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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