Hi there,
I've tried to write a function in Python to generate the Murcko
Framework of a molecule, then remove a ring from the framework. I want
to remove a ring based on the atom ID of the atoms of the ring, rather
than as a substructure so that in the case of a molecule containing
more than one of the same ring, only one ring remains. Therefore I
have used RemoveAtoms to remove each ring atom one by one. My code is
as follows.
def removeRings(mol):
frame = MurckoScaffold.GetScaffoldForMol(mol)
getRings = frame.GetRingInfo()
rings = getRings.AtomRings()
splitFrames = [x for x in range(len(rings))]
for x in range(len(rings)):
editMol = Chem.EditableMol(frame)
for atom in rings[x]:
editMol.RemoveAtom(atom)
splitFrames[x] = editMol.GetMol()
for x in splitFrames:
print Chem.MolToSmiles(x)
However when I use this function I get the following error:
Range Error
idx
Violation occurred on line 143 in file /usr/local/bin/src/
RDKit_2011_03_2/Code/GraphMol/ROMol.cpp
Failed Expression: 0 <= 22 <= 20
I assume that this means that the atom I am trying to remove is not in
the range of the atoms in the framework. I have checked the atom IDs
for all atoms in the framework and all atoms in the rings and they are
within the same range, so I do not understand why I am getting this
error. Can anyone help please?
Many thanks,
Sarah Langdon
PhD student
Cancer Research UK Cancer Therapeutics Unit
Institute of Cancer Research
Haddow Laboratories
15 Cotswold Road
Sutton
Surrey SM2 5NG
Tel: 0208 722 4139
Email: sarah.lang...@icr.ac.uk
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
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