How to generate 3D structures with Marvin Molconverter node?

Member for

3 years 10 months gcincilla

Hi Marvin lovers,

I'm trying to use Marvin Molconverter node to convert smiles to 3D structures. Googling around I found that in the batch version of molconverter this is done using the “-3” option, and “-3:[prehydrogenize]” to output hydrogen atoms explicitly.

Nevertheless when I add these options in the to the "Output Options" box, the Molconverter node triggers the warning “Unknown option(s)”.

Please, can anybody help in this?

Gio

Comments
Fri, 09/30/2016 - 06:57

Member for

9 years 8 months

tohshima

Hi Gio,

Unfortunately, the node doesn't support the option.
The node supports only the Basic export options and specified options for each format.

It's only available in comercial products now.

Best,
Taka

Fri, 09/30/2016 - 09:07

Member for

3 years 10 months

gcincilla

OK Tohshima, thanks for the info.

Wed, 12/07/2016 - 07:42

Member for

9 years 8 months

tohshima

New Free Marvin Nodes has the following enhancment.

 Improvements
  -MolConverter
   Add 'Remove small fragments' options.
   Add 'Cleaning' options.