Re: [Rdkit-discuss] Split molecule into rings and store as mol object/SMILES in list

[Sarah L. <Sar...@ic...>]

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/rdk...@li.../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: sar...@ic...
>>
>>
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