Hi there at RDKit,
I have a set of atom indices from a molecule I want to keep, and any atom
which is not in this list I want to discard.
I thought of implementing this as follows:
#!/usr/bin/env python
from rdkit import Chem
mol = Chem.MolFromSmiles("CCC1CNCC1CC")
keep_atoms = [2,3,4] # assume these exist in the above as an example, you
can print the atom ids to check
edit_mol = Chem.EditableMol(mol)
for atom in mol.GetAtoms():
if atom.GetIdx() not in keep_atoms:
edit_mol.RemoveAtom(atom.GetIdx())
I am not sure this is the best implementation (also because it does not
work), but it's a try.
The end result should be an sdf file with only atoms 2,3,4 from the
original molecule.
When I run the above I get:
[15:45:50]
****
Range Error
idx
Violation occurred on line 143 in file
/opt/RDKit_2011_12_1/Code/GraphMol/ROMol.cpp
Failed Expression: 0 <= 6 <= 5
****
Traceback (most recent call last):
File "./test.py", line 12, in <module>
edit_mol.RemoveAtom(atom.GetIdx())
RuntimeError: Range Error
I cannot quite understand this error. Can anyone shed some light?
I mean this is related to me deleting 3 atoms from the molecule, so it
somehow expects the range to be from 0 <= x <= 5 instead of 0 <= x <= 8...
but why is there this check in place?
Many Thanks
-
Jean-Paul Ebejer
Early Stage Researcher
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