2009/10/9 Daniel Russel drussel@gmail.com

> nt 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. >> > You need some way of traversing the resulting hierarchy and telling what > you are looking at. Say read_pdb returns a Hierarchy. You then have to go > through the children of the node and determine which is a protein and which > is a ligand if you want to do much useful with it. The docs for the read_pdb > function can't possibly specify the answer. If you are writing code that > knows the pdb that is being loaded, then you can hard code it, but that is > not always possible (say you are writing something like modpipe or an > application to handle fitting into em maps). > > Or you load a protein and decide you want to define subdomains. You then > modify the hierarchy to have a node corresponding to the structure. Some > code which alter traverses the hierarchy (such as code to build a simplified > representation), may need to know when it has gotten to the atoms or > residues (it can't assume a constant structure). >

Then you're simply talking about labeling the contents of the Hierarchy. But again, far more useful is to agree on how we are going to organize Hierarchies and how everybody thinks we should treat atomic structures, or structures in general.

> > Together with Keren, I can give suggestions for low resolution structures. >> > Looking forwards to it. > > We'll do

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