Re: [Rdkit-discuss] identify which bonds are rotatable
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Re: [Rdkit-discuss] identify which bonds are rotatable
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From: S.L. C. <sl...@ya...> - 2015-08-10 21:07:32
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Hello Dimitrios, You may also take a look at an earlier entry for a somewhat more sophisticated discussion. http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg03671.html You may like to read the whole thread too. Ling From: Dimitrios Spiliotopoulos <d.s...@bi...> To: Samo Turk <sam...@gm...> Cc: RDKit Discuss <rdk...@li...> Sent: Monday, August 10, 2015 6:38 AM Subject: Re: [Rdkit-discuss] identify which bonds are rotatable Thank you very much, Samo! Have a great day, d. -- Dimitrios Spiliotopoulos, PhD SNF SystemsX.ch Postdoctoral Fellow Department of Biochemistry, University of Zurich Room: Y 44-K-70 Tel: +41 44 635 55 44 Tel: +41 44 635 55 92 Fax: +41 44 635 68 62 On Mon, Aug 10, 2015 at 1:32 PM, Samo Turk <sam...@gm...> wrote: Hi Dimitrios! Yes there is a way. You just have to use smarts pattern for rotatable bond (you can find it in Lipinski module): In [75]: mol = Chem.MolFromSmiles('CCc1cc(OC)ccc1') In [76]: RotatableBond = Chem.MolFromSmarts('[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]') In [77]: mol.GetSubstructMatches(RotatableBond) Out[77]: ((1, 2), (4, 5)) Result are tuples of the indices of the molecule's atoms that match a substructure query. Cheers, Samo On Mon, Aug 10, 2015 at 12:28 PM, Dimitrios Spiliotopoulos <d.s...@bi...> wrote: Hi RDKit users! Is there a way to identify which bonds are rotatable in a small molecule? (in addition to obtaining the number of rotatable bonds via CalcNumRotatableBonds.) Thank you very much in advance! Best wishes, d. -- Dimitrios Spiliotopoulos, PhD SNF SystemsX.ch Postdoctoral Fellow Department of Biochemistry, University of Zurich Room: Y 44-K-70 Tel: +41 44 635 55 44 Tel: +41 44 635 55 92 Fax: +41 44 635 68 62 ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdk...@li... https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdk...@li... https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |
