Is there a way to use free software to convert SMILES strings to structures? So far I've been unsuccessful in finding an open source tool that will convert a large number (>100k) of SMILES strings to a chemical structure.
Is this really only solved by commercial applications?
I would not mind converting through a number of intermediate formats.
Ideally I'd do it with R, but that is the least of my worries.
It's also neither for personal nor academic use.
According to the website, Open Babel should do the trick: Documentation - SMILES, Sourceforge.

For example, the following code will give you a neat SVG file of the molecule benzene:

obabel -:"c1ccccc1" -O benzen.svg


If you experience problems using it, you are welcome to ask more specifically.

Alternatively, you can use a web-query from the national cancer institute. It is easily accessible by the following code

http://cactus.nci.nih.gov/chemical/structure/"structure identifier"/"representation"


For example: benzene, "structure identifier"=c1ccccc1, "representation"=image.

Another open source solution, where you can directly export the structure into a molecular editor is Avogadro. (It uses Open Babel though.)

Depending on the actual problem, however, there might already be more advanced routines.