Hi Sarah,
You can use the GetRingInfo followed by PathToSubmol to get a molecular object.
For example:
>>> from rdkit.Chem import *
>>> mol =
>>> MolFromSmiles('O=C(C(C(O)=O)=CN(C1CC1)C2=C3)C2=CC(F)=C3N(C4)C(C5)CC4N5C')
>>> rings = mol.GetRingInfo().BondRings()
>>> rings
((6, 25, 7), (18, 19, 21, 22, 28), (20, 21, 22, 23, 29), (12, 26, 9, 5, 4, 11),
(27, 16, 14, 13, 26, 10))
>>> MolToSmiles(PathToSubmol(mol, rings[0]))
'C1CC1'
>>> [MolToSmiles(PathToSubmol(mol, ring)) for ring in rings]
['C1CC1', 'C1CCNC1', 'C1CCNC1', 'c1ccncc1', 'c1ccccc1']
Regards,
Eddie
On Sep 15, 2011, at 3:44 AM, Sarah Langdon wrote:
> Hi there,
>
> I would like to split up a molecule into a list of rings (each ring in the
> symSSSR), where each ring is stored as a molecular object (or SMILES) in the
> list.
>
> I have found a previous post
> (http://www.mail-archive.com/[email protected]/msg01054.html)
> which uses Chem.DeleteSubstructs to delete all non-cyclic atoms to leave
> multiple pieces. But I imagine this would leave fused rings as one fragment,
> rather than splitting up the molecule into each individual ring. Is there
> another way to do this which would give me each individual ring, or is there
> a way of splitting fused rings into individual rings after using
> Delete.Substructs?
>
> There is also GetRingInfo, but as far as I can see this only gives you size
> info and atom/bond content of each ring rather than a molecular object or
> SMILES... am I wrong?
>
> Thanks,
>
> Sarah
>
>
> Sarah Langdon
> PhD student
> Cancer Research UK Cancer Therapeutics Unit
> Institute of Cancer Research
> Haddow Laboratories
> 15 Cotswold Road
> Sutton
> Surrey SM2 5NG
>
> Tel: 0208 722 4139
> Email: [email protected]
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