On 9 February 2012 18:19, Rajarshi Guha <[email protected]> wrote:
> The CDK doesn't support SMIRKS yet, so you'd basically have to implement
> the fragmentation rules manually (via atom/bond manipulation)
>
Or you could try the SMIRKS implementation from
http://ambit.sourceforge.net/AMBIT2-LIBS/ambit2-smarts/index.html
It depends on CDK 1.4.5.
Best regards,
Nina
> 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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