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 | edit source]2D structure editing
[edit | edit source]| 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 |
| Ketcher | EPAM Life Sciences | Apache-2.0 | Cross-platform | An open-source web-based chemical structure editor |
| XDrawChem | XDrawChem developers | GNU GPL | Windows, macOS, Linux | A 2D chemical structure drawing tool based on OpenBabel |
3D structure editing
[edit | edit source]| 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. | |
| Avogadro | Avogadro project team | GNU GPL | Windows, macOS, Linux | A 3D molecule editor and visualizer. | |
| 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. | |
| MOE | Chemical Computing Group | Proprietary | Windows, macOS, Linux | Includes 3D molecular sketching, editing, and 2D to 3D conversion. | |
| PyMOL | Schrödinger, Inc. | Proprietary (Open-source version available) | Cross-platform | Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. | |
| SAMSON | OneAngstrom | Proprietary | Windows, macOS, Linux | A modular platform for computational nanoscience, including 3D molecular editing. | 2025 |
| Spartan | Wavefunction, Inc. | Proprietary | Windows, macOS, Linux | Focused on 3D molecular modeling and simulation. | |
| VMD | University of Illinois | Free for non-commercial use | Cross-platform | 3D Molecular visualization tool that includes structure editing through the Molefacture plugin. | |
| YASARA | YASARA Biosciences | Proprietary (Free version available) | Cross-platform | Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities. |
Java Applets
[edit | edit source]| 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 | edit source]| 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
[edit | edit source]Notes and references
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