The CDK doesn't support SMIRKS yet, so you'd basically have to implement
the fragmentation rules manually (via atom/bond manipulation)
On Wed, Feb 8, 2012 at 3:36 PM, lochana menikarachchi <[email protected]>wrote:
>
> Hi All,
>
> Is it possible to fragment a molecule based on set of rules using CDK??
>
> Here is an example rule from a paper:
>
> "Molecules containing an amine group with (at least) an ethylene or
> substituted ethy- lene group separating the nitrogen atom from other
> functional groups, will cleave and lose the nitrogen atom as the
> corresponding amine, and will form the deaminated ion"
>
> Is it possible to define a bunch of such rules and get the list of
> fragment IAtomContainers??
>
> In ChemAxon API, this can be done by defining a set of rules in a XML File
> (Using SMIRKS or RXN) and passing this rules file and molecule to
> Exhaustive Fragmenter..
>
> I wonder whether I can achieve the same functionality using CDK??
>
> Thanks.
>
> Lochana
>
>
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--
Rajarshi Guha
NIH Chemical Genomics Center
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