I have now had quite a good look around the CDK, but some
questions/problems remain.
1) The daylight spec for SMARTS queries implies that the dot is used as
an AND. However, the SQT is either just taking the first fragment or is
using the dot as an OR (I can't tell yet).
([CH3]Br).([OH,O-,$([OX2]([#6])[#6])][CH]1([CH]=[CH][CH]5([CH]4(N([CH3])[CH2][CH2]C25(c3c(O[CH]12)c(O[CH3])[cH][cH]c3[CH2]4)))))
returns every listing that contains BrC. in its SMILES.
2) What is the most efficient way to multithread the SQT? Does a new
instance of the SQT have to be created for each thread?
3) It appears that the SMILES parser doesn't recognize the heavier metals
(e.g. Eu). How much of the periodic table is left out? Is there a way to
capture these atoms without them returning a CDKexception.
4) I am getting AllRingFinder exceptions for phthalocyanine and heme
compounds. What is the current limitation of the AllRingFinder? (I am
aware of the aromaticity detection limitation and I can generally work
around that).
5) What method is used for the IteratingMDLReader to detect ID tags. I
tried using the IMolecule.getproperties() method, but it returned null
strings. I am currently using a v2000 MDL database for this experiment.
6) I would prefer that the IteratingMDLReader return IAtomContainer
objects instead of IMolecule objects, because some mol files contain
multiple molecules. Is this a simple hack of the readers or is there more
to it than that?
P.S. Thanks for all your help so far. I work with very large and very
diverse databases. If there is a bug in any of these classes (at least
under real-world conditions) I am sure to find it. Where do I go to
submit bug reports?
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