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handle multi-frame PDB files #77

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Trajectories can be stored as PDB files (NMR ensembles). MDAnalysis should be 
able to

1) read such a PDB as a trajectory
2) write such a PDB (as a bloated but portable format to exchange trajectories 
and ensembles)

See http://deposit.rcsb.org/depoinfo/print_nmr.html for details, in particular

  "Ensemble structures should be superimposed prior to deposition. The final coordinate file for deposition should contain all the models. A representative model should be identified and placed as the first model in the ensemble. Each model in the deposition should start with a 'MODEL' card and end with an 'ENDMDL' card. Each chain (within each model) should have a 'TER' card at its end."

Original issue reported on code.google.com by orbeckst on 29 Aug 2011 at 2:08

GoogleCodeExporter commented 9 years ago 
(Feel free to grab the ticket!)

Original comment by orbeckst on 19 Nov 2011 at 4:07

GoogleCodeExporter commented 9 years ago 
Hi, I've got a multiframe pdb reader and writer in place (time to replace 
'primitive' with 'basic' ;)?)

upon setting self.frame attribute i get the following error:

  AttributeError: can't set attribute

I'm guessing this is some kind of a read-only parent attribute? How can one 
edit it to update the current frame?

Original comment by jan...@gmail.com on 27 Nov 2011 at 3:57

GoogleCodeExporter commented 9 years ago 
Add the attribute to __slots__.

Original comment by orbeckst on 27 Nov 2011 at 4:52

GoogleCodeExporter commented 9 years ago 
Hi Jan, the latest changes make some of the tests fail. Please run the test 
suite, in particular

    nosetests -v test_atomgroup.py 

but also check the others for good measure and make sure that it passes.
Thanks, Oli

Original comment by orbeckst on 29 Nov 2011 at 11:54

GoogleCodeExporter commented 9 years ago 
Apologies - everything passes now. I dropped the CONECT records for now, I'm 
guessing it will go into the psf._bonds?

Original comment by jan...@gmail.com on 30 Nov 2011 at 3:23

GoogleCodeExporter commented 9 years ago 
I think the PrimitivePDBReader should put the bonds into struct['_bonds'], 
which ends up in Universe._psf['_bonds'] — but you're already doing that in 
http://code.google.com/p/mdanalysis/source/browse/MDAnalysis/topology/PrimitiveP
DBParser.py#90 . So all that needs to be done is to use that information.

I might indeed be worthwhile thinking a bit harder about how to organise 
topological information, especially if we want to add the capability of 
adding/removing/changing a universe. Then we would have basic model building 
capability.

Original comment by orbeckst on 30 Nov 2011 at 6:29

GoogleCodeExporter commented 9 years ago 
Hi Jan,

can you add a test case for the multiframe PDB reader to test_coordinates.py 
that excercises the functionality that you deem ready? You will probably have 
to add a small test file to the test data. At the moment that means checking 
out the branch MDAnalysisTestData and adding the test data into this branch 
(see also Issue 87... but let this not deter you :-) ). I would want to release 
0.7.5 before Christmas.

Once the test case is added you can close this issue (add "closes Issue 77" to 
the commit message to automatically close the issue). You can open a new one 
for the CONECT data and/or merge with Issue 23.

Cheers,
Oli

Original comment by orbeckst on 12 Dec 2011 at 10:37

GoogleCodeExporter commented 9 years ago 
Sweet that we're just the details i needed to finish this up quickly. Already 
pushed out a test file, I'll write some test cases now. Thanks, Oli!

Original comment by jan...@gmail.com on 13 Dec 2011 at 3:53

GoogleCodeExporter commented 9 years ago 
This issue was closed by revision ce1508d14c67.

Original comment by jan...@gmail.com on 14 Dec 2011 at 3:17