<implH> in standardizer

The Version of standardize is 3.1.


I pasted my config file(rule1.xml) and two MRV file.


Please test as the following command:





standardize -c rule1.xml input1.mrv -f mrv -o 1.mrv


standardize -c rule1.xml input2.mrv -f mrv -o 2.mrv





My rule is to keep the wedge H.


You will find implH remove the normal H


and change the wedge H to the normal H at 2.mrv





but keep the wedge H at 1.mrv.





Is it a bug of standardizer?


Best regards

You should specify

Code:

Wedged="true"

in the ImplH task to remove wedged H atoms:

Code:

<implH ID="implh" Charged="True" Isotope="True" Mapped="true" Lonely="true" Radical="true" Wedged="true"/>

or else you can use the Dehydrogenize task to remove lonely, wedged and unspecific H atoms but keep the others (mapped, isotope, ...). You can use Dehydrogenize in the XML config or in a simple action string:

Code:

standardize -c "dehydrogenize" input1.mrv -f mrv -o o1.mrv standardize -c "dehydrogenize" input2.mrv -f mrv -o o2.mrv

Please refer to the Standardizer configuration documentation for configuration issues.

Hi nora





I would like to know


why implH changed the wedge H to the normal H at 2.mrv.

Yes, this is a bug in the release and even in the JChem 3.1.1 release but it has been corrected already - the correction will be available in the next bugfix release, we will let you know when it is ready.