Hi,
On Sat, Feb 20, 2010 at 4:22 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> On 20 February 2010 13:35, Geoffrey Hutchison <ge...@geoffhutchison.net>
> wrote:
>>> http://my.cdash.org/index.php?project=Open%20Babel
>>
>> Here's another failure. This is on the SMILES/SMARTS match test (i.e., all
>> of these SMILES should match themselves when turned into SMARTS).
>>
>> O([P@@](N)(=O)c1ccccc1)CC
>>
>> When I read this in as a SMILES and output as a SMILES, I lose chirality:
>>
>> O(P(=O)(N)c1ccccc1)CC
>>
>> Now if I look at the smartsmatch results
>> (http://my.cdash.org/testDetails.php?test=1816390&build=49366) I can see
>> that each of the failing molecules has a "chiral" non-carbon atom like
>> "c...@]1[c@@H](CCC1)[C@@H]1CCCNC1".
>>
>> In previous versions, we retained these chiral specifiers. I can certainly
>> understand "N" being ignored, but "P" and "S" can definitely be chiral. Does
>> the new stereo analysis ignore all non-carbon atoms for chirality?
>
> I think the answer is probably "yes". I'll look into it. I have a
> feeling that there is some corner case where a lone pair is involved
> in the chirality, but it should be relatively to deal with the general
> case.
Yes, N, P and S are currently skipped. Changing the line below (259,
src/stereo/perception.cpp) makes the smilesmatch test pass (see
Experimental Dashboard). However, I'm not 100% sure what would be the
best option for nitrogen. Detecting chiral (bridge-head) nitrogen
atoms seems complex...
// skip N, P, S
if (atom->IsNitrogen() || atom->IsPhosphorus() || atom->IsSulfur())
continue;
Tim
>> Thanks,
>> -Geoff
>>
>> (Two tests with clear analysis, two tests "failing" due to bug-fixes which
>> have been updated, one left)
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