Hi Ling,
On Mon, Jun 19, 2023 at 3:03 AM Ling Chan <lingtrek...@gmail.com> wrote:
>
> I got some questions about atom indexing. Just wonder if you could help me?
>
> 1. In m3=Chem.CombineMols(m1,m2) , is it guaranteed that the atom
> indices in m3 is equivalent to the indices in m1 followed by the indices in
> m2?
>
> Yes
>
> 1. If I construct an editable mol from m1, is it that the atomic
> indices in the editable mol is equivalent to that in m1? And when I convert
> the editable mol back, suppose the atom indexing is also preserved?
> 2.
>
> Yes
>
> 1. Same as #2, but for an RWMol instead of an editable mol.
>
> Yes
>
> 1. If I delete an "F" atom from an editable mol, is there a way to
> mark the atom in the new mol that was originally bonded to the "F"? I mean,
> if I get its atomic index before the deletion, suppose it won't be
> preserved.
>
> You can set a property on the neighboring atom with something like:
atom.SetProp("F_Neighbor","1")
>
> 1. Similar to #4, but for DeleteSubstructs.
>
> Same answer: you can always use SetProp
> Alternatively, if there is a way to mark atoms, I don't need the atom
> indices anyway.
>
As mentioned, SetProp is great for this. Note that using the property
interface is slower than just relying on the indexing remaining the same,
which you can do in the first two cases.
best regards,
-greg
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