SMILES

“You'll find that life is still worthwhile, if you just smile.” 

― Charles Chaplin

When we say about "SMILES", people might imagine one of this faces :

It does not matter which kind of smiley faces you are thinking right now, we want to introduce you to a new type of  "SMILES". 

Our main character today is the SMILES that stands for the Simplified Molecular Input Line Entry Specification. It is a specification for unambiguously describing the structure of chemical molecule using short ASCII strings. Now, you might be wondering what is the meaning of ASCII right? ASCII is the short form from American Standard Code for Information Interchange. 

Click here if you want to know more information about ASCII from wikipedia.

From graph-based definition, 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 to remove hydrogen atoms and cycles are broken into 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.

Name	SMILES
ethane	CC
carbon dioxide	O=C=O
hydrogen cyanide	C#N
triethylamine	CCN(CC)CC
acetic acid	CC(=O)O
cyclohexane	C1CCCCC1
benzene	c1ccccc1
hydronium ion	[OH3+]
deuterium oxide	[2H]O[2H]
uranium-235	[235U]
E-difluoroethene	F/C=C/F
Z-difluoroethene	F/C=C\F
L-alanine	N[C@@H](C)C(=O)O
D-alanine	N[C@H](C)C(=O)O

               Some examples of SMILES and its name

SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. Examples of molecule editors are ACD/ChemSketch, Accelrys Draw, and Vimol . Two-dimensional editors generate output used as illustrations or for querying chemical databases while three-dimensional molecule editors are used to build molecular models, usually as part of molecular modelling software packages.

SMILES is widely used and computationally efficient as it simple yet comprehensive chemical nomenclature. It uses symbols and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs (HSMG).

Some of the uses of SMILES are:

• Keys for database access
• Mechanism for researchers to exchange chemical information
• Entry system for chemical data
• Part of languages for artificial intelligence or expert systems in chemistry 

So, what we can get by using this SMILES? For example, apart from writing ethane as C2H6, we write it as CC by using SMILES. It is simple right? As you can see, it removed its hydrogen atom. SMILES makes our life easier and simpler in presenting the molecule. =)

Although SMILES seems simple, SMILES differs in several fundamental ways from most chemical nomenclatures and other chemical formats. It is useful to review a few fundamental concepts before digging into the specifics of the SMILES language. 

This post is just a brief view about SMILES. There is a lot of other things about SMILES that we did not discuss yet with you. So, lets try to know and study more about this interesting SMILES. Your effort will not be wasted!

You can view and get more information about SMILES at SMILES.info. Hope you enjoy it!