Using CDK 1.2.2 SMARTSQueryTool and SmilesParser.
the SMARTS query: "[F,Cl,Br,I]C-C=C" doesn't hit the left two
smiles, but does hit the right two smiles. I have also found that the
query hits the sd file related to the right two smiles using
SDV2000Reader, aromaticity detection, and hydrogen adder (I am unsure
whether the sd file was created from the smiles or vice versa). Clearly,
the query shouldn't hit any of these. There seems to be a problem with
aromaticity detection. I have looked through the bug reports and noticed
that Egon's recent patch for sp2 N's might work for the first issue
(haven't tried out the patch yet). Is the coumarin a special case bug? I
noticed DeduceBondSystemTool was mentioned in the comments to another bug
report. Should I be using this tool after parsing SMILES strings and mol
files? Would that make a difference? Daylight's depictmatch service
shows no hits for all four smiles.
Clc1ccc2nccn2c1 <--------> ClC1C=CC2=NC=CN2C=1
FC(F)(F)c1oc2ccccc2c(=O)c1 <----------> FC(F)(F)C1Oc2ccccc2C(=O)C=1
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