Author: michaelbieri
Date: Wed Jul 7 05:04:58 2010
New Revision: 11290
URL: http://svn.gna.org/viewcvs/relax?rev=11290&view=rev
Log:
Merged revisions
11223-11224,11230-11233,11236,11240,11243-11246,11248-11263,11269-11289 via
svnmerge from
svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/1.3
........
r11223 | bugman | 2010-06-08 22:40:49 +1000 (Tue, 08 Jun 2010) | 3 lines
The RDC and PCS correlation plots now do not show deselected spins.
........
r11224 | bugman | 2010-06-09 17:54:56 +1000 (Wed, 09 Jun 2010) | 5 lines
Small fix for the grace.write_xy_header() function.
The symbol numbers now range only between the legal values of 1 to 10.
........
r11230 | bugman | 2010-06-11 21:46:02 +1000 (Fri, 11 Jun 2010) | 3 lines
Bug fix for the control of PyMOL (as a module).
........
r11231 | bugman | 2010-06-11 22:02:28 +1000 (Fri, 11 Jun 2010) | 6 lines
Added a method for translating pymol.cmd.do() commands into specific
pymol.cmd functions.
This prevents problems with commands being executed asynchronously. For
example images were being
saved before ray-tracing was complete.
........
r11232 | bugman | 2010-06-11 22:56:04 +1000 (Fri, 11 Jun 2010) | 6 lines
Reverted r11231 as this is not the best way to control pymol.
The command used was:
svn merge -r11231:11230 .
........
r11233 | bugman | 2010-06-11 23:47:25 +1000 (Fri, 11 Jun 2010) | 5 lines
The PyMOL module pymol.cmd is now available within the pymol user function
class.
This is accessible as pymol.cmd from the prompt/script interface.
........
r11236 | bugman | 2010-06-13 01:33:38 +1000 (Sun, 13 Jun 2010) | 14 lines
Merged r11234 from the 1.3.5 tag into the 1.3 line.
The command used was:
svn merge -r11233:11234 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.5 .
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r11234 | bugman | 2010-06-12 17:23:16 +0200 (Sat, 12 Jun 2010) | 3 lines
Changed paths:
M /tags/1.3.5/scons/manuals.py
Excluded minfx from the API manual compilation.
-----
........
r11240 | bugman | 2010-06-13 02:17:47 +1000 (Sun, 13 Jun 2010) | 6 lines
Manually merged the 1.3.5 CHANGES file back into the main line.
The command used was:
svn merge -r11225:11226 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.5 .
........
r11243 | bugman | 2010-06-16 00:51:24 +1000 (Wed, 16 Jun 2010) | 3 lines
Some function/method docstring epydoc formatting fixes.
........
r11244 | bugman | 2010-06-16 00:56:43 +1000 (Wed, 16 Jun 2010) | 3 lines
The RDC and PCS correlation plots now also show the experimental errors.
........
r11245 | bugman | 2010-06-16 01:05:56 +1000 (Wed, 16 Jun 2010) | 3 lines
Per point comments are now included in the Grace files.
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r11246 | bugman | 2010-06-16 02:48:01 +1000 (Wed, 16 Jun 2010) | 3 lines
Bug fix for the RDC back-calculation function.
........
r11248 | bugman | 2010-06-25 22:16:55 +1000 (Fri, 25 Jun 2010) | 5 lines
Added a function for the pseudo-elliptical cosine function.
This is a numerical approximation generated by series expansion.
........
r11249 | bugman | 2010-06-28 19:39:37 +1000 (Mon, 28 Jun 2010) | 3 lines
The RDCs and PCSs can now be given optimisation weights.
........
r11250 | bugman | 2010-06-28 19:47:58 +1000 (Mon, 28 Jun 2010) | 6 lines
Fix for the relax_io.read_spin_data() function for when None is encountered.
The None values are now returned rather than skipped so that the calling
code can decide what to do
with it.
........
r11251 | bugman | 2010-06-28 19:48:38 +1000 (Mon, 28 Jun 2010) | 3 lines
Fix for the unit tests, the pseudo_ellipse module is now listed in
maths_fns.__all__.
........
r11252 | bugman | 2010-06-28 21:53:02 +1000 (Mon, 28 Jun 2010) | 6 lines
Fix for the get_data() function - the returned data structure is dependent
on the errors.
Instead of a list of x, y, error 1, error 2 with the errors set to None if
non-existent, only the
required errors are returned.
........
r11253 | bugman | 2010-06-29 01:55:59 +1000 (Tue, 29 Jun 2010) | 3 lines
Fix for the Grace write_xy_data() function for when data values of None are
passed in.
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r11254 | bugman | 2010-06-29 17:45:17 +1000 (Tue, 29 Jun 2010) | 3 lines
The alignment tensor optimisation is now optional within the population
N-state model target fn.
........
r11255 | bugman | 2010-06-29 19:07:54 +1000 (Tue, 29 Jun 2010) | 3 lines
Created the align_tensor.fix() user function for fixing the alignment
tensor during optimisation.
........
r11256 | bugman | 2010-06-29 19:12:37 +1000 (Tue, 29 Jun 2010) | 5 lines
The align_tensor.copy() tensor_to arg can now be None.
This is useful for copying between data pipes.
........
r11257 | bugman | 2010-06-29 19:25:58 +1000 (Tue, 29 Jun 2010) | 5 lines
Added the N-state model _minimise_setup_fixed_tensors() method.
This assembles the fixed tensors into an array for use in the maths_fns
code.
........
r11258 | bugman | 2010-06-29 19:48:23 +1000 (Tue, 29 Jun 2010) | 3 lines
The fixed alignment tensors are no longer included in the parameter vector
from _assemble_param_vector().
........
r11259 | bugman | 2010-06-29 20:00:09 +1000 (Tue, 29 Jun 2010) | 3 lines
Fixed for the N-state model target functions for when there is nothing to
optimisise.
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r11260 | bugman | 2010-06-29 20:24:04 +1000 (Tue, 29 Jun 2010) | 3 lines
Fixes for the N-state model introduced by the fixed tensors.
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r11261 | bugman | 2010-06-29 20:24:42 +1000 (Tue, 29 Jun 2010) | 3 lines
Fixes for the N-state model target function setup for when no parameters
are optimised.
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r11262 | bugman | 2010-06-29 22:08:15 +1000 (Tue, 29 Jun 2010) | 3 lines
More fixes for fixed alignment tensors.
........
r11263 | bugman | 2010-06-29 23:45:42 +1000 (Tue, 29 Jun 2010) | 3 lines
Better support for tensor-less N-state model optimisation.
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r11269 | bugman | 2010-07-01 18:25:33 +1000 (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 18:31:10 +1000 (Thu, 01 Jul 2010) | 3 lines
The errors in the correlation plots are now optional.
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r11271 | bugman | 2010-07-01 18:48:48 +1000 (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 18:40:23 +1000 (Fri, 02 Jul 2010) | 3 lines
Added a new system test for the direct optimisation of the paramagnetic
centre.
........
r11273 | bugman | 2010-07-02 18:41:41 +1000 (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.
........
r11274 | bugman | 2010-07-02 18:47:57 +1000 (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.
........
r11275 | bugman | 2010-07-02 18:53:18 +1000 (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 18:54:49 +1000 (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 18:55:42 +1000 (Fri, 02 Jul 2010) | 3 lines
The paramag user function class is now accessible.
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r11278 | bugman | 2010-07-02 18:59:20 +1000 (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 19:50:32 +1000 (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 20:07:05 +1000 (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 21:24:55 +1000 (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 21:31:52 +1000 (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 | 2010-07-03 01:39:21 +1000 (Sat, 03 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.
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r11284 | bugman | 2010-07-03 01:50:23 +1000 (Sat, 03 Jul 2010) | 3 lines
The paramagnetic centre optimisation has been merged into the
func_population() target function.
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r11285 | bugman | 2010-07-03 03:36:51 +1000 (Sat, 03 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 19:38:32 +1000 (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 | 2010-07-04 04:08:53 +1000 (Sun, 04 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 | 2010-07-04 05:56:40 +1000 (Sun, 04 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 | 2010-07-07 02:10:10 +1000 (Wed, 07 Jul 2010) | 3 lines
The N-state model now supports the paramagnetic centre in
return_data_name().
........
Added:
branches/bieri_gui/generic_fns/paramag.py
- copied unchanged from r11289, 1.3/generic_fns/paramag.py
branches/bieri_gui/maths_fns/paramag_centre.py
- copied unchanged from r11289, 1.3/maths_fns/paramag_centre.py
branches/bieri_gui/maths_fns/pseudo_ellipse.py
- copied unchanged from r11289, 1.3/maths_fns/pseudo_ellipse.py
branches/bieri_gui/prompt/paramag.py
- copied unchanged from r11289, 1.3/prompt/paramag.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
- copied unchanged from r11289,
1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/docs/CHANGES
branches/bieri_gui/generic_fns/__init__.py
branches/bieri_gui/generic_fns/align_tensor.py
branches/bieri_gui/generic_fns/grace.py
branches/bieri_gui/generic_fns/pcs.py
branches/bieri_gui/generic_fns/pymol_control.py
branches/bieri_gui/generic_fns/rdc.py
branches/bieri_gui/generic_fns/structure/geometric.py
branches/bieri_gui/info.py
branches/bieri_gui/maths_fns/__init__.py
branches/bieri_gui/maths_fns/n_state_model.py
branches/bieri_gui/maths_fns/rotation_matrix.py
branches/bieri_gui/prompt/__init__.py
branches/bieri_gui/prompt/align_tensor.py
branches/bieri_gui/prompt/interpreter.py
branches/bieri_gui/prompt/pcs.py
branches/bieri_gui/prompt/pymol_control.py
branches/bieri_gui/prompt/rdc.py
branches/bieri_gui/relax_io.py
branches/bieri_gui/scons/manuals.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/align_fit.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/populations.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bieri_gui/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/docs/CHANGES?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/__init__.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/grace.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/pymol_control.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/geometric.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/info.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/maths_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/__init__.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/maths_fns/rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/rotation_matrix.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/__init__.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/interpreter.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pcs.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/prompt/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/pymol_control.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/rdc.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/relax_io.py?rev=11290&r1=11289&r2=11290&view=diff
Modified: branches/bieri_gui/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/scons/manuals.py?rev=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&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=11290&r1=11289&r2=11290&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/align_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/align_fit.py?rev=11290&r1=11289&r2=11290&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py?rev=11290&r1=11289&r2=11290&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=11290&r1=11289&r2=11290&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/missing_data_test.py?rev=11290&r1=11289&r2=11290&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/populations.py?rev=11290&r1=11289&r2=11290&view=diff
r11290 - in /branches/bieri_gui: ./ docs/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ scons/ specific_fns/ test_s...