how to convert cd_structure into a SD record?

I used 'select cd_structure from structure_table where jc_contains(...)...",


and the database returned System.Array with integer numbers. I know this is the compressed record, but how to convert it back to a string with MDL SD format?





Thank you.

Please, check the following thread:


http://www.chemaxon.hu/forum/ftopic529.html.





Look especially at the posting dated Mon Apr 11, 2005 10:05 am.

Here is the screen:

What is the SQL statement triggering this message?

pkovacs wrote:

What is the SQL statement triggering this message?

the command is

Code:

select cd_id, jc_molconvert(cd_structure,'sdf') from structures where jc_contains(cd_smiles,'c1ccccc1')=1;

Thanks

jc_molconvert takes varchar2 arguments. You are trying to use a long raw (cd_structure). I suggest to try something similar to what is proposed in the thread http://www.chemaxon.hu/forum/ftopic529.html as already suggested above.





The next JChem version will introduce full BLOB support. That will allow more flexibility in shaping your SQL statements. Until then you have to go a somewhat more complicated way.

pkovacs wrote:

jc_molconvert takes varchar2 arguments. You are trying to use a long raw (cd_structure). I suggest to try something similar to what is proposed in the thread http://www.chemaxon.hu/forum/ftopic529.html as already suggested above. The next JChem version will introduce full BLOB support. That will allow more flexibility in shaping your SQL statements. Until then you have to go a somewhat more complicated way.

Thanks.





but if I use

Code:

select cd_id, jc_molconvert(cd_smiles,'sdf') from structures where ...

Is there any way to force jc_molconvert to export a structure with 2D coordinates ?





Jun

select cd_id, jc_molconvert(cd_smiles,'sdf -2') from ...

pkovacs wrote:

select cd_id, jc_molconvert(cd_smiles,'sdf -2') from ...

Thanks, however, another problem appeared. This tends to be that the SDF record is too large... Is there any way to bypass this problem?

Blob support in JChem Cartridge will be released very soon (probably as early as next week). In order to take advantage of this new feature, the JChem table must be then created with the cd_structure column being defined as BLOB (instead of LONG RAW, which was the default until recently). One of the new operators will be jc_molconvertbb which will take a BLOB and return a BLOB. This will practically remove the limit on the size of structures.

BLOB support in JChem Cartridge has in the meantime been made available with JChem 3.0.12.