Hi John,
Well, I don't really need it very badly. It was just that a user of my SMARTCyp
program wondered if it could be added to it.
So, if somebody adds it, that would be great. But unfortunately I don't have
the time to do it myself.
Patrik
--------------------------------------------------------------------------
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/
From: John May [mailto:[email protected]]
Sent: 28. april 2013 13:22
To: Patrik Rydberg
Cc: [email protected]
Subject: Re: [Cdk-user] molecule names in smileswriter
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]<mailto:[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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