Author: bugman
Date: Fri Jun 22 13:54:38 2012
New Revision: 17022
URL: http://svn.gna.org/viewcvs/relax?rev=17022&view=rev
Log:
Merged revisions 17017-17021 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17017 | bugman | 2012-06-21 10:36:48 +0200 (Thu, 21 Jun 2012) | 3 lines
The spin ID lookup table has been made private so that it is not included
in the save files.
........
r17018 | bugman | 2012-06-21 21:49:43 +0200 (Thu, 21 Jun 2012) | 5 lines
Fix for reading of BMRB CSA saveframe data - spin IDs generated from the
data now have molecule info.
This is problematic only in certain edge cases, for example a
multi-molecule entry.
........
r17019 | bugman | 2012-06-21 22:05:06 +0200 (Thu, 21 Jun 2012) | 6 lines
Removal of a hack from the generic_fns.bmrb.generate_sequence() function.
This hack was for naming unnamed spins. But this is not needed as the
generic_fns.mol_res_spin.create_spin() function already does this but with
many more safety checks.
........
r17020 | bugman | 2012-06-21 22:18:14 +0200 (Thu, 21 Jun 2012) | 6 lines
Removed a hack from the generic_fns.relax_data.pack_data() function for the
BMRB support.
This calls the generic_fns.bmrb.generate_sequence() function! As non-BMRB
code paths access the
pack_data() function, this is a nasty hack which would have caused problems
in the future.
........
r17021 | bugman | 2012-06-22 13:41:40 +0200 (Fri, 22 Jun 2012) | 26 lines
Creation of a fast molecule, residue and spin data lookup framework using
private metadata.
This consists of two elements: The already existing private lookup table
now at
cdp.mol._spin_id_lookup which is a dictionary with spin IDs as keys and a
list of molecule, residue
and spin indices as values; and a set of private variables within the
molecule, residue and spin
containers which identify the parent container names, numbers and indices.
As all data is private,
it will not be visible to the user or be saved in the XML results and save
files and should be
considered volatile.
All this private metadata is kept up to date via the two new
generic_fns.mol_res_spin functions
metadata_prune() and metadata_update(). For fast operation, these methods
can update specific
container subsets via the mol_index, res_index and spin_index arguments.
All parts of relax which
modify the data pipe's molecule, residue and spin data structure (the
generic_fns.mol_res_spin
functions and test suite) call these two functions as needed. Two
auxiliary functions
spin_id_variants() and spin_id_variants_elim() have been added to create
all possible matching spin
ID strings for a given spin (the second created IDs strings which should no
longer exist).
The speed ups from this change are significant. On one system, the system
and unit tests decrease
from 492.8s/26.4s to 434.3s/25.1s. On another the decrease is from
330.7s/17.4s to 258.9s/15.4s.
In addition, the pipe argument has been added to the
generic_fns.mol_res_spin functions
create_molecule(), create_residue(), create_pseudo_spin() and
create_spin(). Also, the molecule
name will now always be a string! Previously this was allowed to be an
integer. This is needed for
the private metadata functions to operate correctly. A number of unit
tests have been updated for
the changes.
........
Modified:
branches/interatomic/ (props changed)
branches/interatomic/data/__init__.py
branches/interatomic/data/mol_res_spin.py
branches/interatomic/generic_fns/bmrb.py
branches/interatomic/generic_fns/mol_res_spin.py
branches/interatomic/generic_fns/relax_data.py
branches/interatomic/generic_fns/sequence.py
branches/interatomic/specific_fns/model_free/bmrb.py
branches/interatomic/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
branches/interatomic/test_suite/unit_tests/molecule_testing_base.py
branches/interatomic/test_suite/unit_tests/spin_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/interatomic/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/data/__init__.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/data/mol_res_spin.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/bmrb.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/mol_res_spin.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/relax_data.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/sequence.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/model_free/bmrb.py?rev=17022&r1=17021&r2=17022&view=diff
Modified:
branches/interatomic/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/test_suite/unit_tests/molecule_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/unit_tests/molecule_testing_base.py?rev=17022&r1=17021&r2=17022&view=diff
Modified: branches/interatomic/test_suite/unit_tests/spin_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/unit_tests/spin_testing_base.py?rev=17022&r1=17021&r2=17022&view=diff
r17022 - in /branches/interatomic: ./ data/ generic_fns/ specific_fns/model_free/ test_suite/unit_tests/ test_suite/unit_tes...