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?
- The match to the SMARTS is to exclude from the alignment, so did I get
it right if the one below is the procedure to do it, or is there a
SMARTer (sorry, the pun was too tempting) way? Although this seems
similar to the old (non-working) way.
ob = pybel.ob
smarts = pybel.Smarts("[OH]C=O")
atomlist = []
for i in smarts.findall(mol):
for j in i:
atomlist.append(j),
for atom in mol:
if atom.OBAtom.GetIdx() not in atomlist:
reference.append(atom.vector)
ob.OBAlign().SetTarget(reference)
...
- Why ob.OBAlign().GetRMSD() should not work after using
ob.OBAlign().Align() with this procedure? I am not sure why shall I
apply the rotation matrix.
Thanks a lot for your help!
Best,
Pepe
On 30/05/14 19:46, Noel O'Boyle wrote:
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 the molecules to its centroid and applying the
rotation matrix. (I can explain more if this is confusing.)
- Noel
On 24 May 2014 13:14, Giulio Pepe <gp...@cam.ac.uk
<mailto:gp...@cam.ac.uk>> wrote:
Hi there,
I am building a script in python that removes a certain moiety
from two
molecules and calculates the RMSD between the remaining structure.
I am doing this by asking for one or more SMARTS strings to find
in the
molecules, labelling these atoms and deleting them using
OBMol.DeleteAtom(). Then, I align the molecules and find the RMSD
using
the OBAlign() class.
This works fine for some SMARTS string, but for others it gives a very
high and unrealistic RMSD value. I investigated the reason for
this and
I found out that this is caused by a bad alignment of the two
molecules.
I suspect that this is caused by a disordering of the atom labels
caused
by removing certain SMARTS strings. I tested this by printing the
canonical labels.
I tried to renumber the atoms using OBMol.RenumberAtoms(),
unsuccessfully. Symmetry should not be a problem in these molecules.
Did anyone come across this, or have a better solution? I am
attaching a
simplified version of my code below:
import pybel
ob = pybel.ob
mol = [mola,molb]
smarts = [pybel.Smarts("[OH]C=O"),pybel.Smarts("C=C(C#N)C(=O)O")]
for mols in mol:
mols.OBMol.StripSalts()
mols.removeh()
if removemoiety:
for ligands in smarts:
i = 0
todelete = []
for mols in mol:
todelete.append([])
for atom in mols:
for l in ligands.findall(mol[i]):
if atom.OBAtom.GetIdx() in l:
todelete[i].append(atom.OBAtom)
i += 1
j = 0
for mols in todelete:
for atom in mols:
mol[j].OBMol.DeleteAtom(atom)
j += 1
align = ob.OBAlign()
align.SetRefMol(mol[0].OBMol)
align.SetTargetMol(mol[1].OBMol)
align.Align()
print align.GetRMSD()
Thank you very much for your help!
Best,
Pepe
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