How to get agent name?

User a83cdfbe8a

13-10-2010 08:18:06

I write a reactor  as the following image ,I use the method getAgent(),I can get the agent count .but i can not use getPreferredIUPACName() ,it has exception.How can I get "R2"?Thanks!


Exception information:


chemaxon.marvin.plugin.PluginException: chemaxon.marvin.io.MolExportException: Name generation failed: chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$UnsupportedError: Naming is not supported on this structure: unknown pseudo-atom #134


java code:


int num=mol.getAgentCount();


  for(int jj=0;jj<num;jj++){


  plugin.setMolecule(mol.getAgent(jj));


  plugin.run();


   String preferredIUPACNames  = plugin.getPreferredIUPACName();


  }


 

ChemAxon e08c317633

13-10-2010 09:09:34

The agent cannot be named, because it contains an unknown pseudo-atom (see the error message: "Naming is not supported on this structure: unknown pseudo-atom #134"). I suggest you to catch the PluginException in the for loop, and use SMARTS or some other format instead of name if the exception is thrown.


mol.getAgent(jj).toFormat("smarts"); 

Zsolt

User a83cdfbe8a

14-10-2010 05:04:16










Zsolt wrote:

The agent cannot be named, because it contains an unknown pseudo-atom (see the error message: "Naming is not supported on this structure: unknown pseudo-atom #134"). I suggest you to catch the PluginException in the for loop, and use SMARTS or some other format instead of name if the exception is thrown.


mol.getAgent(jj).toFormat("smarts"); 

Zsolt




Thanks.I have tried all Molecule formats,but I  can not get "R2".and I find another problem that :if the structure has pseudo-atom ,use  "plugin.getPreferredIUPACName()", also throw exception.

ChemAxon e08c317633

14-10-2010 12:25:04

The agent ("R2") seems to be an R-group. Without R-group definition (I can't see it on the image) it's absolutely useless. If there is an R-group definition in the molecule, then you can enumerate it with the Markush Enumeration plugin, and then use the result of the enumeration for generating the agent name.


Zsolt