Is it possible to store non saturated by H molecules?

User 5aca842213

12-01-2011 16:36:23

Hello


I'm having a problem when searching substructures containing for example just one H. The molecules are stored, by default saturating all the "empty" bonds with H. Is it possible to store systems without any kind of saturation?


I would like to be able to search for the exact substructure, even if this one just contains one H.


I'm using JChem Base to store molecules and the db_search sample to search them. The application db_search was installed into a Tomcat server.


Thank you very much.


Best regards,

User 5aca842213

12-01-2011 19:59:22

In the searching.jsp I placed this new line, before searcher.run();:

searchOptions.setImplicitHMatching(SearchConstants.IMPLICIT_H_MATCHING_DISABLED);

Before this modification all molecules matches when searching for H. Now no matching hits, and there are molecules with explicit H.

What's missing? Any idea?

Thank you

Best regards

User c1ce6b3d19

12-01-2011 21:25:01

Can you please give us an example of the molecules with "empty" bonds that you are storing?


Perhaps this is a case of explicit vs. implicit hydrogens.


Thanks,


Jon

User 5aca842213

13-01-2011 14:58:41

Just a screen shot of a sample molecule The 3 explicit H of the molecule are not searchable even they exist.

If I draw for example just one H on the search screen nothing is found if I place this code in the searching.jsp
searchOptions.setImplicitHMatching(SearchConstants.IMPLICIT_H_MATCHING_DISABLED);

If the property is enabled, then all the molecules of the database are found. And not all of them have explicit H. I think it's because of the implicit H.

Thank you.

Joan

ChemAxon a3d59b832c

13-01-2011 16:40:39

Hi Joan,


 


Yes, for chemistry it should not matter how the hydrogen is formulated - explicit or implicit. This is why it works like that by default.


And yes, you have found the right searching option to switch off this behaviour, but one further thing needs to be changed to use it in a database. By default, the table standardization contains aromatization and hydrogen removal (changing explicit H to implicit). You have to use a custom standardization that only contains aromatization.


 


For more details, see:


http://www.chemaxon.com/jchem/doc/dev/dbconcepts/index.html#standardizerintegration


 


I attach the needed standardization configuration here.

User 5aca842213

13-01-2011 18:17:48

Thanks a lot!! Now it's working fine!!