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("smi", "CC(Cl)=O")
mol.make3D()
molb.make3D()
mol.removeh()
molb.removeh()
query = ob.CompileMoleculeQuery(mol.OBMol)
mapper = ob.OBIsomorphismMapper.GetInstance(query)
mapping = ob.vpairUIntUInt()
mapper.MapFirst(molb.OBMol, mapping)
print list(mapping)
# Result: ((0, 0), (1, 1), (2, 3), (3, 2))
molb.OBMol.RenumberAtoms([x[1]+1 for x in mapping])
Hopefully something similar will work for you.
- Noel
On 30 November 2012 14:58, dalvarez <algarcia.dan...@gmail.com> wrote:
> 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 = openbabel.OBAlign(False,False)
> align.SetRefMol(S.OBMol)
> align.SetTargetMol(T.OBMol)
> if align.Align():
> OBrotMat = align.GetRotMatrix()
>
> The problem comes when the atom order is not the same in the two files.
> As suggested in other posts, i tried:
>
>> babel input.pdb -O output.pdb --canonical
>
> But it results in a Segmentation Fault, or memory failure due to the large
> number of atoms in the file.
> Anyone can help me working this out? What methods, classes should i use to
> do this job within the script before the alignment?
>
> Thanks in advance!
>
> Daniel
>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/match-atom-order-in-two-pdb-files-of-same-molecule-tp4655723.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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