TPSA from cartridge fails on a structure

Cartridge fail to calculate TPSA for the following structure, however, if I use Marvin Sketcher's Tool menu, it manages to calculate a tpsa value.





select jc_evaluate('CC[C@H]1NC(=O)C(N(C)C(=O)[C@H](C(C)C)N(C)C(=O)[C@H](C(C)C)N(C)C(=O)[C@H](C(C)C)N(C)C(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@@H](C(C)C)N(C)C(=O)[C@H](NC(=O)[C@H](C(C)C)N(C)C(=[0])CN(C)C1=O)C(C)C)[C@H](O)[C@H](C)C\C=C\C','PSA') from dual;





gives error message:





ORA-29532: Java call terminated by uncaught Java exception:


java.lang.RuntimeException: The following exception has been thrown by the


servlet:


Exception: Error while evaluating expression:


PSA


Calculation result is not defined for query molecules.


Calculation result is not defined for query molecules.


ORA-06512: at "JCHEM_CARTRIDGE.JCHEM_CORE_PKG", line 0


ORA-06512: at "JCHEM_CARTRIDGE.EVALUATE_FUNC", line 10

There is a syntax error in your SMILES string. An (=[0]) instead of (=[O]), so a numerical zero instead of a letter.

Seems someone types the smiles by hand!





The error reminds me another problem. I once use molconvert to convert a sdf to smiles, it crashes because one of the structures in the SDF is actually is invalid (can only be represented by smarts as a result). So I have to manually delete that entry in order to obtain smiles for the rest. I just wonder probably molconvert should try to process the whole file and give smarts as the output, then give a warning at the end to alert user to the problem, instead of just quit.

The question remains, I paste the "bad" smiles into Marvin


http://www.chemaxon.com/marvin/doc/dev/example-sketch1.1.html





The use the PSA(2D) tool, it gives 230.30.





So if Marvin is robust enough to handle the smiles, why cartridge has to fail?

We are examining the issue and will get back soon.

Hi,





The [0] SMILES notation (atom with zero weight) was treated as "Any atom" in Marvin, until we have fixed this behaviour. From Marvin 4.1.3 such faulty structures will not be imported.


Sorry for the delayed answer.





Best regards,


Zsolt