These methods are not a very good solution, as they will be true in 99% percent of the cases, or even 100% (why should I call get_is_molecule() if I know that is going to be true all the time ? ). It is far more difficult, but far more useful, to agree of what we expect to get after a PDB, and how we are going to organize our structures in IMP into hierarchies. Together with Keren, I can give suggestions for low resolution structures.
Javi
2009/10/9 Daniel Russel drussel@gmail.com
> 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 >> > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >