Some Stuff

This is expanding on one of the points that Rajarshi made in his blog (which he followed up here ) on the PDB file handling capabilities of the CDK. There are two related topics : reading of PDB format files (the ancient, fixed column-width ATOM files) and the model that these are read into. PDBReader The old PDB format is being replaced with mmCIF and/or PDBML formats. Only there are lots of programs that write out this format, so it makes sense to still support it for a while at least. However, it is a quite nasty format, in some ways. Not so much the fixed column width, but the fact that crystallographers abuse the file format in all sorts of ways. Even simple things like expecting that atom numbers will always increase, may not be true. So it is not easy making a good reader for PDB files. The current CDK one won't read a file with just ATOM records, for example. Think that's reasonable? Well, tough luck for people that made programs that produce simple files like this. A...