Juuso,
I think you will find Chem.PathToSubmol(), which takes a molecule and
sequence of *bond* indices, useful:
In [6]: m = Chem.MolFromSmiles('COCc1ccccc1')
In [8]: sm = Chem.PathToSubmol(m,(0,1))
In [9]: sm.UpdatePropertyCache()
In [10]: sm.Debug()
Atoms:
0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
1 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0
2 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
Bonds:
0 0->1 order: 1 conj?: 0 aromatic?: 0
1 1->2 order: 1 conj?: 0 aromatic?: 0
Best,
-greg
On Tue, Nov 1, 2016 at 11:00 AM, Juuso Lehtivarjo <
juuso.lehtiva...@gmail.com> wrote:
> 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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