Quoting Egon Willighagen <egon.willigha...@gmail.com>: > On Mon, Mar 14, 2011 at 12:55 PM, Jules Kerssemakers > <j.kerssemak...@cmbi.ru.nl> wrote: >> The problem seems to be that the MDLv2000Reader DOESN'T parse the molecule >> properties beyond the "M END" line if asked for an IMolecule, but DOES >> parse them if asked for a IChemFile. > > Correct. That's how it is supposed to happen. The read() method is not > expected to be called multiple times.
That's why I used it to load a single molecule, thinking it was the best way to do... >> I'm guessing the molecule-reading stops after encountering "M END", which >> makes sense as this used to indicate the end of the molecule. Now with SDF >> properties occurring after this terminator-token, things go awry. > > Yes. Didn't I reply that already? :) > > The reason for this is that reading a IMolecule reads a MDL molfile, > which doesn't have any properties as part of the format. > 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". 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 ? >> 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 :) Thanks for your answers anyway :) vincent ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
