Hi,
There is PathToSubmol() although it takes the list of bonds. If you have
atom indices:
bonds = []
> atommap = {}
for i,j in combinations(atom_path, 2):
> b = ParentMol.GetBondBetweenAtoms(i,j)
> if b:
> bonds.append(b.GetIdx())
NewMol = Chem.PathToSubmol(ParentMol, bonds, atomMap=atommap)
atommap is a dictionary populated with atom indicies mapping from ParentMol
to the new one.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
[email protected]
2016-11-01 11:00 GMT+01:00 Juuso Lehtivarjo <[email protected]>:
> Hi All,
>
> Is there a python function (or any simple way whatsoever) to create a
> substructure mol object from another one based on the given atom
> indices? In C++ this could apparently be done with
> getMolFragsWithQuery, but that does not seem to be much used in python
> wrappers...
>
> Best,
> Juuso
>
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