A 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. Computer programs are one component of software, which also includes software documentation, documentation and oth ...

for creating and modifying representations of

chemical structure A chemical structure determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of ...

s. Molecule editors can manipulate chemical structure representations in either a simulated

two-dimensional space In mathematics, a plane is a Euclidean ( flat), two-dimensional surface that extends indefinitely. A plane is the two-dimensional analogue of a point (zero dimensions), a line (one dimension) and three-dimensional space. Planes can arise as ...

three-dimensional space Three-dimensional space (also: 3D space, 3-space or, rarely, tri-dimensional space) is a geometric setting in which three values (called ''parameters'') are required to determine the position of an element (i.e., point). This is the informa ...

, via

2D computer graphics 2D computer graphics is the computer-based generation of digital images—mostly from two-dimensional models (such as 2D geometric models, text, and digital images) and by techniques specific to them. It may refer to the branch of computer ...

3D computer graphics 3D computer graphics, or “3D graphics,” sometimes called CGI, 3D-CGI or three-dimensional computer graphics are graphics that use a three-dimensional representation of geometric data (often Cartesian) that is stored in the computer for th ...

, respectively. Two-dimensional output is used as illustrations or to query

chemical database A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. Types of chemical databases Bioactiv ...

s. Three-dimensional output is used to build molecular models, usually as part of

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sci ...

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 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 or free. Some file format ...

line notation Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature. Chemistry * Cell notation for representation of an electrochemical cell * Dyson / IUPAC (1944) * Hayward (1961) * International Ch ...

. Examples of each include

Molfile Chemical table file (CT File) is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms. ...

and

simplified molecular input line entry specification The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors f ...

(SMILES), respectively. Files generated by molecule editors can be displayed by molecular graphics tools.

Standalone programs

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

Standalone programs

Java Applets

JavaScript embeddable editors

See also

Notes and references

External links