separation of counter ions of additional framents

Hello,

please find attached my code for removing the counter ions. it runs well.

But in the next step I want to store the couniter ion in a separate table. Therefore I changes action string  "keepone" with "removelagest" as described in the standardizer examples. But this crashed. Can you please tell me the action key to remove the large molecule that I can store the counter ions seperately.

Thanks for helping me

ottens

Hi Ottens,

Standardizer is not used in your code example, so we do not have enough information to invastigate the reported issue. Please attach a code example where chemaxon.reaction.Standardizer is used to perform the standardization, and attach the standardizer configuration file/string as well.

Zsolt

Hi Zsolt,

 

oh sorry it was the wrong javaClass. You are right.

as attachement ist the correct javaCode.

 

thanks alot

 

can anyone help please ?

 

thanks

ottens

The attached code (StandardizerTest.java) runs without any error, and produces the attached output (out.sdf).

I'm not sure what dou you mean by  "Therefore I changes action string "keepone" with "removelagest" as described in the standardizer examples. But this crashed.". Pleas attach a code which can be used to reproduce the crash.

Zsolt

Hi Zsolt,

And Again

Here I send you a sd-file and a standardizer configuration file:

1. There an incorrect operation (molecule 2) only for molecule 6 an
     Exception is thrown.

     The molecule coming from sd-file of compound vendors (our raw data).
     Molecule 2 should resulting in a empty record. if there is only one
     fragment it should handled as the largest ! Is there a method to
     count the number of fragments (counterinos and additional
     molecules) in a molecule ?

2. If there are a complex like in molecule 6 than I would prefer to
    separate the whole complex as largest molecule, but without ungroup
    routine in the xml file an Exception is thrown in the standardizer
    gui in the source code nothing is done with the 6th molecule. How can
    we solve this problem ?

3. is it possible to define this xml file also a action string ?

 thanks alot

Ottens

Hi Ottens,

 

1. Removal action of the standardizer can not remove the last fragment of the molecule. If the target molecule has only one fragment, the removal action does not do anything. It seems, that our documentation does not mention this, we will correct the documentation.
For counting the fragments of the molecule, you could use the topology analyzer plugin as described here: http://www.chemaxon.com/marvin/help/calculations/geometrygroup.html#topolanal

2. We are investigating the exception regarding the 6th molecule. It seems to me, that Multiple S-groups are not handled correctly by the Removal action.
I will inform you with the results.

3. Since version 5.11 all XML configurations can be defined as actionstrings. We also have a tool - that is not in the public API yet as interface may change in the upcoming version, but can be used for now - chemaxon.standardizer.configuration.ConfigurationConverter, that can be used from API to convert XML configurations to actionstring configuration.

The actionstring for the provided XML is:
sgroups:ungroup..removal:method=removelargest:measure=atomcount

 

Best Regards,

Imre

 

Hi Imre,

thank you for helping me