Tuesday, 10 December 2013


The Simplified Molecular-Input Line-Entry System or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings ASCII. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. The terms Canonical and Isomeric can lead to some confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive.


The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation while The term Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes,  chirality, and configuration about double bonds.


Graph-based Definition
In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree.

There are some examples of SMILES bonds that can be use:

SMILES BONDS
SYMBOL
SINGLE
-
DOUBLE
=
TRIPLE
#


There are also some example of SMILES and their names:

SMILES
NAME
CC
Ethane
O=C=O
Carbon dioxide
C#N
Hydrogen cyanide
CCN(CC)CC
Triethylamine

Here are some links for tutorial on how to use SMILES:

Here are the examples of SMILES notation using Chemsketch:



Example of complex SMILES using Chemsketch:



HAVE FUN LEARNING SMILES :)


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