IUPAC and traditional name in cartridge

Just install the IUPAC license





1.


select jc_molconvert('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'name') from dual





#>-JC_MOLCONVERT('CC(C)CC1CCC(CC1)C(C)C(O)=O','NAME')---


"2-[4-(2-methylpropyl)phenyl]propanoic acid\n"





Looks good, however, the extra line break "\n" at the end is probably not neccesary.





2.


select jc_molconvert('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'traditionalName') from dual





failed. How do I get traditional name via molconvert?





3.


select jc_evaluate('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'name()') from dual


or


select jc_evaluate('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'traditionalName()') from dual





failed. How do I use name() and tranditionalName as chemical terms?


We are using the latest cartridge version (upgraded two weeks ago).





Error> ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:


java.rmi.RemoteException: Expression name() yields java.lang.String. Expressions must yield one single number!


ORA-06512: at "JCHEM_CART.JCHEM_CORE_PKG", line 96


ORA-06512: at "JCHEM_CART.EVALUATE_FUNC", line 19 (./all_test_full.bee:17)


Error> ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is:


java.rmi.RemoteException: Expression name() yields java.lang.String. Expressions must yield one single number!


ORA-06512: at "JCHEM_CART.JCHEM_CORE_PKG", line 96

Quote:

3. select jc_evaluate('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'name()') from dual or select jc_evaluate('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'traditionalName()') from dual

Please, use jc_evaluate_x instead:

Code:

select jc_evaluate_x('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'chemTerms:traditionalName()') from dual 23:11:40 SQL> / JC_EVALUATE_X('CC(C)CC1CCC(CC1 -------------------------------------------------------------------------------- 2-[4-(2-methylpropyl)phenyl]propanoic acid

Thanks for the quick reply. That addressed question #3 beautifully.

Quote:

2. select jc_molconvert('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'traditionalName') from dual failed. How do I get traditional name via molconvert?

name:t will do the magic here:

Code:

10:00:45 SQL> select jc_molconvert('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'name:t') from dual; JC_MOLCONVERT('CC(C)CC1CCC(CC1 -------------------------------------------------------------------------------- 2-[4-(2-methylpropyl)phenyl]propanoic acid Elapsed: 00:00:00.03

On finding out jc_molconvert syntax in general:





Everything which works for the molconvert command line application should work for jc_molconvert -- with some obvious exceptions such as specifying an output file and the like.





I admit that even knowing this bit of info, I needed some guidance myself to find the answer. The most important trick in this particular case is that you have to look for the answer in the IUPAC Naming documentation instead of the molconvert documentation.





I reproduce the steps here for posterity:





1. Go to the product page: http://www.chemaxon.com/products.html


2. Click on the Calculator plugins menu item in the menu column on the left.


3. Click on the Structure to name item in the unfolding sub-menu items: http://www.chemaxon.com/product/st2name.html


4. Follow the Learn more link: http://www.chemaxon.com/marvin/help/calculations/iupacnaming.html


5. Search for the string molconvert

Quote:

1. select jc_molconvert('CC(C)Cc1ccc(cc1)C(C)C(O)=O', 'name') from dual #>-JC_MOLCONVERT('CC(C)CC1CCC(CC1)C(C)C(O)=O','NAME')--- "2-[4-(2-methylpropyl)phenyl]propanoic acid\n" Looks good, however, the extra line break "\n" at the end is probably not neccessary.

Thank you for making us aware of this. We will provide a fix as soon as possible.





In the meantime, I suggest to use jc_evaluate_x for the same purpose which returns names without the trailing new-line character.

Can one do name-to-structure conversion in cartridge?

E.g:

select jcf.molconvert('bromobenzene', 'smiles:a') from dual

or

select jcf.molconvert('bromobenzene', 'name', 'smiles:a') from dual

(http://www.chemaxon.com/forum/ftopic4725.html).