cis / trans stereochemistry and Exact search

Hello,





I just wanted you to confirm that the following is expected behaviour as of JChem version 3.0.12.





I have two molecules whose SMILES were generated by JChem 3.0.12 as follows:





Oc1ccc(Br)cc1\C=N/NC(=O)c2cnccn2


Oc1ccc(Br)cc1\C=N\NC(=O)c2cnccn2





Clearly one is a 'cis' and the other a 'trans' version according to the SMILES. However, on searching for either using exact match both structures are returned and the fingerprints appear to be identical. Is this the expected behaviour? Is it possible for E/Z information be coded in the fingerprints? Can tetrahedral chirality be coded in the fingerprints?





Cheers,





Daniel.

inhibox wrote:

Is this the expected behaviour?

Yes, if you are using the default settings for the jsp application, it should retrieve both configurations. However, you can fiddle with the setDoubleBondStereoMatchingMode() method:





http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#setDoubleBondStereoMatchingMode(int)


http://www.chemaxon.com/jchem/doc/api/chemaxon/jchem/db/JChemSearch.html#setDoubleBondStereoMatchingMode(int)





See the relevant section of the JChem Query Guide:





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





Alternatively, you may use PERFECT matching instead of EXACT. PERFECT means that all of the molecules' properties must exactly match,


including stereochemistry.





In the Query Guide this section discusses the difference between EXACT and PERFECT modes:





http://www.chemaxon.com/jchem/doc/user/Query.html#otherSearchTypes width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> inhibox wrote: Is it possible for E/Z information be coded in the fingerprints? Can tetrahedral chirality be coded in the fingerprints? Neither E/Z nor chirality information are coded in the fingerprint, but rather the atom by atom search handles these features, which is following the fingerprint screening. (This way it is possible to fine-tune searching stereo features as described above. You can even switch stereo matching off with method setStereoMatching(false).)





Best regards,





Szabolcs

In which JSP page can I make a call to


setDoubleBondStereoMatchingMode in order to set the desired mode


(I've just searched them all for the above string but to no avail)





What are the int input values that this method expects and which mode does each value correspond to?





DBS_NONE: No double bond cis/trans is considered.


DBS_MARKED: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only.


DBS_ALL: All double bonds are checked for cis/trans stereo matching.





Once I have set DBS_ALL via this method, then exact search should distinguish my cis/trans?





Presumably the perfect search is not implemented in the vanilla JSP application? Would this be complicated to implement?

Daniel,





Szilard will soon contact you about the JSP-related questions.

inhibox wrote:

In which JSP page can I make a call to setDoubleBondStereoMatchingMode in order to set the desired mode (I've just searched them all for the above string but to no avail) What are the int input values that this method expects and which mode does each value correspond to? DBS_NONE: No double bond cis/trans is considered. DBS_MARKED: (Default) Double bond cis/trans stereo is checked for double bonds designated by the stereo search flag only. DBS_ALL: All double bonds are checked for cis/trans stereo matching.

These constants are defined in class chemaxon.struc.StereoConstants, and their numerical values are quoted below:

Quote:

DBS_NONE: 2 DBS_MARKED: 1 DBS_ALL: 0

inhibox wrote:

Once I have set DBS_ALL via this method, then exact search should distinguish my cis/trans?

Yes. Alternatively, you can set the "stereo search" square on your query double bonds using the popup menu of the bond. Select menu item "Attributes/Stereo search" for that.





Best regards,


Szabolcs

Hi Dan,





If you do not wish to put the stereo boxes on the double bonds that should be considered as Cis/Trans, you can modify the code the following way to consider stereo for all double bonds:





In the vanilla JSP application look for the line

Code:

searcher = new JChemSearch();

in searching.jsp.





After this line certain options are specified for JChemSearch.


You can also specify here the desired matching mode:

Code:

searcher.setDoubleBondStereoMatchingMode(chemaxon.struc.StereoConstants.DBS_ALL);

Please beware, that before Marvin version 4.0 double bonds with unspecified stereo information (e.g. CC=CC ) will be cleaned to CIS, and will only match CIS configurations in the new matching mode.


From Marvin 4.0 we indicate unspecified double bond stereo with a wiggly bond.





Best regards,





Szilard

Thank you kindly for your comments.





I can and will go ahead and start fiddling now...





Cheers,


Daniel.

Presumably, jcf_equals cartridge function equates to an exact search rather than a perfect search...presumably a perfect search would only be defineable via a user_defined_func which set the method (+more) above as part of it's implementation?

The jcf_equals cartridge function is supposed to do a perfect search. You can do an exact search with

Code:

jcf_compare(<target>,<query>, 't:e')

Peter

The docs for jc(f)_equals:





http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_equals





Peter