Monday, August 10, 2009

Drawing Molecules with SMILES

Lately I have discovered that when drawing 2D or 3D chemical structures, it is often a lot easier to input a SMILES string than to draw it with the GUI. It reminds me of when I first started using Windows (v. 3) - at times I thought it was easier to type a command to tell the computer what I wanted to do instead of hunting through menus and dialogs to find the thing I needed to click.

SMILES is a way of describing a chemical structure on a single line - a LOT like a conventional condensed formula except without the Hydrogens. It is commonly used in database and chemical informatics applications. In an earlier post on Surfactants, I wanted to include the structures of a couple of perfluorinated surfactants. Drawing all 15 fluorines individually was just too tedious, it was much simpler - believe it or not - to type: FC(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=O)O

Drawing large and complex compounds "by hand" is also a hassle - and in some cases very difficult to get a good looking structure. Fortunately, many on line resources (e.g. Wikipedia, PubChem, ChemSpider) list the SMILES string for compounds like morphine:
Earlier in the summer I decided to install Ubuntu on my laptop in addition to Windows so I could run either operating system. One difficulty I have had in moving to Ubuntu is finding chemistry software to replace the programs I usually use on Windows. It turns out that several of the structure programs that I have been using lately will allow me to input a SMILES string.

One program I have been experimenting with lately is Avogadro - an open source project for building and studying 3D chemical structures. Avogadro is available on both Windows and Linux (as well as Mac), which is pretty convenient for me right now. It is a very nice program, they are at version 0.9.7 and plan to release 1.0 in September.

For drawing 2D structures on Windows I use ChemSketch, available as freeware from ACDlabs. On Ubuntu I have tried several 2D structure programs, none that match up to ChemSketch. One that I have used most is BKChem, which I used for the structure of Morphine above.

4 comments:

Bejugam Vinith said...
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DGA said...

The one and ace Norbert Haider has published a great (and GLP) solution for 2D depiction of molecular structures, in ps and png formats

http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2ps.html
http://merian.pch.univie.ac.at/~nhaider/cheminf/mol2png.pl.txt

Free for academic use is csib:
Has all been done, available for many years, supports all planned features of application above plus many more, free for academic use, uses same (but continuously updated) image generation algorithms as in PubChem.
(...).
http://depth-first.com/articles/2008/09/08/smarter-cheminformatics-from-sd-file-to-image-collection-with-chemphoto
http://81.169.131.69/Documentation/csib_man.pdf

Hope this helps. David GarcĂ­a.
http://www.cbm.uam.es/bioweb/David-Garcia.html

Steve W said...

Bejugam, thanks for the complement.

Steve W said...

David, Thanks for the tips.