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
ProgramDeveloper(s)LicensePlatformsInfo
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 GPLWindows, Linuxfreeware
AvogadroAvogadro project teamGNU GPLWindows, macOS, Linux3D molecule editor, visualizer
BALLViewBALL project teamGNU GPL-LGPLWindows, macOS, Linuxviewer, editor, simulation tool
BioclipseBioclipse DevelopersEPLcross-platformJava, Eclipse Rich Client Platform (RCP) based
Biovia DrawMDL Information SystemsProprietaryWindowsDeveloped as ISIS/Draw now owned by Dassault Systèmes[4]
ChemDoodle iChemLabsProprietary cross-platform Java
ChemDrawPerkinElmerProprietaryWindows, macOSEdit chemical structures and reactions
DenebAtelGraphicsProprietaryWindows, LinuxTrial version available; easy to use graphical user interface desktop for packages SIESTA, VASP, QE, etc.
ChemWindowWileyProprietaryWindowsavailable as part of the KnowItAll software environment; Freeware for academic research and teaching
GabeditAbdulrahman AlloucheBSDWindows, macOS, Linux3D molecule editor, visualizer
JChemPaintGNU LGPLcross-platform2D structural formula editor written in Java
Molecular Operating Environment (MOE)Chemical Computing GroupProprietaryWindows, macOS, Linux; SVL programming languagePlatform for molecular modelling / drug discovery applications, with 3D molecular sketching and editing, 2D depiction, and 2D to 3D conversion.
SAMSONInriaProprietaryWindows, macOS, LinuxSoftware platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON)
SpartanWavefunction, Inc.ProprietaryWindows, macOS, Linux
XDrawChemGNU GPLWindows, macOS, Linuxbased on OpenBabel

Java Applets
AppletDeveloper(s)LicenseInfo
JChemPaintGNU LGPLEditor and viewer applets
JME Molecule EditorPeter ErtlProprietaryfreeware available from Molinspiration; Freeware for noncommercial use

JavaScript embeddable editors
ProgramDeveloper LicenseDesktop Browser IE6-7-8Desktop Browser otheriPadiPhoneAndroid Info
Kekulé ProgramKekule.js Lab MIT LicenseYesYesUn­knownUn­knownUn­known
Ketcher EPAM Systems Apache License Un­known Yes Un­known Un­known Un­known originally developed by GGA Software Services before being bought by EPAM Systems

See also

Notes and references
  1. 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.
  2. 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.
  3. 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 (1): 224–232. doi:10.1021/jm030267j. PMID 14695836.
  4. "Biovia Draw datasheet" (PDF). Dassault Systemes. Retrieved 2023-04-25.


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