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

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

Ahh apologise, I misunderstood the question! I thought it seemed a bit simple!

Best,
Nick

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On 21 Apr 2015, at 18:08, James Davidson <J.D...@ve...<mailto:J.D...@ve...>> 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:Nic...@ic...<http://icr.ac.uk>]
Sent: 21 April 2015 17:44
To: James Davidson; rdk...@li...<mailto:rdk...@li...>
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 nic...@ic...<mailto:nic...@ic...> | W www.icr.ac.uk<http://www.icr.ac.uk> | Twitter @ICRnews

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