Dear Noel,
thanks again, this is of great help.
I think the new code is somehow faulty and for some reason it returns
1.79769313486e+308 for any molecule. The updated code is posted at the
end of the message.
The old code worked for what I thought it was molecules with different
labelling.
Hi Giulio,
Problem 1: check out vectorVector3. Initialized with a list of vector3,
e.g. my_vv = ob.vectorVector3([a, b])
Problem 3: What I meant is that the RMSD only takes into account the
aligned coordinates. If you want to include the RMSD of the other
coordinates, you need to work it out your
Dear Noel,
just a few problems I am stuck with, using this procedure:
- SetRef() and SetTarget() need a vector of vector3 objects as argument.
While vector3 is an OpenBabel class, vector is not (I assume it is the
C++ vector?). How do I feed them a vector? Is a python list going to be
fine?
Try using SetRef() and SetTarget() instead with just the coordinates for
the atoms you want to align (in the same order for both, as given by the
match to the Smarts). Afterwards, if you want the RMSD for the whole
molecule, you can manually calculate the whole molecule RMSD by translating
one of t
