Editing Molecule editor

{{short description|Computer program used to create and modify simulated representations of molecular structures}}
A notable '''molecule editor''' is a [[computer program]] for creating and modifying representations of [[chemical structure]]s.<!-- Only for programs/packages with their own article -->

Molecule editors can manipulate chemical structure representations in either a simulated [[Plane (mathematics)|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 database]]s. Three-dimensional output is used to build molecular models, usually as part of [[molecular modelling]] software packages.

Database molecular editors such as Leatherface,<ref>{{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}}</ref> RECAP,<ref>{{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.}}</ref> and Molecule Slicer<ref>{{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}}</ref> 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 ===

{| class="wikitable sortable"
|-
! Program !! Developer(s) !! License !! Platforms !! Info
|-
| [[ACD/ChemSketch]] || [[Advanced_Chemistry_Development|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 (publisher)|Wiley]] || {{proprietary}} || Windows || Freeware for academic research and teaching; part of the KnowItAll software environment
|-
| [[JChemPaint]] || JChemPaint Developers || {{LGPL-lic}} || [[Cross-platform]] || A 2D structural formula editor written in [[Java (programming language)|Java]]
|-
| [[XDrawChem]] || XDrawChem developers || {{GPL-lic}} || Windows, macOS, Linux || A 2D chemical structure drawing tool based on [[OpenBabel]]
|-
|}

=== 3D structure editing ===
{| class="wikitable sortable"
|-
! Program !! Developer(s) !! License !! Platforms !! Info
!Last Release
|-
| [[Amira (software)]] || [[Visage Imaging]]<br>[[Zuse Institute Berlin]] || {{proprietary}} || Windows, macOS, Linux || Includes 3D visualization tools. Trial version available.
|
|-
| [[Ascalaph Designer]] || [[Agile Molecule]] || {{GPL-lic}} || Windows, Linux || A freeware 3D molecule editor.
| {{wikidata|qualifier|preferred|Q4034436|P348|P548=Q2804309|P577}}
|-
| [[Avogadro (software)|Avogadro]] || 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]] || Abdulrahman Allouche || {{BSD-lic}} || Windows, macOS, Linux || A 3D molecule editor with visualization capabilities.
| {{wikidata|qualifier|preferred|single|edit|Q5515367|P348|P548=Q2804309|P577}}
|-
| [[Molecular Operating Environment|MOE]] || [[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]] || [[Schrödinger]] || {{proprietary}} (Open-source version available) || [[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]] || Inria || {{proprietary}} || Windows, macOS, Linux || A modular platform for computational nanoscience, including 3D molecular editing.
| {{wikidata|qualifier|preferred|Q18192364|P348|P548=Q2804309|P577}}
|-
| [[Spartan (chemistry software)|Spartan]] || [[Wavefunction, Inc.]] || {{proprietary}} || Windows, macOS, Linux || Focused on 3D molecular modeling and simulation.
| {{wikidata|qualifier|preferred|Q17084877|P348|P548=Q2804309|P577}}
|-
| [[Visual Molecular Dynamics|VMD]]|| [[University of Illinois]] || Free for non-commercial use || [[Cross-platform]] || 3D Molecular visualization tool that includes structure editing through the Molefacture plugin.
| {{wikidata|qualifier|preferred|edit|Q7936565|P348|P548=Q2804309|P577}}
|-
| [[YASARA]] || YASARA Biosciences || {{proprietary}} (Free version available) || [[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]] ||  || {{LGPL-lic}} || Editor and viewer applets
|-
| [[JME Molecule Editor]] || Peter Ertl || {{proprietary}} || [[freeware]] available from [[Molinspiration]]; [[Freeware]] for noncommercial use
|}

== JavaScript embeddable editors ==

{| class="wikitable"
! Program !! Developer 
!License!! Desktop Browser IE6-7-8 !! Desktop Browser other !! [[iPad]] !! [[iPhone]] !! [[Android (operating system)|Android]] 
!Info
|-
| [[Kekulé Program]] || [[Kekule.js Lab]] 
|[[MIT License]]|| {{yes}} || {{yes}} || {{unk}} || {{unk}} || {{unk}} ||
|-
|}

== See also ==
* [[ChemSpider]]
* [[Comparison of software for molecular mechanics modeling]]
* [[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]]