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 <[email protected]> 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 > <https://github.com/rdkit/rdkit/blob/1bf6ef3d65f5c7b06b56862b3fb9116a3839b229/rdkit/Chem/Lipinski.py#L47> > ): > 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 < > [email protected]> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >
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