Hello all. When traversing a molecule's atoms with atom.GetNeighbors(),
the object returned for an atom is not necessarily the same object
returned when the atom is indexed directly from the molecule. This means
one can't directly compare two atoms as objects found while traversing a
molecule via neighbors to see if they are the same atom. It seems a new
object is created for the atom returned by .GetNeighbors(). Is this
expected behavior and what is the reason for this? I've found that the
comparison can be done by using atom.GetIdx(), but wanted to use the
objects themselves for various reasons. Thanks.
Example:
-------------------------
from rdkit import Chem
m = Chem.MolFromSmiles('C(F)(Cl)(Br)(I)')
atoms = [myatom for myatom in m.GetAtoms()]
for myatom in atoms:
print(myatom.GetIdx(),myatom.GetSymbol(),myatom)
print("The neighbors of {} are:".format(atoms[1].GetSymbol()))
for newatom in atoms[1].GetNeighbors():
print(newatom.GetIdx(),newatom.GetSymbol(),newatom)
print("C0 == C0 ?")
print(atoms[0] == newatom)
Output:
----------------------------
0 C <rdkit.Chem.rdchem.Atom object at 0x7f0d429ca760>
1 F <rdkit.Chem.rdchem.Atom object at 0x7f0d429ca850>
2 Cl <rdkit.Chem.rdchem.Atom object at 0x7f0d429ca940>
3 Br <rdkit.Chem.rdchem.Atom object at 0x7f0d429caa30>
4 I <rdkit.Chem.rdchem.Atom object at 0x7f0d429cab20>
The neighbors of F are:
0 C <rdkit.Chem.rdchem.Atom object at 0x7f0d429cac10>
C0 == C0 ?
False
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