall chemical database edition, manipulation and export (Structure Data File SDF, SMILES, ...) – Free Software (GPL)

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Mobile editor apps

ChemDoodle MobileiChemLabsYesYesYesNoFreeware, integrated with ChemDoodle desktop.
Chirys DrawIntegrated Chemistry DesignYesNoNoNo
Chirys SketchIntegrated Chemistry DesignNoYesNoNo
Elemental (software)DotmaticsYesYesYesNoFreeware
ICEditInfoChemUnknownUnknownYesUnknownbeta version available by InfoChem
3D Molecules Edit & Test for iOSVirtual SpaceYesYesNoNo
3D Molecules Editor for iOSVirtual SpaceYesYesNoNo
3D Molecules View & Edit Lite for iOSVirtual SpaceYesYesNoNoFreeware

See also

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.
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