Hi Patrik,
Doesn't look to be in the default behaviour. As you say the reader loads the
name into the SMIdbNAME but output ignores this and writes the line notation
only. This could easily be done by having a couple of IOOptions but I would
favour using composition and a decorator to achieve this. Either way if you
need this please create a patch and it'll be good to add.
J
On 27 Apr 2013, at 08:16, Patrik Rydberg <[email protected]> wrote:
> Hi all CDK users,
>
> Is there any way to get the SMILESWriter to output the names of the molecules
> as well and not only the smiles?
> The SMILESReader reads the names just fine, but when writing I can’t get them
> to be written, the names are set as properties of the AtomContainers using
> both CDKConstants.TITLE and SMIdbNAME.
> I checked the source code and this might just be missing functionality,
> anyone care to verify that?
>
> CDK version used, 1.4.8. But I cannot see any difference in the SMILESWriter
> code to the newer versions that would affect molecule names being or not
> being written.
>
> Regards,
> Patrik Rydberg
>
> --------------------------------------------------------------------------
> Patrik Rydberg, Associate Professor, Ph.D.
>
> Biostructural Research Group
> Department of Drug Design and Pharmacology
> Faculty of Health and Medical Sciences
> University of Copenhagen
> DK-2100 Copenhagen
>
> http://www.farma.ku.dk/index.php/Patrik-Rydberg/5304/0/
>
>
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