A notable molecule editor is a

computer program A computer program is a sequence or set of instructions in a programming language for a computer to Execution (computing), execute. It is one component of software, which also includes software documentation, documentation and other intangibl ...

for creating and modifying representations of

chemical structure A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target m ...

s. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or

three-dimensional space In geometry, a three-dimensional space (3D space, 3-space or, rarely, tri-dimensional space) is a mathematical space in which three values ('' coordinates'') are required to determine the position of a point. Most commonly, it is the three- ...

, via 2D computer graphics or

3D computer graphics 3D computer graphics, sometimes called Computer-generated imagery, CGI, 3D-CGI or three-dimensional Computer-generated imagery, computer graphics, are graphics that use a three-dimensional representation of geometric data (often Cartesian coor ...

, 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 A file format is a Computer standard, standard way that information is encoded for storage in a computer file. It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary format, pr ...

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

3D structure editing

Java Applets

JavaScript embeddable editors

Notes and references

External links

Molecular structure input on the web

The Chemical Structure Editor: Bridging Chemistry and Cheminformatics
{{DEFAULTSORT:Molecule Editor Chemistry software Computational chemistry