Does the RDKit RMSD Filter node assume the conformers are pre-aligned?

Dear all,

   The question is in the Subject . I would have assumed this information was in the Node Description but this is not the case. 

 

  many thanks

                           John

                        

       

 
 

Hi John,

The molecules do not need to be pre-aligned. The code does a series of standard rigid alignments of the molecules to each other. One alignment is done for each substructure mapping of the molecule onto itself and the best RMS is used in the filter. The multiple alignments are necessary to properly handle symmetric groups. 

You are right that this information should be in the documentation; we will get that fixed.

Best,

-greg