Author: bugman
Date: Fri Oct 2 14:16:40 2015
New Revision: 27955
URL: http://svn.gna.org/viewcvs/relax?rev=27955&view=rev
Log:
Merged revisions 26083-26084,26086,26089-26092,26094,26138 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r26083 | bugman | 2014-09-26 19:42:22 +0200 (Fri, 26 Sep 2014) | 3 lines
Fix for the change of the pipe_control.pipes.test() function to
check_pipe().
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r26084 | bugman | 2014-09-27 00:02:34 +0200 (Sat, 27 Sep 2014) | 5 lines
Small change in the title of the summary table of the frame order
auto-analysis.
'Order parameters' has been replaced by 'Cone half angles' to clarify what
the values really are.
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r26086 | bugman | 2014-09-27 13:07:48 +0200 (Sat, 27 Sep 2014) | 7 lines
Fix for the frame order optimisation target setup printouts.
The 'Numerical integration: ' printout was fixed to 'Quasi-random Sobol'
sequence'. This now
changes to 'SciPy quadratic integration' if cdp.quad_int is set. The text
'PCS' has also been added
for clarification.
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r26089 | bugman | 2014-09-27 16:40:04 +0200 (Sat, 27 Sep 2014) | 6 lines
Removed the call to the frame_order.simulate user function for the rigid
model in the auto-analysis.
There is no motion to simulate in the rigid model, so the
frame_order.simulate user function has no
use.
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r26090 | bugman | 2014-09-27 17:25:28 +0200 (Sat, 27 Sep 2014) | 14 lines
Improvements, fixes, and expansion of the results and data visualisation
file creation.
This is for the frame order auto-analysis. The visualisation() method has
been renamed to
results_output() and its scope expanded. The function previously only
called the
frame_order.pdb_model and frame_order.simulation user functions for
creating PDB representations of
the frame order motions and performing a pseudo-Brownian frame order
dynamics simulate. This has
been extended to also call the results.write user function for outputting
results files and the
rdc.corr_plot and pcs_corr_plot for generating correlation plots of the
measured vs. back-calculated
data.
All parts of the auto-analysis were output files are required now call this
method. This ensures
that all output files are always created, and are placed into the correct
directories.
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r26091 | bugman | 2014-09-27 17:38:25 +0200 (Sat, 27 Sep 2014) | 7 lines
Improvements for the sectioning printouts for the frame order auto-analysis.
The sections now use the lib.text.formatting subtitle() and subsubtitle()
functions to distinguish
them from the output of all the user functions, which use the section(),
subsection() and
subsubsection() functions. New sectioning printouts have been added for
clarity.
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r26092 | bugman | 2014-09-27 17:41:49 +0200 (Sat, 27 Sep 2014) | 6 lines
Possible fixes for the frame order auto-analysis.
This is just in case a user decides to not perform the optimisation
starting with a PCS subset. In
this case, the analysis will now execute correctly.
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r26094 | bugman | 2014-09-30 09:49:39 +0200 (Tue, 30 Sep 2014) | 7 lines
Improvements to the summary table for the frame order auto-analysis.
The rotor and free rotor model motional eigenframe parameter axis_alpha is
now being converted into
spherical angles and reported in the table. This allows the motional
eigenframe of all models to be
easily compared in the table.
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r26138 | bugman | 2014-10-02 15:36:47 +0200 (Thu, 02 Oct 2014) | 6 lines
Created a directory and base PDB system for testing out the PCS information
content.
The base PDB system consists of Ad Bax's CaM domain structures superimposed
onto the open CaM
structure, the N-domain CoM shifted to the origin, and the C-domain CoM
shifted to the z-axis.
........
Added:
trunk/test_suite/shared_data/frame_order/pcs_information_content/
- copied from r26138,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/pcs_information_content/
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/specific_analyses/frame_order/data.py
trunk/specific_analyses/frame_order/optimisation.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27955&r1=27954&r2=27955&view=diff
Modified: trunk/specific_analyses/frame_order/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/data.py?rev=27955&r1=27954&r2=27955&view=diff
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27955&r1=27954&r2=27955&view=diff
r27955 - in /trunk: ./ auto_analyses/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/pcs_information_cont...