Re: [Cdk-devel] IMolecule for SmilesGenerator?

[Rajarshi G. <raj...@gm...>]

Actually,

createSMILES(IMolecule molecule, boolean chiral, boolean
doubleBondConfiguration[])

already handles disconnected components and so essentially ignores the
unspoken 'contract' that IMolecule will not have disconnected
components

On Sat, May 22, 2010 at 5:14 AM, Nina Jeliazkova <ni...@ac...> wrote:
> Hi All,
>
> I might be missing something , but one could generate valid SMILES for
> disconnected components like CCCCCC.CCCCCC and for example have two versions
> of the method with different signatures:
>
> makeSmiles(IAtomContainer) - will generate smiles with dots for disconnected
> compounds.
> makeSmiles(IMolecule)  - will throw an exception if disconnected compounds
>
> Regards,
> Nina
>
> Syed Asad Rahman wrote:
>
> Hi All,
>
> So, if we provide a flag which is set if AtomContainer/Molecule holds
> disconnected components.
> Hence this flag can be checked by underlining implementation (if they need
> connected mols).
>
> Just a thought!
>
>
>
> Hi Rajarshi,
>
> I understood that it is all to do with connectivity. Smiles are only
> valid for connected structures, and IMolecules are specifically meant
> to be connected. This isn't a great way to model the situation, as I
> may have said before, but I can't really imagine a better way to do it
> so I only grumble about it to myself when writing things like:
>
> makeSmiles(container.getBuilder().newInstance(IMolecule.class, container));
>
> however, my guess would be that the design came about when structure
> generators were being made, since intermediate (possibly disconnected)
> structures were AtomContainers, and the fully connected products were
> Molecules.
>
> gilleain
>
> On Sat, May 22, 2010 at 3:40 AM, Rajarshi Guha <raj...@gm...>
> wrote:
>
>
> Hi, is there a reason that SmilesGenerator takes IMolecule and not
> IAtomContainer? It seems a little klunk since given an IAtomContainer
> I can't cast it to IMolecule to use the generator
>
> --
> Rajarshi Guha
> NIH Chemical Genomics Center
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Cdk-devel mailing list
> Cdk...@li...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
>



-- 
Rajarshi Guha
NIH Chemical Genomics Center