Author: bugman
Date: Thu Jul 22 09:35:02 2010
New Revision: 11333
URL: http://svn.gna.org/viewcvs/relax?rev=11333&view=rev
Log:
Merged revisions 11269-11289,11291-11296,11298-11332 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11269 | bugman | 2010-07-01 10:25:33 +0200 (Thu, 01 Jul 2010) | 3 lines
Inverted the x and y axes in the RDC and PCS correlation plots.
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r11270 | bugman | 2010-07-01 10:31:10 +0200 (Thu, 01 Jul 2010) | 3 lines
The errors in the correlation plots are now optional.
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r11271 | bugman | 2010-07-01 10:48:48 +0200 (Thu, 01 Jul 2010) | 3 lines
Better support for RDC and PCS correlation plots with and without errors.
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r11272 | bugman | 2010-07-02 10:40:23 +0200 (Fri, 02 Jul 2010) | 3 lines
Added a new system test for the direct optimisation of the paramagnetic
centre.
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r11273 | bugman | 2010-07-02 10:41:41 +0200 (Fri, 02 Jul 2010) | 5 lines
Renamed the pcs.centre() user function to paramag.centre() in the system
tests.
This is because in the future this paramagnetic centre position is shared
with the PRE.
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r11274 | bugman | 2010-07-02 10:47:57 +0200 (Fri, 02 Jul 2010) | 6 lines
Renamed the pcs.centre() user function to paramag.centre() to abstract for
the PRE.
The paramagnetic centre is shared between different NMR interactions, so
this function has been
abstracted and is no longer PCS dependent.
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r11275 | bugman | 2010-07-02 10:53:18 +0200 (Fri, 02 Jul 2010) | 3 lines
The fix flag is now accepted by the paramag.centre() user function.
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r11276 | bugman | 2010-07-02 10:54:49 +0200 (Fri, 02 Jul 2010) | 3 lines
A few fixes for the paramag prompt code for the change from the PCS.
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r11277 | bugman | 2010-07-02 10:55:42 +0200 (Fri, 02 Jul 2010) | 3 lines
The paramag user function class is now accessible.
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r11278 | bugman | 2010-07-02 10:59:20 +0200 (Fri, 02 Jul 2010) | 3 lines
Fixes for the system tests for the pcs.centre() to paramag.centre() shift.
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r11279 | bugman | 2010-07-02 11:50:32 +0200 (Fri, 02 Jul 2010) | 5 lines
Activated the paramag centre finding system test.
This currently fails as the code to do this does not exist.
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r11280 | bugman | 2010-07-02 12:07:05 +0200 (Fri, 02 Jul 2010) | 3 lines
Fixes for solely specifying that the paramag centre will be optimised.
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r11281 | bugman | 2010-07-02 13:24:55 +0200 (Fri, 02 Jul 2010) | 5 lines
Fix for the RDC back_calc() function for when N=1 in the N-state model.
The bond vector structure was not correct.
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r11282 | bugman | 2010-07-02 13:31:52 +0200 (Fri, 02 Jul 2010) | 6 lines
Bug fix for the RDC back_calc() function - the align_id arg was being
ignored.
The RDCs were being calculated for all tensors, and then assigned to the
align_id key. The results
was that the back-calculated RDCs were for the last tensor, not for
align_id.
........
r11283 | bugman | 2010-07-02 17:39:21 +0200 (Fri, 02 Jul 2010) | 9 lines
Preparation for the optimisation of the paramagnetic centre in the N-state
model.
The calculation of PCS unit vectors and distances has been shifted into the
new
maths_fns.paramag_centre module and into the N-state model maths_fns code.
The API of
maths_fns.n_state_model has been changed so that now atomic positions, the
paramagnetic centre
position, the temperature, and frequency are passed in rather than the PCS
vectors and constants.
The code is now more flexible making it easy to add PRE support.
........
r11284 | bugman | 2010-07-02 17:50:23 +0200 (Fri, 02 Jul 2010) | 3 lines
The paramagnetic centre optimisation has been merged into the
func_population() target function.
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r11285 | bugman | 2010-07-02 19:36:51 +0200 (Fri, 02 Jul 2010) | 5 lines
The paramagnetic centre is now part of the parameter vector for the N-state
model.
Well, only when it is not fixed.
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r11286 | bugman | 2010-07-03 11:38:32 +0200 (Sat, 03 Jul 2010) | 5 lines
N-state models with no parameters are now caught prior to optimisation.
The minimise() method now simply throws a warning and returns without doing
anything.
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r11287 | bugman | 2010-07-03 20:08:53 +0200 (Sat, 03 Jul 2010) | 3 lines
The N-state model calculate() method now stored the back-calculated RDCs
and PCSs and Q factors.
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r11288 | bugman | 2010-07-03 21:56:40 +0200 (Sat, 03 Jul 2010) | 3 lines
The rdc.back_calc() user function without an ID arg will back-calculate
RDCs for all alignments.
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r11289 | bugman | 2010-07-06 18:10:10 +0200 (Tue, 06 Jul 2010) | 3 lines
The N-state model now supports the paramagnetic centre in
return_data_name().
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r11291 | bugman | 2010-07-08 11:45:21 +0200 (Thu, 08 Jul 2010) | 3 lines
Docstring improvements - the geometric info should be in Angstroms.
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r11292 | bugman | 2010-07-08 11:49:35 +0200 (Thu, 08 Jul 2010) | 9 lines
Better support for the optimisation and mapping of the Ln3+ position.
The position is now treated in Angstrom, and is properly scaled. A few
additional API methods have
been added for the mapping of the optimisation space, and a few modified to
support the Ln3+
position.
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r11293 | bugman | 2010-07-08 11:56:42 +0200 (Thu, 08 Jul 2010) | 3 lines
Fix for the Ln3+ position optimisation with no populations, the target
function was overwritten.
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r11294 | bugman | 2010-07-08 13:03:13 +0200 (Thu, 08 Jul 2010) | 5 lines
Fix for the N-state model _assemble_scaling_matrix() method for the
2-domain model.
This is a recently introduced bug. For the 2-domain model, no alignment
parameters are optimised.
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r11295 | bugman | 2010-07-08 13:49:04 +0200 (Thu, 08 Jul 2010) | 3 lines
Changed the alignment tensor parameter scaling back to 1 as this was
slowing down the optimisation.
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r11296 | bugman | 2010-07-08 15:26:24 +0200 (Thu, 08 Jul 2010) | 3 lines
Created the n_state_model.elim_no_prob() to remove structures with zero
probability.
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r11298 | bugman | 2010-07-13 13:28:44 +0200 (Tue, 13 Jul 2010) | 14 lines
Major patch for integrating the GUI into the noe calculation.
This patch is from Michael Bieri (https://gna.org/users/michaelbieri) and
is from file #9490
(https://gna.org/support/download.php?file_id=9490) attached to task #6847
(https://gna.org/task/?6847).
Changes include:
- output filename can be specified
- folder, where results files will be placed, can be specified
- label of hetero nucleus and proton of peak lists and pdb file can be
selected
- sequence is read either by sequence file or pdb file
- removed white spaces and progress output.
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r11299 | bugman | 2010-07-15 13:19:11 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test checking the conversion of alignment tensor to chi
tensor.
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r11300 | bugman | 2010-07-15 13:39:35 +0200 (Thu, 15 Jul 2010) | 3 lines
Fix for the alignment tensor rotation matrix - it is now always in the
right handed universe.
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r11301 | bugman | 2010-07-15 15:26:00 +0200 (Thu, 15 Jul 2010) | 3 lines
Initialising and alignment tensor now adds the ID to the alignment ID list.
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r11302 | bugman | 2010-07-15 15:26:35 +0200 (Thu, 15 Jul 2010) | 3 lines
Wrote the pcs.back_calc() user function back end.
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r11303 | bugman | 2010-07-15 15:29:46 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a severely truncated PDB file for PCS back-calculation with ubiquitin.
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r11304 | bugman | 2010-07-15 15:46:30 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test for the back-calculation of PCSs.
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r11305 | bugman | 2010-07-15 15:46:58 +0200 (Thu, 15 Jul 2010) | 3 lines
Added some unit tests for the pseudo-elliptic cosine function.
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r11306 | bugman | 2010-07-15 17:08:22 +0200 (Thu, 15 Jul 2010) | 5 lines
Fix for the alignment tensor initialisation for when the ID is added to
cdp.align_ids.
This was introduced in r11301. cdp.align_ids was not being checked if the
align ID already exists.
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r11307 | bugman | 2010-07-15 17:23:28 +0200 (Thu, 15 Jul 2010) | 3 lines
The Ln3+ position optimisation system test has been sped up by decreasing
the accuracy.
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r11308 | bugman | 2010-07-15 18:32:33 +0200 (Thu, 15 Jul 2010) | 6 lines
Small fixes and improvements to the rdc.back_calc() user function.
Align IDs are being used instead of RDC IDs so RDCs can be back-calculated
even if measured RDCs are
not present. And spin info is also being checked for better error
reporting to the user.
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r11309 | bugman | 2010-07-15 18:34:04 +0200 (Thu, 15 Jul 2010) | 5 lines
The RDC and PCS back-calculation user fns now add the alignment ID to the
RDC and PCS if absent.
Again this is to allow both data types to be back-calculated in the absence
of measured data.
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r11310 | bugman | 2010-07-15 18:38:18 +0200 (Thu, 15 Jul 2010) | 3 lines
Added a system test to back-calculated RDCs from a PCS derived alignment
tensor.
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r11311 | bugman | 2010-07-16 11:24:28 +0200 (Fri, 16 Jul 2010) | 3 lines
Made a RelaxError less stringent so that the paramagnetic centre can be
unfixed.
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r11312 | bugman | 2010-07-16 11:28:33 +0200 (Fri, 16 Jul 2010) | 3 lines
The align_tensor.delete() user function can now be used to remove all
tensors simultaneously.
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r11313 | bugman | 2010-07-16 19:12:36 +0200 (Fri, 16 Jul 2010) | 3 lines
Fixed the align_tensor.delete() arg unit test to accept None as an arg.
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r11314 | bugman | 2010-07-16 19:13:13 +0200 (Fri, 16 Jul 2010) | 3 lines
Pre-defined probabilities can now be used in the 'fixed' N-state model
optimisation.
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r11315 | bugman | 2010-07-19 11:42:30 +0200 (Mon, 19 Jul 2010) | 5 lines
For for a bug introduced in the last revision (r11314).
The fixed probabilities were not being set for the Ln3+ optimisation case.
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r11316 | bugman | 2010-07-19 11:59:05 +0200 (Mon, 19 Jul 2010) | 3 lines
Large speed ups of the Ln3+ position finding system test.
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r11317 | bugman | 2010-07-19 15:35:24 +0200 (Mon, 19 Jul 2010) | 9 lines
Created compile_1st_matrix_pseudo_ellipse() for numerically making the 1st
degree frame order matrix.
A number of new supplementary functions have been added for this numerical
approximation:
part_int_daeg1_pseudo_ellipse_xx()
part_int_daeg1_pseudo_ellipse_yy()
part_int_daeg1_pseudo_ellipse_zz()
tmax_pseudo_ellipse()
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r11318 | bugman | 2010-07-19 17:36:43 +0200 (Mon, 19 Jul 2010) | 3 lines
Fix for the print_frame_order_2nd_degree() fn, sys.stdout overwriting now
works.
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r11319 | bugman | 2010-07-19 18:04:13 +0200 (Mon, 19 Jul 2010) | 6 lines
Created compile_2nd_matrix_pseudo_ellipse() for numerically making the 2nd
degree frame order matrix.
A series of part_int_daeg2_pseudo_ellipse_**() supplementary functions have
been added for this
numerical approximation. The function is also unit tested.
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r11320 | bugman | 2010-07-19 18:39:18 +0200 (Mon, 19 Jul 2010) | 6 lines
Removal of the T23 transpose from compile_2nd_matrix_pseudo_ellipse() and
an index shift of -1.
The removal of the transpose has changed all of the indices in
part_int_daeg2_pseudo_ellipse_xx().
These indices now start at zero for easier debugging.
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r11321 | bugman | 2010-07-19 18:42:38 +0200 (Mon, 19 Jul 2010) | 3 lines
Reordering of the part_int_daeg2_pseudo_ellipse_xx() functions.
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r11322 | bugman | 2010-07-19 19:18:42 +0200 (Mon, 19 Jul 2010) | 3 lines
Added a debugging print out to test_compile_2nd_matrix_pseudo_ellipse().
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r11323 | bugman | 2010-07-19 19:19:18 +0200 (Mon, 19 Jul 2010) | 3 lines
Clean up of the maths functions in part_int_daeg2_pseudo_ellipse_xy().
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r11324 | bugman | 2010-07-21 11:24:16 +0200 (Wed, 21 Jul 2010) | 3 lines
Added support for the pseudo-elliptic cone model in the frame order user
function and specific code.
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r11325 | bugman | 2010-07-21 11:46:03 +0200 (Wed, 21 Jul 2010) | 3 lines
Removed the docstring linewrapping in the frame order maths_fns module.
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r11326 | bugman | 2010-07-21 13:28:41 +0200 (Wed, 21 Jul 2010) | 3 lines
Alphabetical arrangement of the functions in the frame_order_matrix_ops
module.
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r11327 | bugman | 2010-07-21 13:36:52 +0200 (Wed, 21 Jul 2010) | 3 lines
Modified compile_2nd_matrix_pseudo_ellipse() to rotate and return the frame
order matrix.
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r11328 | bugman | 2010-07-21 13:38:29 +0200 (Wed, 21 Jul 2010) | 5 lines
Created the func_pseudo_ellipse() optimisation target fn. for the
pseudo-elliptic cone model.
The structure of the Frame_order class has been simplified for handling
multiple frame order models.
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r11329 | bugman | 2010-07-21 13:43:49 +0200 (Wed, 21 Jul 2010) | 3 lines
Fix for the frame order grid_search() method - the pseudo-elliptic
parameters were incorrectly named.
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r11330 | bugman | 2010-07-21 13:54:01 +0200 (Wed, 21 Jul 2010) | 7 lines
Bug fix for the frame order grid search - the non-linear grid search is now
performed.
Previously the minfx.grid.grid() function was being used, causing the
custom grid to be ignored.
Now minfx.grid.grid_point_array() is being used allowing the non-regular
grid to be used.
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r11331 | bugman | 2010-07-21 14:52:37 +0200 (Wed, 21 Jul 2010) | 3 lines
Bug fix for the frame order grid_search() method - the point grid is now
properly constructed.
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r11332 | bugman | 2010-07-21 16:32:58 +0200 (Wed, 21 Jul 2010) | 3 lines
Fix for the _assemble_param_vector() method - the pseudo-ellipse parameter
vector was not being created.
........
Added:
branches/multi_processor_merge/generic_fns/paramag.py
- copied unchanged from r11332, 1.3/generic_fns/paramag.py
branches/multi_processor_merge/maths_fns/paramag_centre.py
- copied unchanged from r11332, 1.3/maths_fns/paramag_centre.py
branches/multi_processor_merge/prompt/paramag.py
- copied unchanged from r11332, 1.3/prompt/paramag.py
branches/multi_processor_merge/test_suite/shared_data/structures/trunc_ubi_pcs.pdb
- copied unchanged from r11332,
1.3/test_suite/shared_data/structures/trunc_ubi_pcs.pdb
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
- copied unchanged from r11332,
1.3/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
- copied unchanged from r11332,
1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
- copied unchanged from r11332,
1.3/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
- copied unchanged from r11332,
1.3/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
- copied unchanged from r11332,
1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_pseudo_ellipse.py
- copied unchanged from r11332,
1.3/test_suite/unit_tests/_maths_fns/test_pseudo_ellipse.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/auto_analyses/noe.py
branches/multi_processor_merge/data/align_tensor.py
branches/multi_processor_merge/generic_fns/__init__.py
branches/multi_processor_merge/generic_fns/align_tensor.py
branches/multi_processor_merge/generic_fns/frame_order.py
branches/multi_processor_merge/generic_fns/pcs.py
branches/multi_processor_merge/generic_fns/rdc.py
branches/multi_processor_merge/maths_fns/__init__.py
branches/multi_processor_merge/maths_fns/frame_order.py
branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py
branches/multi_processor_merge/maths_fns/n_state_model.py
branches/multi_processor_merge/prompt/__init__.py
branches/multi_processor_merge/prompt/align_tensor.py
branches/multi_processor_merge/prompt/frame_order.py
branches/multi_processor_merge/prompt/interpreter.py
branches/multi_processor_merge/prompt/n_state_model.py
branches/multi_processor_merge/prompt/pcs.py
branches/multi_processor_merge/prompt/rdc.py
branches/multi_processor_merge/specific_fns/frame_order.py
branches/multi_processor_merge/specific_fns/n_state_model.py
branches/multi_processor_merge/test_suite/system_tests/n_state_model.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/align_fit.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/multi_processor_merge/test_suite/system_tests/scripts/n_state_model/populations.py
branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_align_tensor.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/auto_analyses/noe.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/align_tensor.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/__init__.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/align_tensor.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/generic_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/frame_order.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/pcs.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/rdc.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/maths_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/__init__.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/frame_order.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/n_state_model.py?rev=11333&r1=11332&r2=11333&view=diff
Modified: branches/multi_processor_merge/prompt/__init__.py
[... 47 lines stripped ...]
r11333 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ generic_fns/ maths_fns/ prompt/ specific_fns/ test_suit...