Hi,
Fredrik- thanks, that's working for me now.
I am using the following simple python script to run the rmsd calcs on two
conformers from two files:
import pybel
file1 = 'conf1.mol2'
file2 = 'conf2.mol2'
ref = pybel.readfile('mol2', file1).next()
tar = pybel.readfile('mol2', file2).next()
align=pybel.ob.OBAlign()
align.SetRefMol(ref.OBMol)
align.SetTargetMol(tar.OBMol)
align.Align()
rmsd=align.GetRMSD()
print rmsd
Just thought this might be helpful for any other new people reading.
Cheers,
Scott
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