Our friends from Pfizer published this in 2005 regarding most common salts (ions) in the CSD. http://www.ncbi.nlm.nih.gov/pubmed/16136575 (freely available)
Just a pointer, maybe you are (ever) interested in augmenting this list... On 28 June 2011 18:32, Greg Landrum <[email protected]> wrote: > Dear JP, > > On Tue, Jun 28, 2011 at 5:32 PM, JP <[email protected]> wrote: >> Something is not quite clear to me in the remove salts functionality - >> particularly the dontRemoveEverything flag. >> >> Watch out for this case (everything removed): >>>>> remover = SaltRemover() >>>>> len(remover.salts)>1 >> True >>>>> mol = Chem.MolFromSmiles('CC(=O)O.[Na]') >>>>> res = remover.StripMol(mol) >>>>> res.GetNumAtoms() >> 0 >> >> JP -- why does this return 0 ?! why is the CC(=O)O part stripped here? > > because acetic acid is one of the counterions present in the salt > definition file. Take a look at $RDBASE/Data/Salts.txt > If you want to create your own definitions, you can create a salt > stripper from them like this: > remover = SaltRemover(defnFilename='my_salt_file.txt') > >> dontRemoveEverything helps with this by leaving the last salt: >>>>> res = remover.StripMol(mol,dontRemoveEverything=True) >>>>> res.GetNumAtoms() >> 4 >> > > It's the acetic acid: > [4]>>> m = Chem.MolFromSmiles('CC(=O)O.[Na]') > > [5]>>> res = rm.StripMol(m,dontRemoveEverything=True) > > [6]>>> Chem.MolToSmiles(res) > Out[6] 'CC(=O)O' > > The reason that is left instead of the Na is because the Na comes > first in the Salts.txt file, so it's removed first. There are some > notes about this at the top of that file. > > -greg > ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
