Author: bugman
Date: Wed Jun 16 10:12:25 2010
New Revision: 11247
URL: http://svn.gna.org/viewcvs/relax?rev=11247&view=rev
Log:
Merged revisions
11185-11189,11206-11210,11223-11224,11230-11233,11236,11240,11243-11245 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11185 | bugman | 2010-05-11 16:48:07 +0200 (Tue, 11 May 2010) | 3 lines
Added some checks to properly inform the user as to what data is missing.
........
r11186 | bugman | 2010-05-14 15:53:21 +0200 (Fri, 14 May 2010) | 3 lines
Docstring fix for the vect_dist_spherical_angles() function.
........
r11187 | bugman | 2010-05-18 14:15:13 +0200 (Tue, 18 May 2010) | 5 lines
Added a check for the RDC RMS based Q-factor.
This is to check that relax matches both of Pales' Q-factors - which it
does.
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r11188 | bugman | 2010-05-18 17:54:30 +0200 (Tue, 18 May 2010) | 3 lines
Broke some nasty circular import caused by importing the generic_fns.grace
module.
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r11189 | bugman | 2010-05-18 18:32:14 +0200 (Tue, 18 May 2010) | 3 lines
Set names are now only written if they are not None.
........
r11206 | bugman | 2010-05-19 10:49:53 +0200 (Wed, 19 May 2010) | 8 lines
Created the rdc.corr_plot() and pcs_corr_plot() user functions.
These are for creating correlation plots of measured vs. back-calculated
RDCs and PCSs.
A couple of N-state model methods (return_grace_string() and
return_units()) were added to allow the
user functions to work.
........
r11207 | bugman | 2010-05-19 11:31:30 +0200 (Wed, 19 May 2010) | 6 lines
Added a maximum global iteration arg and check into the
dauvergne_protocol.py module.
This was requested by Michael in the commit for r11194 at
https://mail.gna.org/public/relax-commits/2010-05/msg00022.html.
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r11208 | bugman | 2010-05-20 09:24:42 +0200 (Thu, 20 May 2010) | 16 lines
Bug fix for catching the looping around the universal solution in the
dauvergne_protocol module.
This was first identified by Seb in the post at
https://mail.gna.org/public/relax-users/2007-09/msg00010.html (Message-id:
<46EEA6B2.90606@xxxxxxxxx>).
The problem was the automatic looping over optimisation cycles in the
full_analysis.py script. This
code is now in the dauvergne_protocol auto_analyses module. The issue was
a never-ending looping
around the universal solution (the optimisation minimum combined with
Occam's razor or the model
selection minimum). This should now be caught and the protocol terminated
at the end of the first
completed loop. The fix was to compare the chi2, selected models,
diffusion tensor, and model-free
parameters to every iteration, starting from the first. This will not be
optimal if the protocol is
interrupted in the middle of one such loop, but will just mean that a few
extra iterations will be
required to complete the loop.
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r11209 | bugman | 2010-05-21 16:17:46 +0200 (Fri, 21 May 2010) | 3 lines
Modified the relax checklist to include minfx bundling.
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r11210 | bugman | 2010-05-21 16:59:46 +0200 (Fri, 21 May 2010) | 3 lines
More updates to the release checklist.
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r11223 | bugman | 2010-06-08 14:40:49 +0200 (Tue, 08 Jun 2010) | 3 lines
The RDC and PCS correlation plots now do not show deselected spins.
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r11224 | bugman | 2010-06-09 09:54:56 +0200 (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.
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r11230 | bugman | 2010-06-11 13:46:02 +0200 (Fri, 11 Jun 2010) | 3 lines
Bug fix for the control of PyMOL (as a module).
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r11231 | bugman | 2010-06-11 14:02:28 +0200 (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.
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r11232 | bugman | 2010-06-11 14:56:04 +0200 (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 .
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r11233 | bugman | 2010-06-11 15:47:25 +0200 (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 | 2010-06-12 17:33:38 +0200 (Sat, 12 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.
-----
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r11240 | bugman | 2010-06-12 18:17:47 +0200 (Sat, 12 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 .
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r11243 | bugman | 2010-06-15 16:51:24 +0200 (Tue, 15 Jun 2010) | 3 lines
Some function/method docstring epydoc formatting fixes.
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r11244 | bugman | 2010-06-15 16:56:43 +0200 (Tue, 15 Jun 2010) | 3 lines
The RDC and PCS correlation plots now also show the experimental errors.
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r11245 | bugman | 2010-06-15 17:05:56 +0200 (Tue, 15 Jun 2010) | 3 lines
Per point comments are now included in the Grace files.
........
Modified:
branches/cst/ (props changed)
branches/cst/auto_analyses/dauvergne_protocol.py
branches/cst/docs/CHANGES
branches/cst/docs/Release_Checklist
branches/cst/generic_fns/grace.py
branches/cst/generic_fns/pcs.py
branches/cst/generic_fns/pymol_control.py
branches/cst/generic_fns/rdc.py
branches/cst/generic_fns/structure/geometric.py
branches/cst/info.py
branches/cst/maths_fns/n_state_model.py
branches/cst/maths_fns/rotation_matrix.py
branches/cst/prompt/pcs.py
branches/cst/prompt/pymol_control.py
branches/cst/prompt/rdc.py
branches/cst/scons/manuals.py
branches/cst/specific_fns/n_state_model.py
branches/cst/test_suite/system_tests/n_state_model.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/cst/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/auto_analyses/dauvergne_protocol.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/CHANGES?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/Release_Checklist?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/grace.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/pcs.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/pymol_control.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/rdc.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/structure/geometric.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/info.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/n_state_model.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/maths_fns/rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/maths_fns/rotation_matrix.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/pcs.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/prompt/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/pymol_control.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/prompt/rdc.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/scons/manuals.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/specific_fns/n_state_model.py?rev=11247&r1=11246&r2=11247&view=diff
Modified: branches/cst/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/system_tests/n_state_model.py?rev=11247&r1=11246&r2=11247&view=diff
r11247 - in /branches/cst: ./ auto_analyses/ docs/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ scons/ specific_fn...