As a followup to my email, Javi had raised issues concerning the choice of names of HierarchyType. It is problematic to have such a type label (as a protein is a molecule, but it is complicated to express such a reslationship). I propose removing the Hierarchy::get_type() method and HierarchyType type and replacing it with methods like - get_is_protein() (true for any piece of protein) - get_is_molecule() (true for any molecule) - get_is_residue() - get_is_atom() - get_is_assembly() (not sure if we want this) etc...
Something else to think about for Tuesday.
> I'm not entirely sure I agree (witness the last developers > meeting :-). But am ambivalent. It could be structured better though > which would help things converge faster. > > That said, we have several outstanding questions: > - do we have PROTEINs which can contain CHAINs or just PROTEINS > (which are chains). This we should probably just find something > authorative and use it. I don't much care either way. > > - what are the most useful things for one or more read_pdb functions > to return? For this we should come up with standard usage cases. I > would propose a couple here: > - someone is running through lots of PDB files and wants to load > one protein from each file. To do this, it would be nice to have a > function which loads a protein from the pdb and returns a hierarchy > containing only that protein. Whether this protein has one or more > chains depends on the answer to the first question > - load the whole structure from a pdb complete with many proteins > and ligands and other molecules. For this it is useful to be able to > read everything from one PDB model record. > - take one piece of the pdb and use it (such as a chain or > ligand). For this it is nice not to have to dissect a hierarchy. > - load a bunch of model records from a single pdb and deal with > all the molecules in each record. > > Any other cases? Think about it and we will discuss it on Tuesday. > > A proposal to think which handles the above cases is: > - one function which reads a protein from a pdb > - one function which reads everything from one model record in a pdb > and returns it in a list/vector