ChemAxon Forum Archive » Structure manipulation: Reactor, Metabolizer

jc_react and Extended smiles format

User 7b0ee04e66

16-07-2007 13:08:35

Hi,





I am trying to remove the charges from NH+ with the reaction below





Code:
select JC_React('[N;+1:1]([H])>>[N:1]', 'C[C@@H]1CCC([NH3+])C[C@@H]1C |r|', 'method:a..outFormat:cxsmiles')from dual






and the result is C[C@@H]1CCC(N)C[C@@H]1C, which means that I have lost the fact was the stereochemistry in my molecule was relative.





I have also tried


Code:
select JC_React('[N;+1:1]([H])>>[N:1]', 'C[C@H]([NH2+]C1CC[C@@H](C)[C@@H](C)C1)C(O)=O |a:1|', 'method:a..outFormat:cxsmiles') from dual






In that case, I get the error message below


Code:
ORA-29532: Java call terminated by uncaught Java exception: java.lang.Exception: The following exception has been thrown by the servlet:


Exception:


Some features of [#6][C@H](NC1CC[C@@H]([#6])[C@@H]([#6])C1)C(O)=O cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format.


ORA-06512: at "JCHEM.JCHEM_CORE_PKG", line 320


ORA-06512: at "JCHEM.REACT_FUNC", line 11






How can I specify that my reagents are Extended Smiles in the Option part?





Thanks


Catherine





PS I have tried this with JChem 3.2.6

ChemAxon d76e6e95eb

16-07-2007 13:21:07

Thanks for reporting this issue, we are examining the problem and will get back to you soon.

ChemAxon aa7c50abf8

17-07-2007 16:25:37

Catherine,





Please, replace the double dots between the options in the third parameter with space:





Code:
select JC_React('[N;+1:1]([H])>>[N:1]', 'C[C@@H]1CCC([NH3+])C[C@@H]1C |r|', 'method:a outFormat:cxsmiles')from dual






Thanks


Peter

User 7b0ee04e66

17-07-2007 16:38:38

Hi Peter,


Thanks a lot. It works.


To clarify, when do we need to use '..' between parameters?


Does this ever apply to reactions options? Or does it only apply to Standardizer options?


Thanks


Catherine

ChemAxon aa7c50abf8

17-07-2007 16:58:14

Catherine,





The default separator is the space character for the options of jc_react. You can use a custom separator, though, to make the pattern resemble that of the Standardizer actions:





Code:
select JC_React('[N;+1:1]([H])>>[N:1]', 'C[C@@H]1CCC([NH3+])C[C@@H]1C |r|', 'sep=.. method:a..outFormat:cxsmiles')from dual






(There is a space after sep=.. to mark the end of the separator string -- barely visible here.)





Please, see:


http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_react and


http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html#option_list_parameter





Without the custom separator the options string 'method:a..outFormat:cxsmiles' is interpreted as the option 'method' having the value of 'a..outFormat:cxsmiles' -- which is actually a bug in jc_react (should rather throw an exception). I will fix this.





Thanks


Peter

User 7b0ee04e66

18-07-2007 08:07:13

Thanks, this was very useful


Catherine