Re: [Cdk-user] cutting a functional group from a molecule

[RzmmDX <rz...@ya...>]

ok, i tried the UniversalIsomorphismTester and used the
getSubgraphAtomsMaps() method, however it seems to contain null rMaps while
getSubgraphMaps() returns the bond no. correctly, so m i using it wrongly?

Rajarshi Guha-3 wrote:
> 
> 
> On Jul 8, 2007, at 11:28 AM, RzmmDX wrote:
> 
>>
>> i been using the fragmenter class made by Rajarshi Guha.
>>
>> i parse this smiles string "C(CC(C(=O)O)N)CNC(=NO)N" it has 2 hydroxyl
>> groups,
>> how do i break the bond that bonds the hydroxyl group to the molecule?
> 
> The trick will be to identify the -OH group (either by SMARTS or by  
> hand). Once you have the hydroxyl O atom, you can get all the bonds  
> connected to it (getConnectedBonds) and then choose that bond whose  
> other atom is a C. You can then remove that bond.
> 
> Of course, this will result in 3 disconnected components. If just  
> want to remove the -OH's then make sure to remove the O's as well
> 
> -------------------------------------------------------------------
> Rajarshi Guha  <rg...@in...>
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> -------------------------------------------------------------------
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>                 --  E.B. Ross
> 
> 
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