jcsearch example (exact vs. perfect)

The table that gives examples between EXACT and PERFECT searches on this[1] page says the the following should be a hit for EXACT but not PERFECT. The EXACT match doesn't hit for me. Should it, or is the documentation inaccurate? I'm using jcsearch 3.0.10.








jcsearch -t:e -s "C\C=C\C(C)O" -q "C\C=C/C(C)O"

















[1] http://www.chemaxon.com/jchem/doc/user/Query.html#searchtypes

Actually the table is meant to be used with an mrv or molfile query.





The corresponding smarts search would be:

Code:

$ jcsearch -t:e -s "C\C=C\C(C)O" -q "[#6][#6]=[#6][#6]([#6])[#8]" C\C=C\C(C)O

or SMILES:

Code:

$ jcsearch -t:e -s "C\C=C\C(C)O" -q "CC=CC(C)O{smiles:}" C\C=C\C(C)O

(Both of them match.)





Background:


In MDL terminology the double bond stereo information is only considered when the double bond has a stereo search flag. (It is also called stereo care flag, and is depicted as a square on the double bond.) I guess this was introduced to avoid unintentional stereo searching. (In the MDL system you draw the query, so the query inherently will hold an information about cis/trans stereochemistry based on the coordinates of the query atoms.)





On the other hand, in the Daylight systems, SMILES/SMARTS queries do not have coordinates, so the search always considers the cis/trans features of the query if specified.





As the ChemAxon searching tries to be compatible with both systems, the above behavior corresponds to the searching with setDoubleBondStereoMatchingMode(SearchConstants.DBS_MARKED) (jcsearch option: --doubleBondStereo:M). This means that the behavior depends on the format of the query.





This option can also be set to DBS_NONE (ignore all double bonds, --doubleBondStereo:N) and DBS_ALL (consider all double bonds, not just the flagged ones, --doubleBondStereo:A).





See the relevant sections of the query guide:





http://www.chemaxon.com/jchem/doc/user/Query.html#cisTrans





http://www.chemaxon.com/jchem/doc/user/Query.html#daylMDLDiff





All the best,


Szabolcs