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 execute. Computer programs are one component of software, which also includes documentation and other intangible components.
A computer program ...
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 ...
or
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 or
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 t ...
, 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
Bioactivi ...
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 or
line notation. Examples of each include
Molfile 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
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekul ...
tools.
Standalone programs
Java Applets
JavaScript embeddable editors
See also
*
ChemSpider
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.
Database
The database contains information on more than 100 million molecules from over 270 data sources including:
* EPA DSSTox
* U.S. Food and D ...
*
Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
See also
* Car–Parrinello molecular dynamics
* Comparison of force-field implementations
*Comparison of nucleic acid simulation software ...
*
Molecular design software Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''.
In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemi ...
Notes and references
External links
Molecular structure input on the webThe Chemical Structure Editor: Bridging Chemistry and Cheminformatics
{{DEFAULTSORT:Molecule Editor
Chemistry software
Computational chemistry