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:nicholas.fi...@icr.ac.uk] > Sent: 21 April 2015 17:44 > To: James Davidson; rdkit-discuss@lists.sourceforge.net > 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 nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews > > ________________________________________ > From: James Davidson [j.david...@vernalis.com] > Sent: 21 April 2015 17:06 > To: rdkit-discuss@lists.sourceforge.net > 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 > > __________________________________________________________ > ____________ > PLEASE READ: This email is confidential and may be privileged. It is intended > for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it is > unauthorised and may be unlawful. If you have received this email in error, > please notify the sender or postmas...@vernalis.com. Email is not a secure > method of communication and the Company cannot accept responsibility for > the accuracy or completeness of this message or any attachment(s). Please > check this email for virus infection for which the Company accepts no > responsibility. 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The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 0000 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
