Searching for nonsensical stereochemistry

I've noticed that chemists are registering compounds with nonsensical stereochemistry and I want to perform a search to identify how extensive this problem is. I am looking for ideas on crafting jc_compare statements that will work to identify the following nonsensical substructures:

• up,down, or squiggle wedge bonds drawn starting from heteroatoms (e.g. O,N,S)


• up,down, or squiggle wedge bonds drawn starting from aromatic carbons

I've tried queries similar to the following without any success -- this returns results without considering how the stereochemistry is drawn.

SELECT * FROM CHEMREG.COMPOUND

WHERE jc_compare(COMPOUND, 'FORMAT

  DRAWER



  2  1  0  0  0  0  0  0  0  0999 V2000

    0.0000   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    0.0000    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

  2  1  1  1      

M  END

','t:s  exactStereoMatching:Y stereoSearchType:s absoluteStereo:a') = 1

Dear customer,

Could we recommend to use our Structure Checker tool (also available from JChem Oracle Cartridge) to filter out these molecules with nonsensical stereochemistry ? See, for example, the incorrect tetrahedral stereo checker.

In cartridge, it is available through the jc_evaluate_x operator.

Example for checking:

select jc_evaluate_x('input_molecule',  'chemTerms:check("incorecttetrahedralstereo")') from dual;

for checking and fixing:

select jc_evaluate_x('input_molecule',  'chemTerms:fix("incorecttetrahedralstereo->clearwegde")') from dual;

Best regards,
Krisztina

EDIT: Does the StrucutreChecker require a license different than the JChem Cartridge license?

 

Thanks for the fast reply. I like your idea or using the StructureChecker, however i am not able to get it to work.

 

Taking your example I tried:

SELECT jc_evaluate_x('c1ccccc1', 'chemTerms:check("incorecttetrahedralstereo")') FROM DUAL

and then I tried fixing the spelling of "correct":

SELECT jc_evaluate_x('c1ccccc1', 'chemTerms:check("incorrecttetrahedralstereo")') FROM DUAL

 

Both give the same error (below). What am I missing here?

ORA-29532: Java call terminated by uncaught Java exception: chemaxon.jchem.cartridge.oresident.nonidxscan.NonIdxScanException: RemoteException occurred in server thread; nested exception is: 

	java.rmi.RemoteException: chemaxon.nfunk.jep.ParseException: Error while evaluating expression:

check("incorrecttetrahedralstereo")

    The provided checker configuration contains errors. The indexes of invalid checkers: 1-InvalidChecker .

ORA-06512: at "JCHEM.JCHEM_CLOB_PKG", line 34

ORA-06512: at "JCHEM.EXEC_FUNCV", line 44

ORA-06512: at "JCHEM.EVALUATEX_FUNC", line 7

29532. 00000 -  "Java call terminated by uncaught Java exception: %s"

*Cause:    A Java exception or error was signaled and could not be

           resolved by the Java code.

*Action:   Modify Java code, if this behavior is not intended.

Sorry, the correct name of the checker is incorrecttetrahedralstereo. This checker will find the incorrectly drawn tetrahedral stereo centers.

Furthermore, we recommend to apply the wedgeclean standardizer action as part of the standardizer configuration set for the table (as std_config or std_conf:sql  CREATE INDEX parameter) .

Krisztina

One more supplement: there is an additional wedge bond checker implemented in Structure Checker: nonstereowedgebond

Best regards,

Krisztina

Hello Krisztina,  your suggestions are appreciated. 

However I am still getting that same error message (shown in my prev post) when I try:

SELECT jc_evaluate_x('c1ccccc1', 'chemTerms:check("incorrecttetrahedralstereo")') FROM DUAL


or


SELECT jc_evaluate_x('c1ccccc1', 'chemTerms:check("nonstereowedgebond")') FROM DUAL

My last guess is that these Cartridge functions require a separate license. Does that make any sense?

Yes, it does. Structure Checker license is needed.

Krisztina