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MolConvert options?
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Evert

Joined: 15 Feb 2008
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Link to postPosted: Tue Aug 09, 2011 1:57 pmPost subject: MolConvert options? Reply with quote

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

Szilard
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Joined: 21 May 2004
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Link to postPosted: Wed Aug 10, 2011 5:45 pmPost subject: Reply with quote

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

Evert

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Link to postPosted: Thu Aug 11, 2011 10:08 amPost subject: Reply with quote

Hi,

The Standardizer node presumably requires a license?

Szilard
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Link to postPosted: Thu Aug 11, 2011 11:02 pmPost subject: Reply with quote

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.


 
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