Molecule editor

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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.

Standalone programs[edit]

Program Developer(s) License Platforms Info
Accelrys Draw Accelrys Proprietary Windows freeware version available; includes name2structure and structure2name, InChI naming, and canonical SMILES
ACD/ChemSketch ACD/Labs Proprietary Windows A chemically intelligent drawing interface that allows drawing almost any chemical structure including organics, organometallics, polymers, and Markush structures. freeware version available
Amira (software) Visage Imaging
Zuse Institute Berlin
Proprietary Windows, macOS, Linux 14-day trial version available
Ascalaph Designer Agile Molecule GNU GPL Linux, Windows freeware
ArgusLab Mark Thompson (author) Proprietary Windows freeware
Avogadro Avogadro project team GNU GPL Linux, macOS, Windows 3D molecule editor, visualizer
BALLView BALL project team GNU GPL-LGPL Linux, macOS, Windows viewer, editor, simulation tool
Bioclipse Bioclipse Developers EPL cross-platform Java, Eclipse Rich Client Platform (RCP) based
BKChem Beda Kosata GNU GPL cross-platform 2D molecule editor written in Python
ChemDoodle iChemLabs Proprietary Linux, macOS, Windows Complete chemical publishing system for drawing chemical structures, reactions, spectra and more. Free trial available.
ChemDraw PerkinElmer Proprietary macOS, Windows Edit chemical structures and reactions
Deneb AtelGraphics Proprietary Linux, Windows Trial version available; easy to use graphical user interface desktop for packages SIESTA, VASP, QE, etc.
Elemental (software) Dotmatics Proprietary Windows, iOS freeware for PCs, iPhone, iPad
ICEdit InfoChem Proprietary Windows Edit chemical structures and reactions
Chemtool GNU GPL Linux, Unix 2D editor for chemical structural formulas, written in C using GTK
ChemWindow Bio-Rad Proprietary available as part of the KnowItAll software environment; Freeware for academic research and teaching
Gabedit Abdulrahman Allouche BSD Linux, macOS, Windows 3D molecule editor, visualizer
ICM-Chemist MolSoft Proprietary Windows, macOS, Linux Easy to use graphical user interface desktop chemistry editor
JChemPaint GNU LGPL cross-platform 2D structural formula editor written in Java
HyperChem Hypercube, Inc. Proprietary Windows 3D molecule editor, visualizer
KnowItAll Bio-Rad Proprietary Windows Freeware for academic research and teaching
lhendraw Lennard Wasserthal GNU GPL Linux chemdraw cdx/cdxml compatible FOSS clone, search function
MAPS (molecular software) Scienomics Proprietary cross-platform Build complex molecular (molecules, metal complexes, polymers...) and periodic (crystal, surface, interface, CNT, nanosystems...) systems, generate amorphous conformations. Read SMILES and 3D formats (pdb, xyz, cif...).
MarvinSketch/View ChemAxon Proprietary cross-platform commercial and freeware versions. Chemical editor and viewer, desktop version (Java Beans)
MarvinSpace ChemAxon Proprietary cross-platform commercial and freeware versions. 3D macromolecular visualization and ligand editing, desktop version (Java Beans)
MedChem Designer Simulations Plus Proprietary Windows freeware – includes free S+logP, S+logD(7.4), TPSA, PEOE sigma charges, HBD, HBA, and Rule of 5 calculations.
Molecular Operating Environment (MOE) Chemical Computing Group Proprietary Windows, Linux, Mac; SVL programming language Platform for molecular modelling / drug discovery applications, with 3D molecular sketching and editing, 2D depiction, and 2D to 3D conversion.
molsKetch GNU GPL cross-platform multiplatform editor, based on Qt4
MOLTEMPLATE BSD 3-clause Linux, macOS, Windows General text-based molecule builder for LAMMPS
ODYSSEY Wavefunction, Inc. Proprietary macOS, Windows
SAMSON Inria Proprietary Windows, Linux, macOS Software platform for integrated computational nanoscience. Customized with SAMSON Elements (modules for SAMSON)
SketchEl GNU GPL cross-platform editor, Java, available on SourceForge
Smormo-Ed BSD Linux, Windows, available on SourceForge
Spartan Wavefunction, Inc. Proprietary Linux, macOS, Windows
StruMM3D Exorga, Inc. Proprietary Windows
Vimol ISC BSD, Linux, macOS, Windows Powerful, with vim-like interface
XDrawChem GNU GPL Linux, macOS, Windows based on OpenBabel
Zem (software) Example GNU GPL Linux, macOS, Windows based on OpenBabel

Java Applets[edit]

Applet Developer(s) License Info
Accelrys JDraw Accelrys Proprietary commercial and freeware versions for nonprofit use
ICEdit InfoChem Proprietary Edit chemical structures and reactions
JChemPaint GNU LGPL Editor and viewer applets
JME Molecule Editor Peter Ertl Proprietary freeware available from Molinspiration; Freeware for noncommercial use
MarvinSketch ChemAxon Proprietary commercial and freeware versions. Chemical editor applet implementation
MarvinSpace ChemAxon Proprietary commercial and freeware versions. 3D macromolecular visualization and ligand editing
SDA ACD/Structure Drawing Applet ACD/Labs Proprietary commercial and freeware versions
ChemWriter Metamolecular Proprietary Version 1 needs Java plug-in, version 2 needs no browser plug-ins
SketchEl GNU GPL, available on SourceForge
Chemis3D Didier Collomb Proprietary
MolEdit MolSoft Proprietary HTML5 editor allows drawing 2D chemical structure inside a web browser's page; needs no plug-ins (like Java); works in any modern HTML5 compatible browser with JavaScript enabled, including mobile platforms; lightweight, intuitive
FlaME: Flash Molecular Editor Pavel Dallakian, Norbert Haider Freeware for noncommercial use

JavaScript embeddable editors[edit]

Program Developer Desktop Browser IE6-7-8 Desktop Browser other iPad iPhone Android Windows Phone
AngularDrawChem Michał Malik Unknown Yes No No No Unknown Draw organic structures and reaction schemes in SVG, available online and as AngularJS module; open-source (MIT)
ChemDoodle Web Components iChemLabs Yes Yes Yes Yes Yes Unknown HTML5 chemistry web components including viewers, animations, interactive components and editors; uses Canvas and WebGL graphics. Free and open source under GPL v3.0 license
ChemDraw JS PerkinElmer No Yes Unknown Unknown Unknown Unknown The JavaScript version of ChemDraw
ChemWriter 3 Metamolecular No Yes Yes Unknown Unknown Unknown
Elemental (software) Dotmatics Yes Yes Yes Yes Yes Unknown proprietary software
ICEdit InfoChem No Yes Yes Yes Yes Yes Edit chemical structures and reactions
Ketcher [h[GGA Software Services]] Yes Yes Unknown Unknown Unknown Unknown Written using SVG/VML via Raphaël.js. Open source initiative.
LAI4D Lai4d Systems No Yes Yes Yes Yes Yes Free light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type.
Marvin JS ChemAxon No Yes Unknown Unknown Unknown Unknown The JavaScript version of MarvinSketch; has somewhat less features than Java-based version at present
Molinspiration WebME molecule editor Yes Yes Unknown Unknown Unknown Unknown proprietary software
JSDraw Scilligence Yes Yes Yes Yes Yes Unknown
JSME Peter Ertl Yes Yes Yes Yes Yes Unknown Supports drag and drop on HTML5 compatible desktop browsers to import and export MOL and RXN files. The editor can generate SMILES and InChI.
VectorMol Sciformation Unknown Yes Unknown Unknown Yes Unknown Written using SVG/VML via Raphaël.js; supports drag and drop on HTML5 compatible desktop browsers to import MOL and RXN files. Integrated structure optimizers. License is CC-BY-NC-SA
WebMolKit Molecular Materials Informatics No Yes No No No No Also core library for SketchEl2. License is GPL.

Online editors[edit]

Program Developer Info
AngularDrawChem Michał Malik open-source (MIT) editor for drawing organic structures and reaction schemes in SVG, available on-line and as an AngularJS module
ICEdit InfoChem free trial, edit chemical structures and reactions
LAI4D Lai4d Systems Free light 3D CAD tool (viewer and designer) for the web that includes a "molecule" entity type.
MolEdit MolSoft HTML5 editor allows drawing 2D chemical structure inside a web browser's page; needs no plug-ins (like Java); works in any modern HTML5 compatible browser with JavaScript enabled, including mobile platforms; lightweight, intuitive
MolView Herman Bergwerf Free software. Built for desktops, tablets and smartphones. Integrates some online databases including PubChem, RCSB, the NCI/CADD Chemical Identifier Resolver and the Crystallography Open Database.
Marvin molecule editor and viewer ChemAxon proprietary software. Supports all major formats and structure/query features. This Java implementation also includes unlimited structure based predictions for a range of properties (pKa, logD, name<>structure, etc.).
Molecular Editor and Image Sharer Based on JChemPaint; allows storing generated images on a server
PubChem online molecule editor supports SMILES, SMARTS, InChI, and all common chemical file formats.
MolEditor | Ambinter Small chemical database edition, manipulation and export (Structure Data File SDF, SMILES, ...) – Free Software (GPL)

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Mobile editor apps[edit]

Program Developer iPad iPhone Android BlackBerry Info
ChemDoodle Mobile iChemLabs Yes Yes Yes No Freeware, integrated with ChemDoodle desktop.
ChemJuice IDBS Yes Yes No No
Chirys Draw Integrated Chemistry Design Yes No No No
Chirys Sketch Integrated Chemistry Design No Yes No No
Elemental (software) Dotmatics Yes Yes Yes No Freeware
ICEdit InfoChem Unknown Unknown Yes Unknown beta version available by InfoChem
3D Molecules Edit & Test for iOS Virtual Space Yes Yes No No
3D Molecules Editor for iOS Virtual Space Yes Yes No No
3D Molecules View & Edit Lite for iOS Virtual Space Yes Yes No No Freeware

See also[edit]

Notes and references[edit]

  1. ^ Kenny, P.W.; Sadowski, J. (2005) Structure modification in chemical databases Chemoinformatics in drug discovery (editor: Oprea, T.I.), 271-285 (Wiley).
  2. ^ Lewell, X.Q.; Judd, D.B; Watson, S.P.; Hann, M.M. (1998) RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry J. Chem. Inf. Comput. Sci. 38, 511-522.
  3. ^ Vieth, M.; Siegel, M.G.; Higgs, R.E.; Watson, I.A.; Robertson, D.H.; Savin, K.A.; Durst, G.L.; Hipskind; P.A. (2004) Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs J. Med. Chem. 47, 224-232.

External links[edit]