User d8da4712c1
22-07-2013 14:40:55
Please refer to this post cause I can't change it's section
User d8da4712c1
22-07-2013 14:40:55
Please refer to this post cause I can't change it's section
ChemAxon aa7c50abf8
22-07-2013 16:41:25
Hello,
Do the SQL queries return the same result consistently -- meaning the one with benzene always returns zero hits and the one with naphthalene always return 6 hits?
Thanks,
Peter
User d8da4712c1
22-07-2013 17:34:10
Yes Peter
ChemAxon aa7c50abf8
23-07-2013 08:14:38
Please, could you post
1.) the output of the following SQL:
select jchem_core_pkg.getenvironment from dual;
2.) the SQL which you used to create the JChem index
?
Thanks,
Peter
User d8da4712c1
23-07-2013 08:20:56
I'm using the default index, created by Jchem installation.
GETENVIRONMENT
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Oracle environment:
Oracle Database 11g Release 11.2.0.3.0 - 64bit Production
PL/SQL Release 11.2.0.3.0 - Production
CORE 11.2.0.3.0 Production
TNS for Linux: Version 11.2.0.3.0 - Production
NLSRTL Version 11.2.0.3.0 - Production
JChem owner: SYSADMIN
JChem Server environment:
Java VM vendor: Oracle Corporation
Java version: 1.7.0_19
Java VM version: 23.7-b01
JChem version: 6.0.1
JChem Index version: 6000000
JDBC driver version: 11.1.0.7.0-Production
1 rows selected
ChemAxon aa7c50abf8
23-07-2013 08:39:01
Do you use default standardization on the structure table?
User d8da4712c1
23-07-2013 08:53:53
no custom one.
ChemAxon abe887c64e
23-07-2013 10:03:27
Hello,
It seems that JChem's default standardizer actions (aromatization and removing explicit hydrogens) are missing from the applied standardizer configuration file. Please add these two actions to the config file and change the settings of the table accordingly.
See documentation about default standardization: https://www.chemaxon.com/jchem/doc/user/query_standard.html
See documentation about table settings: http://www.chemaxon.com/jchem/doc/admin/#table_settings
Best regards,
Krisztina
User d8da4712c1
23-07-2013 10:37:09
It works now, thanks.
User d8da4712c1
23-07-2013 10:48:18
We don't understand why we should apply (remove explicit hydro. ) cause in some cases the user don't want so!
ChemAxon abe887c64e
23-07-2013 11:05:06
Yes, sorry, I have to add that removing explicit hydrogens is not so compulsory as aromatization, but helps to compare the hydogens in the later search processes.
Remove explicit hydrogen action converts explicit hydrogens to implicit ones, and has more options for specifying which hydrogens to remove (bridgehead, charged, isotopic, lonely, wedged, ...). See:
https://www.chemaxon.com/marvin/help/developer/core/hydrogens.html
Best regards,
Krisztina
ChemAxon 9c0afc9aaf
23-07-2013 12:05:26
| idrissdev wrote: |
We don't understand why we should apply (remove explicit hydro. ) cause in some cases the user don't want so! |
The reason we include and recommend this in the default standardization is performance.
The target graph will be smaller, thus the search is faster, and the structure consumes less memory in the structure cache.
Also the cd_smiles field will be shorter, so it's less likely that it cannot fit into the column size (e.g. 4000 for VARCHAR2), which would mean a NULL value, and greatly increased search time on these structures.
In practice it's probably not too common to import structures with explicit H atoms drawn everywhere, but it's a good practice to include this action.
Of course we do not remove the H atoms where they could mean a diffrece: this action is never executed on the query structure and by default H atoms with extra info are kept (e.g. isotopes, etc.)
Szilard
User d8da4712c1
23-07-2013 12:35:49
Ok thanks, but why did that affect our search results?
User d8da4712c1
23-07-2013 14:21:02
Another bug with the same results issue, what I did ?--> I deleted all structures from the table then inserted them again, the search results give the same problem mentionned above.
the problem is resolved only when I go to jchemanager (after the insertion is done) --> table option then apply a standerdizer ( with or without the new two rules)
Thanks.
ChemAxon aa7c50abf8
23-07-2013 15:05:18
I am afraid I don't understand. You said earlier that changing the Standardizer configuration helps. And now you seem to say that until you change the Standardizer configuration, you don't see a change in the search behaviour. This second observation seems consistent with the first to me. Where is the problem?
Thanks,
Peter
User d8da4712c1
23-07-2013 15:11:41
it works when, I do this in order:
1-Insert structures
2-go to jchemanager ---> table options ---> modify the standerdizer xml config file ( if the two rules are there ---> remove them, if the two rules are not there ---> add them )
3-apply the new standerdizer rules
4-search results ---> good.
it doesn't work:
1-delete all structure from jchem table
2-insert them again
3-search results ---> same problem mentionned at first post.
4-I tried to do this with standerdizer with or without new two rules
Hope that helps.
Thanks.
Regards,
Idris
ChemAxon aa7c50abf8
23-07-2013 15:36:53
In the "doesn't work" case, you do step #4 (changing the Standardizer configuration) the same way as step #2 in the "works" case, don't you. I.e. you use the JChem Manager and modify the Standardizer XML configuration file in the table options menu, correct?
Peter
User d8da4712c1
23-07-2013 15:38:43
Yes, but I only do it before the insertion.
ChemAxon aa7c50abf8
23-07-2013 15:56:36
You commit your work after done with both the deletions and the inserts, correct?
User d8da4712c1
23-07-2013 15:57:37
Yes
User d8da4712c1
23-07-2013 15:58:17
Like I said it's the same problem, so it only doesn't work with some requests.
ChemAxon aa7c50abf8
23-07-2013 16:01:15
Did you do the inserts and the deletes with JChem Manager?
User d8da4712c1
23-07-2013 16:05:41
no, inserts with my php script and deletes with sql.
ChemAxon aa7c50abf8
23-07-2013 16:13:54
Your PHP script uses jc_insert I assume, correct?
Please, could you post the SQL you used to delete the structures?
Thanks,
Peter
User d8da4712c1
23-07-2013 16:15:49
Delete * from sub_structure;
Yes jc_insert.
User d8da4712c1
23-07-2013 16:19:08
delete from sub_structure;
ChemAxon aa7c50abf8
23-07-2013 16:20:12
You should use jc_delete to delete from JCB structure tables that will be searched using JChem Cartridge. Does the problem persist, if you use jc_delete?
User d8da4712c1
25-07-2013 09:16:46
It works now, thank you so much ^_^