On Mon, Mar 14, 2011 at 1:48 PM, Vincent Le Guilloux
<vincent.le-guill...@univ-orleans.fr> wrote:
> Here I don't understand: if I reefer to the documentation of the
> MDLv2000Reader class, this class "Reads a molecule from an MDL MOL or SDF
> file".
Yeah, I guess that's an issue of where to put the parantheses...
should be updated, I think:
"Reads (a molecule from an MDL molfile) or (a MDL SD file)."
Or, even more correct:
"Reads a {@link IMolecule) from an MDL molfile or a {@link IChemFile}
from an MDL SD file."
> Although no particular documentation is provided on how properties are
> handled, I was guessing that this was the class to use when one want to read
> a single molecule available in the SDF format.
>
> Was my guess a wrong one ?
I never anticipated that someone might want to read just the first
molecule in a SD file :)
BTW, I don't think you're wrong... the documentation is and the CDK
library is in not providing decent feedback...
>>> The IChemFileReader of course has to continue beyond the M-END, because
>>> there may be more molecules, in this process it "accidentally" encounters
>>> the properties, which it then (correctly) associates with the previous
>>> molecule.
>>
>> Properties are only part of the MDL SD file specification, and thus
>> read when reading a SD file.
>
> Which is the case here... There is clearly something I'm missing here, sorry
> for that if its obvious or already explained elsewhere :)
No, it's kinda new :) That's the funny thing with the CDK... most bug
reports are reflecting unanticipated use cases :)
> Thanks for your answers anyway :)
That's what we have this mailing list for (and the book).
Anyway, I will file bug/feature reports for:
1. split SDFReader from MDLV2000Reader (if not in master already; need
to check that)
2. have IChemObjectReader.read() throw an EOF exception when called a
second time
3. clearer JavaDoc, as outlined above
Jules, Vincent, did I miss anything?
Thanx for discussing these things in detail! This is what the CDK
needs to make progress! (Well, and matching patches following the
bug/feature reports, of course ;)
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
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