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On Tuesday 08 June 2004 11:31, Miguel wrote: > [complain] > > Jmol would have recognized the element type if the PDB had bothered to > follow their own file format specification of 1996 and had filled in > columns 77-78 with the element symbol.
This was a later addition - not in the original format.
> > [/complain] > > If you feel that it is truly justified, I could try mapping ?C, ?N and ?O > to carbon, nitrogen, and oxygen. > > However, we will be unable to map AC because: > > AC = Ac = actinium > > Do you have any recommendations as to how we can address this problem?
Please do not do this!
The examplify the *very bad* situation with PDB files, I know someone who had a friend implement a PDB parser that parses the whole PDB database... And for several PDB entries, it has a special one-entry-only parser !!!
I recommend that you do not make extensions for invalid PDB files. I spent 2 weeks in Brookhaven (the previous home of the PDB) about 8 years ago looking at this problem. Their own format had varied enough over the years that it was a major problem to reconcile all *their* files. Add to this the many creative deviations for other "PDB" files and it is a nightmare.
IMO you should implement the current specification to whatever extent you have energy for and report deviations from this with warnings or errors. XML took precisely this approach. If it doesn't obey the spec it's broken. So an XML parser can be as little as 20K (AElfred) while HTML parsers can be huge because they have to cope with broken legacy
Best
P.
Egon
- -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6
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