Author: michaelbieri
Date: Fri Jul 23 01:30:02 2010
New Revision: 11339
URL: http://svn.gna.org/viewcvs/relax?rev=11339&view=rev
Log:
Merged revisions 11298-11332,11334-11338 via svnmerge from
svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/1.3
........
r11298 | bugman | 2010-07-13 21:28:44 +1000 (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.
........
r11299 | bugman | 2010-07-15 21:19:11 +1000 (Thu, 15 Jul 2010) | 3 lines
Added a system test checking the conversion of alignment tensor to chi
tensor.
........
r11300 | bugman | 2010-07-15 21:39:35 +1000 (Thu, 15 Jul 2010) | 3 lines
Fix for the alignment tensor rotation matrix - it is now always in the
right handed universe.
........
r11301 | bugman | 2010-07-15 23:26:00 +1000 (Thu, 15 Jul 2010) | 3 lines
Initialising and alignment tensor now adds the ID to the alignment ID list.
........
r11302 | bugman | 2010-07-15 23:26:35 +1000 (Thu, 15 Jul 2010) | 3 lines
Wrote the pcs.back_calc() user function back end.
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r11303 | bugman | 2010-07-15 23:29:46 +1000 (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 23:46:30 +1000 (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 23:46:58 +1000 (Thu, 15 Jul 2010) | 3 lines
Added some unit tests for the pseudo-elliptic cosine function.
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r11306 | bugman | 2010-07-16 01:08:22 +1000 (Fri, 16 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.
........
r11307 | bugman | 2010-07-16 01:23:28 +1000 (Fri, 16 Jul 2010) | 3 lines
The Ln3+ position optimisation system test has been sped up by decreasing
the accuracy.
........
r11308 | bugman | 2010-07-16 02:32:33 +1000 (Fri, 16 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.
........
r11309 | bugman | 2010-07-16 02:34:04 +1000 (Fri, 16 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.
........
r11310 | bugman | 2010-07-16 02:38:18 +1000 (Fri, 16 Jul 2010) | 3 lines
Added a system test to back-calculated RDCs from a PCS derived alignment
tensor.
........
r11311 | bugman | 2010-07-16 19:24:28 +1000 (Fri, 16 Jul 2010) | 3 lines
Made a RelaxError less stringent so that the paramagnetic centre can be
unfixed.
........
r11312 | bugman | 2010-07-16 19:28:33 +1000 (Fri, 16 Jul 2010) | 3 lines
The align_tensor.delete() user function can now be used to remove all
tensors simultaneously.
........
r11313 | bugman | 2010-07-17 03:12:36 +1000 (Sat, 17 Jul 2010) | 3 lines
Fixed the align_tensor.delete() arg unit test to accept None as an arg.
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r11314 | bugman | 2010-07-17 03:13:13 +1000 (Sat, 17 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 19:42:30 +1000 (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 19:59:05 +1000 (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 23:35:24 +1000 (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()
........
r11318 | bugman | 2010-07-20 01:36:43 +1000 (Tue, 20 Jul 2010) | 3 lines
Fix for the print_frame_order_2nd_degree() fn, sys.stdout overwriting now
works.
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r11319 | bugman | 2010-07-20 02:04:13 +1000 (Tue, 20 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 | 2010-07-20 02:39:18 +1000 (Tue, 20 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 | 2010-07-20 02:42:38 +1000 (Tue, 20 Jul 2010) | 3 lines
Reordering of the part_int_daeg2_pseudo_ellipse_xx() functions.
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r11322 | bugman | 2010-07-20 03:18:42 +1000 (Tue, 20 Jul 2010) | 3 lines
Added a debugging print out to test_compile_2nd_matrix_pseudo_ellipse().
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r11323 | bugman | 2010-07-20 03:19:18 +1000 (Tue, 20 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 19:24:16 +1000 (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 19:46:03 +1000 (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 21:28:41 +1000 (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 21:36:52 +1000 (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 21:38:29 +1000 (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 21:43:49 +1000 (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 21:54:01 +1000 (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 22:52:37 +1000 (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 | 2010-07-22 00:32:58 +1000 (Thu, 22 Jul 2010) | 3 lines
Fix for the _assemble_param_vector() method - the pseudo-ellipse parameter
vector was not being created.
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r11334 | bugman | 2010-07-22 19:09:04 +1000 (Thu, 22 Jul 2010) | 6 lines
Bug fix for the func_pseudo_ellipse() target function.
The overwriting of the permanent storage data structures was killing the
optimisation of the average
domain position. Now temporary data structures are used for the functions
which return numpy arrays.
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r11335 | bugman | 2010-07-22 19:12:22 +1000 (Thu, 22 Jul 2010) | 5 lines
The same bug fix of r11334 has now been applied to the func_rigid() and
func_iso_cone() target fns.
The temporary data structures are no longer clobbering the permanent
storage structures.
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r11336 | bugman | 2010-07-22 19:38:26 +1000 (Thu, 22 Jul 2010) | 3 lines
Modified the test_compile_2nd_matrix_pseudo_ellipse() unit test to match
the new fn syntax.
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r11337 | bugman | 2010-07-22 23:57:03 +1000 (Thu, 22 Jul 2010) | 3 lines
Silenced the scipy.integrate.quad() warnings by setting the full_output arg
to 1.
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r11338 | bugman | 2010-07-23 02:26:42 +1000 (Fri, 23 Jul 2010) | 3 lines
Limit arrays are now sent into the minfx generic interface for limiting
simulated annealing.
........
Added:
branches/bieri_gui/test_suite/shared_data/structures/trunc_ubi_pcs.pdb
- copied unchanged from r11338,
1.3/test_suite/shared_data/structures/trunc_ubi_pcs.pdb
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
- copied unchanged from r11338,
1.3/test_suite/system_tests/scripts/n_state_model/A_to_chi.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
- copied unchanged from r11338,
1.3/test_suite/system_tests/scripts/n_state_model/pcs_back_calc.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
- copied unchanged from r11338,
1.3/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
branches/bieri_gui/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
- copied unchanged from r11338,
1.3/test_suite/unit_tests/_maths_fns/test_frame_order_matrix_ops.py
branches/bieri_gui/test_suite/unit_tests/_maths_fns/test_pseudo_ellipse.py
- copied unchanged from r11338,
1.3/test_suite/unit_tests/_maths_fns/test_pseudo_ellipse.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/noe.py
branches/bieri_gui/data/align_tensor.py
branches/bieri_gui/generic_fns/align_tensor.py
branches/bieri_gui/generic_fns/frame_order.py
branches/bieri_gui/generic_fns/paramag.py
branches/bieri_gui/generic_fns/pcs.py
branches/bieri_gui/generic_fns/rdc.py
branches/bieri_gui/maths_fns/frame_order.py
branches/bieri_gui/maths_fns/frame_order_matrix_ops.py
branches/bieri_gui/maths_fns/n_state_model.py
branches/bieri_gui/prompt/align_tensor.py
branches/bieri_gui/prompt/frame_order.py
branches/bieri_gui/specific_fns/frame_order.py
branches/bieri_gui/specific_fns/n_state_model.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
branches/bieri_gui/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/bieri_gui/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/noe.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/data/align_tensor.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/align_tensor.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/generic_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/frame_order.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/generic_fns/paramag.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/paramag.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/pcs.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/rdc.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/frame_order.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/frame_order_matrix_ops.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/n_state_model.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/align_tensor.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/prompt/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/frame_order.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/frame_order.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=11339&r1=11338&r2=11339&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/n_state_model.py?rev=11339&r1=11338&r2=11339&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py?rev=11339&r1=11338&r2=11339&view=diff
Modified:
branches/bieri_gui/test_suite/unit_tests/_prompt/test_align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/unit_tests/_prompt/test_align_tensor.py?rev=11339&r1=11338&r2=11339&view=diff
r11339 - in /branches/bieri_gui: ./ auto_analyses/ data/ generic_fns/ maths_fns/ prompt/ specific_fns/ test_suite/shared_dat...