Dear James,
I tried to be helpful and show you how I do it with GetAdjacencyMatrix, however
I ran into my old friend the segmentation fault 11 as there is still some weird
error with this function.
Here's what I have though, should work for you.
>>> from rdkit import Chem
>>> m =
>>> Chem.MolFromSmiles('CC[C@H](CO)NC1=NC(=C2C(=N1)N(C=N2)C(C)C)NCC3=CC=CC=C3')
>>> atomIdx1 = 0
>>> atomIdx2 = 10
>>> print(Chem.GetAdjacencyMatrix(m)[atomIdx1][atomIdx2])
Segmentation fault: 11
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter
@ICRnews
________________________________________
From: James Davidson [[email protected]]
Sent: 21 April 2015 17:06
To: [email protected]
Subject: [Rdkit-discuss] Python GetShortestPath()?
Dear All,
I might be having a ‘moment’ here, but for the life of me I can’t seem to find
the equivalent of RDKit::MolOps::getShortestPath exposed in python(?).
I want to pass in two atom ids, and get back a list of atom ids in the shortest
path. I could possibly try to roll my own by using GetDistanceMatrix() and
GetAdjacencyMatrix(), but I think I may struggle(!).
So, any pointer to GetShortestPath() greatly appreciated!
Kind regards
James
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