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 | |
|---|---|---|---|---|---|
| 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 |
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.