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.
| Program | Developer(s) | License | Platforms | Info | |
|---|---|---|---|---|---|
| Windows | A chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available. | ||||
| Windows | Formerly ISIS/Draw, now owned by Dassault Systèmes. Focuses on 2D chemical structure editing.[4] | ||||
| PerkinElmer | Windows, macOS | Primarily for editing 2D chemical structures and reactions | |||
| JChemPaint Developers | A 2D structural formula editor written in Java | ||||
| Windows | Freeware for academic research and teaching; part of the KnowItAll software environment | ||||
| XDrawChem Developers | Windows, macOS, Linux | A 2D chemical structure drawing tool based on OpenBabel | |||
| MarvinSketch | Chemaxon | Proprietary | Cross-platform | Comprehensive chemical editor for drawing, querying, and displaying chemical structures | |
| Herman Bergwerf | Copyright | Lightweight 2D chemical editor with 3D visualizer integrated with external databases like PubChem |
| Program | Developer(s) | License | Platforms | Info | Last Release | |
|---|---|---|---|---|---|---|
| Avogadro project team | Windows, macOS, Linux | A 3D molecule editor and visualizer. | ||||
| BALL project team | Windows, macOS, Linux | 3D molecular modeling, visualization, and editing tool. | ||||
| Abdulrahman Allouche | Windows, macOS, Linux | A 3D molecule editor with visualization capabilities. | ||||
| Windows, Linux | A freeware 3D molecule editor. | |||||
| Windows, macOS, Linux | Includes 3D molecular sketching, editing, and 2D to 3D conversion. | |||||
| Inria | Windows, macOS, Linux | A modular platform for computational nanoscience, including 3D molecular editing. | ||||
| Windows, macOS, Linux | Focused on 3D molecular modeling and simulation. | |||||
| Windows, macOS, Linux | Includes 3D visualization tools. Trial version available. | |||||
| Deneb | AtelGraphics | Windows, Linux | GUI for simulation packages, including 3D editing. | |||
| (Open-source version available) | Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. | |||||
| ChimeraX | Free for academic use | A molecular graphics tool for visualization, analysis, and basic 3D modeling. | ||||
| IQmol | Andrew Gilbert | A molecular editor with visualization capabilities, designed to work with Q-Chem. | ||||
| VMD | Free for non-commercial use | 3D Molecular visualization tool that includes structure editing through the Molefacture plugin. | ||||
| HyperChem | Hypercube, Inc. | Windows, Linux | A 3D molecular modeling tool with quantum chemistry and molecular dynamics features. Discontinued. | |||
| Chemcraft | Chemcraft developers | Visualization and analysis tool for quantum chemistry and molecular structures. | ||||
| YASARA Biosciences | (Free version available) | Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities. | ||||
| Biovia Discovery Studio | Advanced molecular modeling platform with features for 3D visualization, simulations, and drug discovery. | |||||
| Biovia Materials Studio | A 3D editing and visualization tool specifically designed for materials science applications. | |||||
| CrystalMaker | CrystalMaker Software Ltd | Designed for building, visualizing, and analyzing crystal structures in 3D. | ||||
| Py-ChemShell | CSE Collaboration | LGPL3 | A 3D editor for preparing quantum mechanical and molecular mechanics calculations. | |||
| Molecular Constructor | Alexander Teplukhin | Freeware | Windows, macOS, Linux, Android, iOS | A free 3D molecular builder and editor with geometry optimization features. | ||
| WebMO | WebMO LLC | Proprietary (Free version available) | Browser-based | A web-based interface for computational chemistry packages with integrated 3D molecular editor. | ||
| Miew | EPAM Systems | MIT License | Browser-based | A 3D molecular viewer and editor designed for visualization and editing of large molecular complexes. |
| Applet | Developer(s) | License | Info | |
|---|---|---|---|---|
| Editor and viewer applets | ||||
| Peter Ertl | freeware available from Molinspiration; Freeware for noncommercial use |
| Program | Developer | License | Desktop Browser IE6-7-8 | Desktop Browser other | Info | ||||
|---|---|---|---|---|---|---|---|---|---|
| MIT License | |||||||||
| Ketcher | EPAM Systems | Apache License | Originally developed by GGA Software Services before being bought by EPAM Systems |