[Cdk-devel] New Canonical SMILES Generator now in CVS

[Christoph S. <ste...@ic...>]

Dear Colleagues,

due to a generous contribution by Oliver Horlacher we do now have the 
long awaited canonical SMILES generator. Oliver works for the company 
Therastrat (http://www.therastrat.com), a theragenomics company located 
in the Basel area of Switzerland. We would also like to thank the 
Therastrat company officials for their consent.

Some technical notes:

In order to use the canonical SMILES generator you need to properly 
configure the atoms in the molecule for which you want to generate the 
SMILES. The SmilesGenerator needs to know the correct atomic mass in 
order to generate the correct SMILES notation and it also needs to know 
the implicite hydrogen count in order to generate the canonical order of 
atoms.

For the first problem I have added a convenience method to 
ElementFactory. After reading or generating your molecule, you can now do:

try
{
	new ElementFactory().configureAtoms(molecule);
}
catch(Exception exc)
{
	exc.printStackTrace();
}

in order to get all the relevant fields in atom filled.

IMPORTANT: This does, however, not fill in the proper hydrogen count.

For this and I guess for many other applications, we are in urgent need 
for a HydrogenCountAssigner.class. Does anyone have a general way of 
doing this (see other posting)?

Cheers,

Chris

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..