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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