Re: [Rdkit-discuss] Python GetShortestPath()?

[Nicholas F. <Nic...@ic...>]

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 nic...@ic... | W www.icr.ac.uk | Twitter @ICRnews

________________________________________
From: James Davidson [J.D...@ve...]
Sent: 21 April 2015 17:06
To: rdk...@li...
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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