As you found, the --canonical solution is not at all the efficient way
to do this. Here's the proper way to do this using Tim's
OBIsomorphismMapper (which uses the VF2 graph matching algorithm I
believe).
import pybel
ob = pybel.ob
mol = pybel.readstring("smi", "CC(=O)Cl")
molb = pybel.readstring(
Hi there,
I'm trying to obtain a rotation matrix between two pdb files containing the
same protein. For many of them the following script works perfectly:
# Load files in OBMol
S = next(pybel.readfile('pdb',struc))
S.removeh()
T = next(pybel.readfile('pdb',target))
T.removeh()
# Align
align = op
