# Molecule editor > Mediated Wiki article. Canonical URL: https://mediated.wiki/source/Molecule_editor > Markdown URL: https://mediated.wiki/source/Molecule_editor.md > Source: https://en.wikipedia.org/wiki/Molecule_editor > Source revision: 1353273054 > License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) {{Short description|Program for simulating chemical structures}} A '''molecule editor''' is a [computer program](/source/computer_program) for creating and modifying representations of [chemical structure](/source/chemical_structure)s. Molecule editors can manipulate chemical structure representations in either a simulated [two-dimensional space](/source/Plane_(mathematics)) or [three-dimensional space](/source/three-dimensional_space), via [2D computer graphics](/source/2D_computer_graphics) or [3D computer graphics](/source/3D_computer_graphics), respectively. Two-dimensional output is used as illustrations or to query [chemical database](/source/chemical_database)s. Three-dimensional output is used to build molecular models, usually as part of [molecular modelling](/source/molecular_modelling) software packages. Database molecular editors such as Leatherface,{{cite book|doi=10.1002/3527603743.ch11|chapter=Structure Modification in Chemical Databases|title=Chemoinformatics in Drug Discovery|pages=[https://archive.org/details/isbn_9783527307531_0/page/271 271–285]|series=Methods and Principles in Medicinal Chemistry|year=2005|last1=Kenny|first1=Peter W.|last2=Sadowski|first2=Jens|isbn=9783527307531|url=https://archive.org/details/isbn_9783527307531_0/page/271}} RECAP,{{cite journal|doi=10.1021/ci970429i|pmid=9611787|title=RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry|journal=Journal of Chemical Information and Computer Sciences|volume=38|issue=3|pages=511–522|year=1998|last1=Lewell|first1=Xiao Qing|last2=Judd|first2=Duncan B.|last3=Watson|first3=Stephen P.|last4=Hann|first4=Michael M.}} and Molecule Slicer{{cite journal|doi=10.1021/jm030267j|pmid=14695836|title=Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs|journal=Journal of Medicinal Chemistry|volume=47|pages=224–232|year=2004|last1=Vieth|first1=Michal|last2=Siegel|first2=Miles G.|last3=Higgs|first3=Richard E.|last4=Watson|first4=Ian A.|last5=Robertson|first5=Daniel H.|last6=Savin|first6=Kenneth A.|last7=Durst|first7=Gregory L.|last8=Hipskind|first8=Philip A.|issue=1}} 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](/source/file_format) or line notation. Examples of each include [Molfile](/source/Molfile) and [simplified molecular input line entry specification](/source/simplified_molecular_input_line_entry_specification) (SMILES), respectively. Files generated by molecule editors can be displayed by [molecular graphics](/source/molecular_graphics) tools. == Standalone programs == === 2D structure editing === {| class="wikitable sortable" |- ! Program !! Developer(s) !! License !! Platforms !! Info |- | [ACD/ChemSketch](/source/ACD%2FChemSketch) || [ACD/Labs](/source/Advanced_Chemistry_Development) || {{proprietary}} || Windows || A chemically intelligent drawing interface allowing creation of 2D structures for organics, organometallics, polymers, and Markush structures. Freeware version available. |- | [BIOVIA Draw](/source/BIOVIA_Draw) || [Dassault Systèmes](/source/Dassault_Syst%C3%A8mes) || {{proprietary}} || Windows || Successor of [ISIS/Draw](/source/ISIS%2FDraw). |- | [ChemDraw](/source/ChemDraw) || Revvity Signals || {{proprietary}} || Windows, macOS || Primarily for editing 2D chemical structures and reactions |- | [ChemWindow](/source/ChemWindow) || [Wiley](/source/Wiley_(publisher)) || {{proprietary}} || Windows || Freeware for academic research and teaching; part of the KnowItAll software environment |- | [JChemPaint](/source/JChemPaint) || JChemPaint Developers || {{LGPL-lic}} || [Cross-platform](/source/Cross-platform) || A 2D structural formula editor written in [Java](/source/Java_(programming_language)) |- | [XDrawChem](/source/XDrawChem) || XDrawChem developers || {{GPL-lic}} || Windows, macOS, Linux || A 2D chemical structure drawing tool based on [OpenBabel](/source/OpenBabel) |} === 3D structure editing === {| class="wikitable sortable" |- ! Program !! Developer(s) !! License !! Platforms !! Info !Last Release |- | [Amira (software)](/source/Amira_(software)) || [Visage Imaging](/source/Visage_Imaging)
[Zuse Institute Berlin](/source/Zuse_Institute_Berlin) || {{proprietary}} || Windows, macOS, Linux || Includes 3D visualization tools. Trial version available. | |- | [Ascalaph Designer](/source/Ascalaph_Designer) || [Agile Molecule](/source/Agile_Molecule) || {{GPL-lic}} || Windows, Linux || A freeware 3D molecule editor. | {{wikidata|qualifier|preferred|Q4034436|P348|P548=Q2804309|P577}} |- | [Avogadro](/source/Avogadro_(software)) || Avogadro project team || {{GPL-lic}} || Windows, macOS, Linux || A 3D molecule editor and visualizer. | {{wikidata|qualifier|preferred|single|edit|Q851800|P348|P548=Q2804309|P577}} |- | Deneb || AtelGraphics || {{proprietary}} || Windows, Linux || GUI for simulation packages, including 3D editing. | |- | [Gabedit](/source/Gabedit) || Abdulrahman Allouche || {{BSD-lic}} || Windows, macOS, Linux || A 3D molecule editor with visualization capabilities. | {{wikidata|qualifier|preferred|single|edit|Q5515367|P348|P548=Q2804309|P577}} |- | [MOE](/source/Molecular_Operating_Environment) || [Chemical Computing Group](/source/Chemical_Computing_Group) || {{proprietary}} || Windows, macOS, Linux || Includes 3D molecular sketching, editing, and 2D to 3D conversion. | {{wikidata|qualifier|preferred|Q28447694|P348|P548=Q2804309|P577}} |- | [PyMOL](/source/PyMOL) || [Schrödinger, Inc.](/source/Schr%C3%B6dinger_(company)) || {{proprietary}} (Open-source version available) || [Cross-platform](/source/Cross-platform) || Popular molecular visualization tool with basic 3D editing capabilities for structural analysis. | {{wikidata|qualifier|preferred|single|edit|Q1373457|P348|P548=Q2804309|P577}} |- | [SAMSON](/source/SAMSON) || OneAngstrom || {{proprietary}} || Windows, macOS, Linux || A modular platform for computational nanoscience, including 3D molecular editing. | 2025 |- | [Spartan](/source/Spartan_(chemistry_software)) || [Wavefunction, Inc.](/source/Wavefunction%2C_Inc.) || {{proprietary}} || Windows, macOS, Linux || Focused on 3D molecular modeling and simulation. | {{wikidata|qualifier|preferred|Q17084877|P348|P548=Q2804309|P577}} |- | [VMD](/source/Visual_Molecular_Dynamics)|| [University of Illinois](/source/University_of_Illinois) || Free for non-commercial use || [Cross-platform](/source/Cross-platform) || 3D Molecular visualization tool that includes structure editing through the Molefacture plugin. | {{wikidata|qualifier|preferred|edit|Q7936565|P348|P548=Q2804309|P577}} |- | [YASARA](/source/YASARA) || YASARA Biosciences || {{proprietary}} (Free version available) || [Cross-platform](/source/Cross-platform) || Molecular graphics and modeling software focused on structural biology, with extensive 3D capabilities. | {{wikidata|qualifier|preferred|edit|Q8049645|P348|P548=Q2804309|P577}} |- |} == Java Applets == {| class="wikitable" ! Applet !! Developer(s) !! License !! Info |- | [JChemPaint](/source/JChemPaint) || || {{LGPL-lic}} || Editor and viewer applets |- | [JME Molecule Editor](/source/JME_Molecule_Editor) || Peter Ertl || {{proprietary}} || [freeware](/source/freeware) available from [Molinspiration](/source/Molinspiration); [Freeware](/source/Freeware) for noncommercial use |} == JavaScript embeddable editors == {| class="wikitable" ! Program !! Developer !License!! Desktop Browser IE6-7-8 !! Desktop Browser other !! [iPad](/source/iPad) !! [iPhone](/source/iPhone) !! [Android](/source/Android_(operating_system)) !Info |- | [Kekulé Program](/source/Kekul%C3%A9_Program) || [Kekule.js Lab](/source/Kekule.js_Lab) |[MIT License](/source/MIT_License)|| {{yes}} || {{yes}} || {{unk}} || {{unk}} || {{unk}} || |- |} == See also == * [ChemSpider](/source/ChemSpider) * [Comparison of software for molecular mechanics modeling](/source/Comparison_of_software_for_molecular_mechanics_modeling) * [Molecular design software](/source/Molecular_design_software) == Notes and references == {{Reflist|30em}} ==External links== * [https://dx.doi.org/10.1186/1758-2946-2-1 Molecular structure input on the web] * [http://metamolecular.com/chemwriter/articles/the-chemical-structure-editor-bridging-chemistry-and-cheminformatics/ The Chemical Structure Editor: Bridging Chemistry and Cheminformatics] {{DEFAULTSORT:Molecule Editor}} Category:Chemistry software Category:Computational chemistry --- Adapted from the Wikipedia article [Molecule editor](https://en.wikipedia.org/wiki/Molecule_editor) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Molecule_editor?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.