Re: [Rdkit-discuss] rotatable bond

[Maciek W. <ma...@wo...>]

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
>
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