Hi Eddie,
Thanks, that's exactly what I needed.
Sarah
On 16 Sep 2011, at 00:24, Eddie Cao wrote:
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
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