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

ProgramDeveloper(s)LicensePlatformsInfo
ACD/ChemSketchACD/LabsProprietaryWindowsA chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available.
BIOVIA DrawDassault SystèmesProprietaryWindowsSuccessor of ISIS/Draw.
ChemDrawRevvity SignalsProprietaryWindows, macOSPrimarily for editing 2D chemical structures and reactions
ChemWindowWileyProprietaryWindowsFreeware for academic research and teaching; part of the KnowItAll software environment
JChemPaintJChemPaint DevelopersGNU LGPLCross-platformA 2D structural formula editor written in Java
XDrawChemXDrawChem developersGNU GPLWindows, macOS, LinuxA 2D chemical structure drawing tool based on OpenBabel

3D structure editing

ProgramDeveloper(s)LicensePlatformsInfoLast Release
Amira (software)Visage Imaging Zuse Institute BerlinProprietaryWindows, macOS, LinuxIncludes 3D visualization tools. Trial version available.
Ascalaph DesignerAgile MoleculeGNU GPLWindows, LinuxA freeware 3D molecule editor.2009
AvogadroAvogadro project teamGNU GPLWindows, macOS, LinuxA 3D molecule editor and visualizer.1 April 2026
DenebAtelGraphicsProprietaryWindows, LinuxGUI for simulation packages, including 3D editing.
GabeditAbdulrahman AlloucheBSDWindows, macOS, LinuxA 3D molecule editor with visualization capabilities.27 July 2021
MOEChemical Computing GroupProprietaryWindows, macOS, LinuxIncludes 3D molecular sketching, editing, and 2D to 3D conversion.June 2024
PyMOLSchrödinger, Inc.Proprietary (Open-source version available)Cross-platformPopular molecular visualization tool with basic 3D editing capabilities for structural analysis.1 February 2025
SAMSONOneAngstromProprietaryWindows, macOS, LinuxA modular platform for computational nanoscience, including 3D molecular editing.2025
SpartanWavefunction, Inc.ProprietaryWindows, macOS, LinuxFocused on 3D molecular modeling and simulation.
VMDUniversity of IllinoisFree for non-commercial useCross-platform3D Molecular visualization tool that includes structure editing through the Molefacture plugin.30 November 2016
YASARAYASARA BiosciencesProprietary (Free version available)Cross-platformMolecular graphics and modeling software focused on structural biology, with extensive 3D capabilities.5 October 2024

Java Applets

AppletDeveloper(s)LicenseInfo
JChemPaintGNU LGPLEditor and viewer applets
JME Molecule EditorPeter ErtlProprietaryfreeware available from Molinspiration; Freeware for noncommercial use

JavaScript embeddable editors

ProgramDeveloperLicenseDesktop Browser IE6-7-8Desktop Browser otheriPadiPhoneAndroidInfo
Kekulé ProgramKekule.js LabMIT LicenseYesYesUnknownUnknownUnknown

See also

Notes and references

External links