On Wed, Feb 17, 2010 at 12:58 AM, Geoffrey Hutchison <[email protected]> wrote: > One of my (unstated) goals with Open Babel is to support as many file formats > as possible. Leave no chemical data behind and process it as accurately as > possible.
Let there be no mistake here... I do not like to leave behind any data either! The reason why format specifications are important to me (open or not, see below), is that most of them cause *modeling error* ... and that's get pushed in the your statistical analysis, so, in order to do the latter properly, and fairly judge the quality of the modeling, you *must* know the error involved in reading the data from disk. Some format are better than others, have less limitatations, more flexible: CML is very flexible, and information loss is just minimal; (Open)SMILES does not handle coordinates, and will never handle conformational variance properly... That's the kind of thing that matters to me... > I support MDL, CDX, MOL2, and other formats which might be considered > "non-open" by Egon. ... and to a much lesser extend if a format is open or not! So, offense taken here! I brought the whole discussion up, just I feel the current *guidelines* are not enough for me to decide what is open and what is not... it is not me who made claims in the Blue Obelisk wiki (well, I hope not)... I cannot find good arguments to say that Daylight SMILES, MDL, ... are not as Open as some of the specification that we deem Open... I am only fairly sure about OpenSMILES... the rest is to me undecided yet. > No offense to Egon, but he's not part of the OB project. No offense taken on not being OB contributor. In a multi-universe where I'd have a subtle knife not to just move between worlds, but also back and forth in time, I'd be a happy OB contributor... > (Sadly, Blue Obelisk = BO, which is an easy typo...) I am still loving to see a proper OpenBabel plugin for Bioclipse... > I like Peter's comments about "rough consensus and running code." That's very > much in line with my view. Tests are also welcome. I recapitulate my note on this, and take OpenBabel as a lead here... OpenBabel *is* the "rough concensus and running code" for MDL/Symyx molfile, Daylight SMILES, CDX, ... And this is my point all along... Open Source is making a strong point for existing formats (which is good), and as such, makes existing rules on Open Specifications/Standards less useful... Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
