problem of standardization

Hi,

 

I insert structure via jchem manager 6.0.1 and i have a xml file for business rules (standardizer_CN.xml)

I remark that some structures are not correctly standardized (see file : 2013-12-17_12.sdf before insertion and 2013-12-17_12_st.sdf after ) .

The rule Z-aro-N-oxide2 is not well applied for the 2 first molecules and the rule iodoxy is not applied for the third molecule.

 

I try to run :

 

standardize -c standardizer_CN.xml 2013-12-17_12.sdf -f sdf -o 2013-12-17_12_st.sdf

 

the same problem ...

 

with files

with files 

Hi,

I move your question to the forum of Standardizer questions. Your question will be answered soon.

Best regards,

Krisztina

Hi,

In case of the iodoxy rule, you should modify your transformation in order to fit the third molecule. One "A" atom (any atom except H) should be changed to "AH" (any atom including H) in the transformation rule. I have attached the new transformation.

As for the Z-aro-N-oxide2 rule, what is your expected result? What are the desired forms of your first two molecules? Could you please specify? Because in my opinion this rule works as defined in the transformation.

Best wishes,

Ágnes

you are right : my business rule Z-aro-N-oxide2 is incorrect.

and for odoxy rule, you are right too.

Hi,

 

I thought that rule aromatize is applied in structure by default.

In my xml file, this rule "aromatize" is not defined. So could you confirm i have to add this rule to the xml file?

 

Thanks

Custom standardization overwrites the default. So, please add removeexplicitH and aromatize actions to your xml file.  It is recommended to place aromatize as the last action.

Best regards,

Krisztina

Hi,

 

Thanks but in it is written here : http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#noteOrder

 

that In most cases it is best to put it first in the configuration for aromatization rule...

Yes, you are right, the most important issue is, that -  after the execution of the standardization steps - the structure must be in aromatized form.

Krisztina