MolConvert options?

Hi,

I was hoping to be able to use the MolConverter Knime node to strip explicit hydrogens from SD files, but it seems that the options that can be used with command-line molconvert (-Y for removing explicit hydrogens) are not supported. Or are they?

Thanks

Hi,

In a command-line tool it makes more sense to mix different functionality into one unit.

In a pipeline environment it's ususally better to keep functions separated.

You can remove the explicit H atoms with the Standardizer node - have you tried it yet ?

 

Best,

 

Szilard

Hi,

The Standardizer node presumably requires a license?

HomerE wrote:

Hi, The Standardizer node presumably requires a license?

Yes, you need a license for the JChem Extension nodes.

(opposed to the Marvin nodes which are free)

However H removal and some other simple actions do not need an additional Standardizer license.

http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#notes

 

Some Standardizer actions ("aromatize", "aromatize:b", "dearomatize", "addexplicitH", "removeexplicitH", "wedgeclean","convertwedgeinterpretation") do not require a license key: standardization composed of these actions only can be run unlimited even without license.