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
Files generated by molecule editors can be displayed by molecular graphics tools.
Standalone programs
2D structure editing
| 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. |
BIOVIA Draw |
Dassault Systèmes | Proprietary | Windows | Successor of ISIS/Draw. |
| ChemDraw | Revvity Signals | 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
| 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. | 22 January 2025 
|
| 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. | 1 February 2025
|
| 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
| 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
| 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 |
See also
Notes and references
- ISBN 9783527307531.
- PMID 9611787.
- PMID 14695836.