SSS including H atoms

Hello,





We are running query.jpg (attached) and get hits.jpg (attached) from our JCHEM table.





We are wondering why some of the query H atoms are not being considered (apparently/please confirm) in the hits set generation. In particular why do we see OMe when we have clearly specified OH? Other points on the Benzene ring where H is specified we can see other substitution?





Is there a flag/switch to force consider H? The Underlying database is probably only heteroatoms hydrogenated state...do I need a hydrogenated version of the column for this search to work as expected?





Thanks for any comments,





Cheers,


Daniel.

Daniel, Do you have a custom standardization configuration on the table?





Cheers, Szabolcs

Yes we do and it does include dehydrogenation in the action string.





Is this the issue we have?





Cheers,


Daniel.

Most probably. Please make sure that the hydrogens are only removed from the database structures and not from queries. For this, you have to use the Groups tag:

Code:

<RemoveExplicitH ID="dehydrogenize" Groups="target"/>

See the documentation for more details: http://www.chemaxon.com/jchem/doc/user/Query.html#standardizationDB





Please also note that only explicit hydrogens of the query are used by substructure search. You have to draw them explicitly if you want to search them, or assign the appropriate H, X or s query property. See: http://www.chemaxon.com/jchem/doc/user/Query.html#explH


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





Best regards,


Szabolcs

Hello,





We are still concerned about the apparent behaviour of this SSS?


If we use the following query.jpg with explicit defined H - It seems we get the following hits which include O-C bond where we might expect O-H this is unexpected - can somebody please explain this situation? Is it a standardization issue? The fingerprints are aromatized but not hydrogenised?





Thank you





Daniel.

Hi Daniel,





Can you post here the standardization configuration on the table?





Szabolcs

Here we go:





<?xml version="1.0" encoding="UTF-8"?>


<!-- Standardizer configuration file -->





<StandardizerConfiguration Version ="0.1">


<Actions>


<Removal ID="keepOne" Method="keepLargest" Measure=""/>


<Action ID="aromatize" Act="aromatize"/>


<Transformation ID="A" Structure="[O:2]=[N:1]=O>>[O-:2][N+:1]=O"/>


<Transformation ID="B" Structure="[c:1][O:2][c:3](=[O:4])-[c:5]-[c:6]>>[c:1][O:2][C:3](=[O:4])[CH:5]=[c:6]"/>


<Transformation ID="C" Structure="N=[N:1]#[N:2]>>N=[N+:1]=[N-:2]"/>


<Transformation ID="D" Structure="O=C1CC=CC=C1>>OC1=CC=CC=C1"/>


<Transformation ID="E" Structure="[H:4][O:3][C:1]#[C:2]>>[H:4][C:2]=[C:1]=[O:3]"/>


<Transformation ID="F" Structure="[C][O-]>>CO"/>


<Transformation ID="G" Structure="[c][O-]>>CO"/>


<Transformation ID="H" Structure="C[N+:1][H:2]>>C[N:1]"/>


<Transformation ID="I" Structure="c[N+:1][H:2]>>c[N:1]"/>


<Action ID="aromatize" Act="aromatize"/>


<RemoveExplicitH ID="removeH" Charged="true" Radical="true" Mapped="true"/>


</Actions>


</StandardizerConfiguration>





Perhaps this bit is causing the issue?


RemoveExplicitH ID="removeH"

Yes. See my post above: http://www.chemaxon.com/forum/viewpost11365.html#11365





You must use Groups="target" for the RemoveExplicitH rule.





In the next major version (5.0) we plan to modify Standardizer so that it will always treat RemoveExplicitH specially: it will ignore this rule for the queries, regardless of the Groups setting.





Szabolcs

JChem 5.0 is out.





From now on, the RemoveExplicitH action will not cause trouble, because there is no special precaution to do any more.





Regards,


Szabolcs