Daniel - I assume that most people just gave up on reading this entire
tread (I know I almost did ...) , as it is too long with many brunches
that were never resolved.
It would be a good idea to send on Monday a remainder with the topics
for discussion and the proposed solutions, even better as a wiki page
so others can add their solutions as well.
I will add the low-res perspective once you will post your ideas :)
Keren.
On Oct 8, 2009, at 9:59 PM, Daniel Russel wrote:
On Oct 8, 2009, at 9:21 PM, Dina Schneidman wrote:
completely agree. these are resolved much faster by talking :)
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