From: Christoph S. <ste...@eb...> - 2008-08-28 14:32:11
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Hi Raphael, very toughtful email - thanks! I think we should proceed as you suggested (branch, test, merge) Cheers, Chris Raphael A. Bauer wrote: > Nina Jeliazkova wrote: >> Rajarshi Guha wrote: >>> On Aug 21, 2008, at 11:23 AM, Christoph Steinbeck wrote: >>> >>> >>>> I suggest that, like in so many cases, we adopt the Perl TIMTOWTDI > .... >>> Once again I don't personally use PDB files, but given that BioJava >>> focuses on that type of stuff, I am assuming that its implementation >>> is more complete - but I may be totally wrong. In any case, if it is >>> the case that the BioJava code is more complete, that should be the >>> recommended way >>> >>> >>>> The question is: Who writes the mapper :-) >>>> >>> Who's using the CDK and PDB files? :) >>> >> or who might be using in the future ... it is hard to predict beforehand >> all possible ways a library can be used. IMHO, I would prefer Perl way :) > > hi, > > > meep. i am currently using the pdb reader and writer for some smaller > projects :) > > some quick comments on the issues from my side: > > 1. biojava / jmol readerwriter vs cdk readerwriter > hmm. i don't know what is the better way to do it actually. the major > point is how difficult it will be to maintain the internal data > structure converters between biojava and cdk (a minor point is the > "philosophical question"). and if nobody apart from me is actually using > the "biological" pdb file format then it is definitely not worth the > effort to establish the converter, integrate biojava into the build > process and so on). > > 2. things we can do immediately > - i have some fixes to the writer that enable roundtripping > - i have some fixes to the reader to enable the reading of files without > full header (many programs actually produce only 3d coordinates in a pdb > style). > => raphael should commit this to a branch for testing and so on (btw who > is raphael? me? oh...) > > 3. things that are ugly > - pdb is ugly because there is a standard, but many break it (.. not the > first time i hear this argument). > - as far as i can remember the cdk reader relies on a "PROTEIN" > containing line in the file and does not do anything if that magic word > is not present... simply not relying on this fixes many problems > (relates to 2. and "roundtripping"). > > > some conclusions > - first i am committing some branched code for reading writing - you can > comment on that, any maybe that solves many issues we are currently > discussing. (this will not happen until mid of september because i am > out of office). > - if that does not suit the needs of the larger cdk community we can > start a discussion if we want to wrap the biojava reader and writer or > do anything else... > > > thanks to rajarshi for starting the discussion :) > > raphael > > > > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |