Author: bugman
Date: Wed Oct 22 15:39:59 2014
New Revision: 26357
URL: http://svn.gna.org/viewcvs/relax?rev=26357&view=rev
Log:
Merged revisions 26334-26348 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26334 | bugman | 2014-10-22 09:47:22 +0200 (Wed, 22 Oct 2014) | 9 lines
Modified the atomic position handling in
pipe_control.structure.main.load_spins_multi_mol().
The multiple molecule merging functionality of the structure.load_spins
user function now handles
missing atomic positions differently. The aim is that the length of the
spin container position
variable is fixed for all spins to the number of structures, as the N-state
model analysis assumes
this equal length for all spins. When data is missing, the atomic position
for that structure is
now set to None. This will require other modifications in relax to support
this new design.
........
r26335 | bugman | 2014-10-22 10:08:50 +0200 (Wed, 22 Oct 2014) | 6 lines
Modified the interatom.unit_vectors user function backend to handle missing
atomic positions.
This is to match the structure.load_spins user function change whereby
missing atomic positions are
now set to the value of None.
........
r26336 | bugman | 2014-10-22 10:21:18 +0200 (Wed, 22 Oct 2014) | 6 lines
Fix for the atomic position handling in
pipe_control.structure.main.load_spins_multi_mol().
The dimensionality of the position structure returned by the structural
object atom_loop() method
needed to be reduced.
........
r26337 | bugman | 2014-10-22 10:47:48 +0200 (Wed, 22 Oct 2014) | 9 lines
The structure.load_spins user function now stores the number of states in
cdp.N.
This is to help the specific analyses which handle ensembles of structures.
With the introduction
of the from_mols argument to the structure.load_spins user function, the
number of states is now not
equal to the number of structural models, as the states can now come from
different structures of
the same model. Therefore the user function will now explicitly set cdp.N
to the number of states
depending on how the spins were loaded.
........
r26338 | bugman | 2014-10-22 11:02:30 +0200 (Wed, 22 Oct 2014) | 7 lines
Clean up and speed up of the N_state_model.test_CaM_IQ_tensor_fit system
test.
All output files are now set to 'devnull' so that the system test no longer
creates any files within
the relax source directories. And the optimisation settings have been
decreased to hugely speed up
the system test.
........
r26339 | bugman | 2014-10-22 11:36:57 +0200 (Wed, 22 Oct 2014) | 6 lines
Bug fix for the lib.arg_check.is_float_matrix() function.
The check for a numpy.ndarray data structure type was incorrect so that
lists of numpy arrays were
failing in this function. Rank-2 arrays were not affected.
........
r26340 | bugman | 2014-10-22 11:38:09 +0200 (Wed, 22 Oct 2014) | 6 lines
Expanded the lib.arg_check.is_float_matrix() function by adding the
none_elements argument.
This matches a number of the other module functions, and allows for entire
rows of the matrix to be
None.
........
r26341 | bugman | 2014-10-22 11:44:55 +0200 (Wed, 22 Oct 2014) | 8 lines
Lists of lists containing rows of None are now better supported by the
lib.xml functions.
The object_to_xml() function will now convert the float parts to IEEE-754
byte arrays, and the None
parts will be stored as None in the <ieee_754_byte_array> list node. The
matching xml_to_object()
method has also been modified to read in this new node format. This
affects the results.write and
state.save user functions (as well as the results.read and state.load user
functions).
........
r26342 | bugman | 2014-10-22 14:00:50 +0200 (Wed, 22 Oct 2014) | 5 lines
Added spacing after the minimise.grid_search user function setup printouts.
This is for better spacing for the next messages from the specific analysis.
........
r26343 | bugman | 2014-10-22 14:01:58 +0200 (Wed, 22 Oct 2014) | 5 lines
Speed up of the N_state_model.test_CaM_IQ_tensor_fit system test.
This test is however still far too slow.
........
r26344 | bugman | 2014-10-22 14:22:11 +0200 (Wed, 22 Oct 2014) | 7 lines
Added printouts to pipe_control.pcs.return_pcs_data() and
pipe_control.rdc.return_rdc_data().
These functions now accept the verbosity argument which if greater than 0
will activate printouts of
how many RDCs or PCSs have been assembled for each alignment. This will be
useful for user feedback
as the spin verses interatomic data container selections can be difficult
to understand.
........
r26345 | bugman | 2014-10-22 14:26:17 +0200 (Wed, 22 Oct 2014) | 8 lines
The verbosity argument for the N-state model optimisation is now propagated
for more printouts.
The argument for the calculate() and minimise() API methods is now sent into
specific_analyses.n_state_model.optimisation.target_fn_setup(), and from
there into the
pipe_control.pcs.return_pcs_data() and pipe_control.rdc.return_rdc_data()
functions. That way the
number of RDCs and PCSs used in the N-state model is reported back to the
user for better feedback.
........
r26346 | bugman | 2014-10-22 14:34:35 +0200 (Wed, 22 Oct 2014) | 6 lines
Updated the N_state_model.test_CaM_IQ_tensor_fit system test so it operates
correctly as a GUI test.
All user functions are now executed through the special self._execute_uf()
method to allow either
the prompt interpreter or the GUI to execute the user function.
........
r26347 | bugman | 2014-10-22 14:37:25 +0200 (Wed, 22 Oct 2014) | 6 lines
Modified the N_state_model.test_CaM_IQ_tensor_fit system/GUI test for
implementing a new feature.
The 'spin_selection' argument has been added to the interatom.define user
function. This will be
used to carry the spin selections over into the interatomic data containers.
........
r26348 | bugman | 2014-10-22 14:52:21 +0200 (Wed, 22 Oct 2014) | 6 lines
Implemented the spin_selection Boolean argument for the interatom.define
user function.
This has been added to the frontend with a description, and to the backend.
When set, it allows the
spin selections to define the interatomic data container selection.
........
Modified:
branches/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/lib/arg_check.py
branches/space_mapping_refactor/lib/xml.py
branches/space_mapping_refactor/pipe_control/interatomic.py
branches/space_mapping_refactor/pipe_control/minimise.py
branches/space_mapping_refactor/pipe_control/pcs.py
branches/space_mapping_refactor/pipe_control/rdc.py
branches/space_mapping_refactor/pipe_control/structure/main.py
branches/space_mapping_refactor/specific_analyses/n_state_model/api.py
branches/space_mapping_refactor/specific_analyses/n_state_model/optimisation.py
branches/space_mapping_refactor/test_suite/system_tests/scripts/n_state_model/CaM_IQ_tensor_fit.py
branches/space_mapping_refactor/user_functions/interatom.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/space_mapping_refactor/lib/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/arg_check.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/lib/xml.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/lib/xml.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/interatomic.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/minimise.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/pcs.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/rdc.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/pipe_control/structure/main.py?rev=26357&r1=26356&r2=26357&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/n_state_model/api.py?rev=26357&r1=26356&r2=26357&view=diff
Modified:
branches/space_mapping_refactor/specific_analyses/n_state_model/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/specific_analyses/n_state_model/optimisation.py?rev=26357&r1=26356&r2=26357&view=diff
Modified:
branches/space_mapping_refactor/test_suite/system_tests/scripts/n_state_model/CaM_IQ_tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/scripts/n_state_model/CaM_IQ_tensor_fit.py?rev=26357&r1=26356&r2=26357&view=diff
Modified: branches/space_mapping_refactor/user_functions/interatom.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/user_functions/interatom.py?rev=26357&r1=26356&r2=26357&view=diff
r26357 - in /branches/space_mapping_refactor: ./ lib/ pipe_control/ pipe_control/structure/ specific_analyses/n_state_model/...