On Mon, Dec 17, 2012 at 12:42 AM, Peter Gedeck <[email protected]>wrote:
> hello Paul
>
> If you look at your fragments you see that in your decomposition you have
> overlapping fragments:
>
> set(['[3*]OCC(O[3*])C1CC1', '[4*]CC([4*])C1CC1', '[3*]Oc1ncncn1',
> '[14*]c1ncncn1', '[3*]OCC([4*])C1CC1', '[3*]OC(C[4*])C1CC1',
> '[3*]OC1CNC1', '[15*]C1CNC1'])
>
> This indicated that the fragmentation did not go down to the smallest
> fragments but stopped at a minimum fragment size of 2 to 4.
>
Peter's right, this has to do with the minimum fragment size. You can see
it here:
In [9]: BRICS.BRICSDecompose(base,minFragmentSize=4)
Out[9]:
set(['[3*]OCC(O[3*])C1CC1',
'[4*]CC([4*])C1CC1',
'[3*]Oc1ncncn1',
'[14*]c1ncncn1',
'[3*]OCC([4*])C1CC1',
'[3*]OC(C[4*])C1CC1',
'[3*]OC1CNC1',
'[15*]C1CNC1'])
> You can seer this from the fact that the ether oxygen is not included in
> the list. This gives two options, either you set the argument or the
> default has changed. The second one would probably be captured by a test so
> my guess is the first one. if it's the second one I take the blame as Greg
> would never do this.
>
Or I changed the tests after changing the default... ;-)
The question should be relatively easy to answer by browsing SVN, but the
sourceforge svn browser is so awful that it's painful to do so.
-greg
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