Hi Toby,
One additional note on what Greg wrote:
you can define another smarts pattern for the identification of rotatable
bonds:
Lipinski.RotatableBondSmarts = Chem.MolFromSmarts("...")
Some smarts from the literature:
Daylight:
[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]-&!@[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]
Chemaxon: [!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]
Best,
Grégori
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