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 edit

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 Windows, Linux freeware
Avogadro Avogadro project team GNU GPL Windows, macOS, Linux 3D molecule editor, visualizer
BALLView BALL project team GNU GPL-LGPL Windows, macOS, Linux viewer, editor, simulation tool
Bioclipse Bioclipse Developers EPL cross-platform Java, Eclipse Rich Client Platform (RCP) based
Biovia Draw MDL Information Systems Proprietary Windows Developed as ISIS/Draw now owned by Dassault Systèmes[4]
ChemDoodle iChemLabs Proprietary cross-platform Java
ChemDraw PerkinElmer Proprietary Windows, macOS Edit chemical structures and reactions
Deneb AtelGraphics Proprietary Windows, Linux 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 Windows, macOS, Linux 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, macOS, Linux; 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, macOS, Linux Software platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON)
Spartan Wavefunction, Inc. Proprietary Windows, macOS, Linux
XDrawChem GNU GPL Windows, macOS, Linux based on OpenBabel

Java Applets edit

Applet Developer(s) License Info
JChemPaint GNU LGPL Editor and viewer applets
JME Molecule Editor Peter Ertl Proprietary freeware available from Molinspiration; Freeware for noncommercial use

JavaScript embeddable editors edit

Program Developer License Desktop Browser IE6-7-8 Desktop Browser other iPad iPhone Android Info
Kekulé Program Kekule.js Lab MIT License Yes Yes Un­known Un­known Un­known
Ketcher EPAM Systems Apache License Un­known Yes Un­known Un­known Un­known originally developed by GGA Software Services before being bought by EPAM Systems

See also edit

Notes and references edit

  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.

External links edit

  • Molecular structure input on the web
  • The Chemical Structure Editor: Bridging Chemistry and Cheminformatics