[Rdkit-discuss] GetMolFrags asMols with persistent atom indexes

[Joshua M. <jos...@be...>]

Hey All,

I am chopping parts out of molecules and picking up the pieces using the
Chem.GetMolFrags() function.
I would like to separate fragments into distinct mol objects but keep the
original atom indexes however setting the asMols=True flag seems to reset
the indexes, is this expected behaviour? Is there a way around this?

Here's some code:

In [1]: from rdkit import Chem

In [2]: m = Chem.MolFromSmiles('c1ccccc1.CCO')

In [3]: Chem.GetMolFrags(m)
Out[3]: ((0, 1, 2, 3, 4, 5), (6, 7, 8)) <----- desired indexes

In [4]: frags = Chem.GetMolFrags(m, asMols=True)

In [5]: for frag in frags:
   ...:     print([a.GetIdx() for a in frag.GetAtoms()])
   ...:
[0, 1, 2, 3, 4, 5]
[0, 1, 2] < ------ indexes have been reset


Many thanks in advance,
Josh