Hi Gosia,

you may want to look at the CombineMols() function in the rdmolops module. If you make a single molecule out of the two fragments, then you should manage to get what you are looking for.


Cheers,
p.

On 06/21/17 14:47, gosia olejniczak wrote:
dear RDKit experts,

is it possible to calculate RMSD value between two non-covalent molecular complexes?

For instance:
complex1: X(conformer1) + H2O
complex2: X(conformer2) + H2O

i tried GetBestRMS and GetO3A.Align but the program clearly neglects H2O and calculates the RMSD only between X(conformer1) and X(conformer2)

thank you!
best regards,
gosia


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