From: Raphael A. B. <rap...@ch...> - 2008-08-27 15:31:55
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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 |