Molecule editor
A notable 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]2D structure editing
[edit]| Program | Developer(s) | License | Platforms | Info |
|---|---|---|---|---|
| ACD/ChemSketch | ACD/Labs | Proprietary | Windows | A chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available. |
| ChemDraw | PerkinElmer | Proprietary | Windows, macOS | Primarily for editing 2D chemical structures and reactions |
| ChemWindow | Wiley | Proprietary | Windows | Freeware for academic research and teaching; part of the KnowItAll software environment |
| JChemPaint | JChemPaint Developers | GNU LGPL | Cross-platform | A 2D structural formula editor written in Java |
| XDrawChem | XDrawChem developers | GNU GPL | Windows, macOS, Linux | A 2D chemical structure drawing tool based on OpenBabel |
3D structure editing
[edit]| Program | Developer(s) | License | Platforms | Info | Last Release |
|---|---|---|---|---|---|
| Amira (software) | Visage Imaging Zuse Institute Berlin |
Proprietary | Windows, macOS, Linux | Includes 3D visualization tools. Trial version available. | |
| Ascalaph Designer | Agile Molecule | GNU GPL | Windows, Linux | A freeware 3D molecule editor. | 2009 |
| Avogadro | Avogadro project team | GNU GPL | Windows, macOS, Linux | A 3D molecule editor and visualizer. | 10 February 2024 
|
| Deneb | AtelGraphics | Proprietary | Windows, Linux | GUI for simulation packages, including 3D editing. | |
| Gabedit | Abdulrahman Allouche | BSD | Windows, macOS, Linux | A 3D molecule editor with visualization capabilities. | 27 July 2021
|
| MOE | Chemical Computing Group | Proprietary | Windows, macOS, Linux | Includes 3D molecular sketching, editing, and 2D to 3D conversion. | June 2024 |
| PyMOL | Schrödinger | Proprietary (Open-source version available) | Cross-platform | Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. | 9 April 2024
|
| SAMSON | Inria | Proprietary | Windows, macOS, Linux | A modular platform for computational nanoscience, including 3D molecular editing. | 2024 |
| Spartan | Wavefunction, Inc. | Proprietary | Windows, macOS, Linux | Focused on 3D molecular modeling and simulation. | 14 May 2024 |
| VMD | University of Illinois | Free for non-commercial use | Cross-platform | 3D Molecular visualization tool that includes structure editing through the Molefacture plugin. | 30 November 2016
|
| YASARA | YASARA Biosciences | Proprietary (Free version available) | Cross-platform | Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities. | 5 October 2024
|
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]- ^ 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 (1): 224–232. doi:10.1021/jm030267j. PMID 14695836.