jcsearch question

Hello,


I am trying to run jcsearch on a database and I use

Code:

jcsearch -q "SMARTS" -t:e -f smiles:TCD_ID DB:Compounds

How should I modify the query so that I get the CD_ID from the Compounds database in the output. Currently, it only gives me the smiles string of the hit and not the CD_ID





Thanks

Hi,




jcsearch does not have an option to export data fields.


In fact it is a quite simple command-line application, mostly used only for testing.




Have you tried Instant JChem yet ?


http://www.chemaxon.com/product/ijc.html />


It's easy to install, and it comes with a sophisticated GUI, where you export the current hits, and can specify the fields to export, their order and the file format to export to.




On the other hand if you are looking for a back-end solution, calling jcsearch is not efficient at all, not only because it start a new JVM (Java Virtual Machine), but since non-cached mode is deprecated it loads the cache for the whole DB table during each run, and it's lost when the program exits.


I rather suggest using JChemSearch from our API in this case directly from the application:


http://www.chemaxon.com/jchem/doc/api/chemaxon/jchem/db/JChemSearch.html

http://www.chemaxon.com/jchem/doc/guide/search/index.html />


Best regards,




Szilard

My task is that I have abt 50K compounds in a file and I would like to compare each compound in the file with a database of abt 7 million compounds. I was using a batch command to parse the file and compare each compound with the database. When I used compr, I ran out of Java heap space. So I tried jcsearch which is slow but works fine. I am not certain how instantjchem can help me with this task.


Thanks!

Instant JChem has an "Overlap Analysis" function that lets you compare the contents of 2 databases for similar or identical compounds. This might be quite useful for what you are doing.


See here for details:


http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/performing_overlap_analysis.html />


However a database of 7M compounds is going to need a lot of memory (Java heap space of probably getting on for 1GB) so may not be practical unless you have a "big" machine. But I guess you could break it down into smaller chunks, though obviously this is not ideal.




I suggest you try it one a smaller test set first to see if it meets you needs.




Tim

I guess Instant JChem would be the tool for you. (It can also access JChem tables remotely in mySql and Oracle databases.)





Still, I just checked the code of jcsearch, and the cd_id was available in the right place. So it only needed one line of code to set it in the output. Your proposed syntax above will work in the next JChem release. (Please note that no other fields will be available.)

Dear Chemaxon,





I can't obtain CD_ID with de jcsearch 5.0.02.1 ?





Is it normal ?





Thanks,





Karim.

Yes, jcsearch is not prepared to return data fields in the way as in the question above. However, there is an option to return the cd_id only (without the structure):

Quote:

$ jcsearch -q CCCCCCC -f :Tcd_id DB:jchem_table 14 17 48 94

I hope this helps,


Szabolcs

Sorry, you are right, it used to work before. We will check.

I don't understand ....sorry.





It works or not ? I want to have "cd_id" in result with jcsearch.





Karim.

Sorry for making the confusion. It is working in 5.0.2.1 if only the cd_id is requested:

Quote:

$ jcsearch -q CCCCCCC -f :Tcd_id DB:jchem_table 14 17 48 94

We will check why the "-f smiles:TCD_ID" option stopped working, and will fix soon.





Best regards,


Szabolcs

OK, thanks Szabolcs !





Karim.

tdudgeon wrote:

Instant JChem has an "Overlap Analysis" function that lets you compare the contents of 2 databases for similar or identical compounds. This might be quite useful for what you are doing. See here for details: http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/performing_overlap_analysis.html /> However a database of 7M compounds is going to need a lot of memory (Java heap space of probably getting on for 1GB) so may not be practical unless you have a "big" machine. But I guess you could break it down into smaller chunks, though obviously this is not ideal. I suggest you try it one a smaller test set first to see if it meets you needs. Tim

I just tried this link as I am interested in an overlap analysis of two databases and the related federated search acroxx multiple databases. I get an error indicating the page is not available.

 

Thanks,

Jim

Oops, our web site has been reorganized in the meantime. I am sorry for the inconvenience.

 

The current URL-s are:

Overlap analysis:

http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemistry_functions/performing_overlap_analysis.html

 

Federated search:

http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/managing_data/queries/federated.html

 

(It is also possible to navigate from the main page using menus: Documentation -> Users Guide -> Instant JChem etc.)

 

I will also edit the above posts to point to the correct URL.

Best regards,

Szabolcs