Question: drawing chemical from smile 2D/3D
gravatar for Stane
8 weeks ago by
Stane20 wrote:


I have been drawing chemical from smile using python package rdkit and I was wondering if it could be possible to do the same from R as I am using R much more in my work. I played with ChemmineR which seems great but I can't figure out how to make it work fully.

first if I try converting my smile to sdf I get this error 

Error in validObject(.Object) : 
  invalid class “SDFset” object: invalid object for slot "ID" in class "SDFset": got class "NULL", should be or extend class "character"

It seems that installing ChemmineOB solve this problem and the plot function let me see the basic structure of my chemical but then trying to get better figure using the visualize function return the following error : An error occured. Please try again

Finally there is the 3D function generate3DCoords which seems to work but then how to plot it ? because using the plot function is not showing anything useful.








ADD COMMENTlink modified 8 weeks ago by Thomas Girke1.6k • written 8 weeks ago by Stane20
gravatar for Thomas Girke
8 weeks ago by
Thomas Girke1.6k
United States
Thomas Girke1.6k wrote:

The online structure viewing via sdf.visualize() is working again. The server needed a restart. Thanks for letting us know.

Please note, the structure rendering functionalities in ChemmineR and the affiliated online service are for 2D encodings, 3D representations are not expected to look good. If you need 3D support then you may want to consider using a standalone structure rendering tool like Avogadro ( 


ADD COMMENTlink written 8 weeks ago by Thomas Girke1.6k

Thank you Thomas for your help the recommendation about Avogadro !

ADD REPLYlink written 7 weeks ago by Stane20
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