On Wed, Jan 20, 2016 at 5:33 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> On 01/20/2016 03:55 PM, Peter S. Shenkin wrote:
> > On Wed, Jan 20, 2016 at 3:06 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
> > wrote:
> >> As much as PDB wants the old busted PDB format gone, they
> >> are not offering a usable alternative that I know of.
> > Such as: a JSON file ...
>
> JSON encodes a single string. That is a problem for sending larger files
> over the net, say, an NMR structure of a larger molecule with 100 models
> in the file.
>
That's not a problem, conceptually, because you can have an array of
structures. Any hierarchical format has a verbosity problem due to
duplication of metadata, but for use as an interchange format, I don't see
this as a big problem.
Actually, though, you could imagine having a JSON file encoding only the
conventions to be used when reading or writing pdb files. So it would
encode the dialect. Then APIs could be provided to read the dialect JSON
file and then read or write the PDB file using the dialect -- similar,
conceptually, to the way Python handles different dialects of .csv file.
CSV is a good format for tabular data, and you can send rows
> incrementally, but a typical application requires some small amount of
> metadata as well. For example, the full sequence -- that does not fit
> into a single-table format like CSV.
Right, but each structure in the JSON array can have its own metadata
blocks for data that are not 1:1 with atoms.
ASN.1 provides a nice alternative but it has issues, too. (Mainly, the fact
that it's fallen into obscurity.)
-P.
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