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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