Ahh apologise, I misunderstood the question! I thought it seemed a bit simple!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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On 21 Apr 2015, at 18:08, James Davidson
<[email protected]<mailto:[email protected]>> wrote:
Hi Nick,
Well on the plus side I don't get a segfault(!)
On the minus side - unfortunately I think this approach only gives the length
of the shortest path, rather than a list of the atom ids in the shortest path.
Kind regards
James
-----Original Message-----
From: Nicholas Firth [mailto:[email protected]<http://icr.ac.uk>]
Sent: 21 April 2015 17:44
To: James Davidson;
[email protected]<mailto:[email protected]>
Subject: RE: Python GetShortestPath()?
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)NCC
3=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]<mailto:[email protected]> | W
www.icr.ac.uk<http://www.icr.ac.uk> | Twitter @ICRnews
________________________________________
From: James Davidson [[email protected]<mailto:[email protected]>]
Sent: 21 April 2015 17:06
To:
[email protected]<mailto:[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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