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, RECAP, and Molecule Slicer 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
2D structure editing
Program Developer(s) License Platforms Info ACD/ChemSketch ACD/Labs Windows A chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available. alvaSketcher Alvascience , free Windows, macOS, Linux 2D molecular structure editor supporting drawing, editing, fragment transformations, SMILES and MDL V2000. BIOVIA Draw Dassault Systèmes Windows Successor of ISIS/Draw. ChemDraw Revvity Signals Windows, macOS Primarily for editing 2D chemical structures and reactions ChemWindow Wiley Windows Freeware for academic research and teaching; part of the KnowItAll software environment JChemPaint JChemPaint Developers Cross-platform A 2D structural formula editor written in Java XDrawChem XDrawChem developers Windows, macOS, Linux A 2D chemical structure drawing tool based on OpenBabel
3D structure editing Program Developer(s) License Platforms InfoLast Release Amira (software) Visage ImagingZuse Institute Berlin Windows, macOS, Linux Includes 3D visualization tools. Trial version available. Ascalaph Designer Agile Molecule Windows, Linux A freeware 3D molecule editor. Avogadro Avogadro project team Windows, macOS, Linux A 3D molecule editor and visualizer. Deneb AtelGraphics Windows, Linux GUI for simulation packages, including 3D editing. Gabedit Abdulrahman Allouche Windows, macOS, Linux A 3D molecule editor with visualization capabilities. MOE Chemical Computing Group Windows, macOS, Linux Includes 3D molecular sketching, editing, and 2D to 3D conversion. PyMOL Schrödinger, Inc. (Open-source version available) Cross-platform Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. SAMSON OneAngstrom Windows, macOS, Linux A modular platform for computational nanoscience, including 3D molecular editing. 2025 Spartan Wavefunction, Inc. 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 (Free version available) Cross-platform Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities.
Java Applets
Applet Developer(s) License Info JChemPaint Editor and viewer applets JME Molecule Editor Peter Ertl 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
See also ChemSpider Comparison of software for molecular mechanics modeling Molecular design software
Notes and references
External links Molecular structure input on the web The Chemical Structure Editor: Bridging Chemistry and Cheminformatics