Hi Paul,
Thanks for the comments!
I may have jumped in a bit too enthusiastically with this - having
tested with the single "walk through" example from the paper. Having
now seen rather strange predictions for a lot of in-house molecules, I
have started to do what I should have done at the start - actually
reproduce the full test set (also in the supporting info
http://pubs.acs.org/doi/suppl/10.1021/ci8001815) - something is clearly
up, because most don't agree(!)
At the moment, I am presuming this is down to the SMARTS modifications
that I made. I will look into this further when I have some more time -
for now, here are the changes I think I made - roughly in the order that
I found them (I found the piece of paper where I had scrawled them
down!)
#G6 = #8,#16,#34,#52,#84
i = $(*!-*)
#X = !#1;!#6
!#G4 = !#6;!#14;!#32;!#50;!#82
#G7 = #9,#17,#35,#53,#85
#N = #8,#7,#9,#17,#35
!#N = !#8;!#7;!#9;!#17;!#35
!i = !$(*!-*)
q3 = $(*(@*)(@*)@*)
But there is also maybe an additional, more fundamental, issue - the
SMILES in the supporting test-set suggest that the molecules need
pre-'washing'. More precisely - bases appear in the list as their
conjugate acids - which means there still needs to be a 'gross'
assessment of possible basic centres (SMARTS), then a corresponding
mono-protonation prior to pKa calculation.
Kind regards
James
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