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

[Rajarshi G. <rg...@in...>]

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

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Rajarshi Guha  <rg...@in...>
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