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

Program	Developer(s)	License	Platforms	Info
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
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
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.
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
JChemPaint		GNU LGPL	cross-platform	2D structural formula editor written in Java
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.
SAMSON	Inria	Proprietary	Windows, Linux, macOS	Software platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON)
Spartan	Wavefunction, Inc.	Proprietary	Linux, macOS, Windows
XDrawChem		GNU GPL	Linux, macOS, Windows	based on OpenBabel

Java Applets

Ap	JChemPaint		GNU LGPL	Editor and viewer applets
JME Molecule Editor	Peter Ertl	Proprietary	freeware available from Molinspiration; Freeware for noncommercial use

JavaScript embeddable editors

Program	Developer	Desktop Browser IE6-7-8	Desktop Browser other	iPad	iPhone	Android	Windows Phone
Kekulé Program	Kekule.js Lab	Yes	Yes	Unknown	Unknown	Unknown	Unknown	Published under the MIT License

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.

External links

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[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: 224–232. doi:10.1021/jm030267j. PMID 14695836.