Re: [Rdkit-discuss] rotatable bond
Open-Source Cheminformatics and Machine Learning
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From: Maciek W. <ma...@wo...> - 2018-03-09 13:06:12
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Hi Mariana, You can do exactly what this function is doing - counting matches of a SMARTS definition of rotatable bond. For a bond you can check if it matches mentioned SMARTS. The definition is here: http://www.rdkit.org/Python_Docs/rdkit.Chem.Lipinski-module.html SMARTS_DEF = '[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]' > bond = mol.GetBondWithIdx(5) # Get any bond in a molecule > rot_mol = Chem.MolFromSmarts(SMARTS_DEF) > rot_bond = rot_mol.GetBondWithIdx(0) > if bond.Match(rot_bond): > print(rotatable) Note there are more advanced definitions of such bonds, above example is taken from RDKit's Lipinski module. ---- Pozdrawiam, | Best regards, Maciek Wójcikowski ma...@wo... 2018-03-09 13:56 GMT+01:00 Mariana Assmann <mar...@gm...>: > Hi everyone, > > is it possible to check for a single bond if it is rotatable? I only found > a function to calculate the total number of rotatable bonds in the > molecule, but nothing specific to a selected bond. > > Best regards, > Mariana > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > |