Hi Brian,
when you fetch a Chem.Atom object from a Chem.Mol a Python object is
created on-the-fly that wraps the underlying C++ object.
Every time you do this, a new Python object is created. This does not apply
only to GetNeighbors(); please see an example below:
In [1]: from rdkit import Chem
In [2]: mol = Chem.MolFromSmiles("C")
In [3]: a0_1 = mol.GetAtomWithIdx(0)
In [4]: a0_2 = mol.GetAtomWithIdx(0)
In [5]: a0_1 == a0_2
Out[5]: False
In [6]: a0_1
Out[6]: <rdkit.Chem.rdchem.Atom at 0x7fd2de00e5d0>
In [7]: a0_2
Out[7]: <rdkit.Chem.rdchem.Atom at 0x7fd2de0195d0>
In [8]: a0_1.GetIdx() == a0_2.GetIdx()
Out[8]: True
In short, you cannot rely on comparing Chem.Atom object identity, but you
can certainly rely on their index.
Cheers,
p.
On Fri, Jan 8, 2021 at 5:00 AM Brian Peterson <brian.peter...@molsight.com>
wrote:
> 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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