Commits for the relax NMR molecular dynamics analysis software. ()

edward | 17 May 2013 11:20

r19700 - in /branches/relax_disp/test_suite/shared_data/dispersion/Hansen: ./ 500_MHz/ 800_MHz/

Author: bugman
Date: Fri May 17 11:20:10 2013
New Revision: 19700

URL: http://svn.gna.org/viewcvs/relax?rev=19700&view=rev
Log:
Now all of the Hansen CPMG data is present as truncated Sparky peak lists.

Added:
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in.bis_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in.bis_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/133.33.in.bis_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/533.33.in.bis_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/933.33.in.bis_trunc
Modified:
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/truncate_data.py

Added: branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_trunc
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_trunc?rev=19700&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_trunc (added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in.bis_trunc
Fri May 17 11:20:10 2013
 <at>  <at>  -1,0 +1,4  <at>  <at> 
+Assignment    w1         w2      Data Height
+
+GLY70N-HN    108.972    7.112    1.6276208e+04

(Continue reading)

edward | 17 May 2013 11:18

r19699 - in /branches/relax_disp/test_suite/shared_data/dispersion/Hansen: ./ 500_MHz/ 800_MHz/

Author: bugman
Date: Fri May 17 11:17:59 2013
New Revision: 19699

URL: http://svn.gna.org/viewcvs/relax?rev=19699&view=rev
Log:
The truncated Hansen CPMG data is now in the form of Sparky peak lists.

Modified:
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/1000.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/200.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/266.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/333.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/400.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/466.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/600.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/66.667.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/666.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/733.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/800.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/866.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/reference.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/1000.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/133.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/200.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/266.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/333.33.in_trunc

(Continue reading)

edward | 17 May 2013 11:12

r19698 - in /branches/relax_disp/test_suite/shared_data/dispersion/Hansen: ./ 500_MHz/ 800_MHz/

Author: bugman
Date: Fri May 17 11:12:53 2013
New Revision: 19698

URL: http://svn.gna.org/viewcvs/relax?rev=19698&view=rev
Log:
Created truncated data files of the Hansen CPMG data.

This consists of residues 70 and 71 and will be used to massively speed up the system tests.

Added:
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/1000.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/133.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/200.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/266.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/333.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/400.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/466.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/533.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/600.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/66.667.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/666.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/733.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/800.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/866.67.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/933.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/500_MHz/reference.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/1000.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/133.33.in_trunc
    branches/relax_disp/test_suite/shared_data/dispersion/Hansen/800_MHz/200.in_trunc

(Continue reading)

edward | 17 May 2013 11:02

r19697 - /branches/relax_disp/specific_analyses/relax_disp/parameters.py

Author: bugman
Date: Fri May 17 11:02:52 2013
New Revision: 19697

URL: http://svn.gna.org/viewcvs/relax?rev=19697&view=rev
Log:
Finally Monte Carlo simulations for the relaxation dispersion models now work.

This was a simple fix for the specific_analyses.relax_disp.parameters.param_index_to_param_info()
function.

Modified:
    branches/relax_disp/specific_analyses/relax_disp/parameters.py

Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=19697&r1=19696&r2=19697&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Fri May 17 11:02:52 2013
 <at>  <at>  -511,7 +511,7  <at>  <at> 

     # All other parameters.
     else:
-        param_name = names[index-2]
+        param_name = spins[0].params[index]

     # Return the data.
     return param_name, spin_index

(Continue reading)

edward | 17 May 2013 10:47

r19696 - in /branches/relax_disp: ./ test_suite/unit_tests/package_checking.py

Author: bugman
Date: Fri May 17 10:47:59 2013
New Revision: 19696

URL: http://svn.gna.org/viewcvs/relax?rev=19696&view=rev
Log:
Merged revisions 19695 via svnmerge from 
svn+ssh://bugman@.../svn/relax/trunk

........
  r19695 | bugman | 2013-05-17 10:47:20 +0200 (Fri, 17 May 2013) | 12 lines

  Fix for the package checking as part of the unit tests.

  This was identified from the bug report #20820 (https://gna.org/bugs/?20820) submitted by Troels E.
  Linnet (https://gna.org/users/tlinnet).

  The problem was that on some systems, the full path is required for checking the presence of the
  directories which are the sub-packages of the main package being checked.  The result was that 
  checking for the package in the __all__ list was skipped.

  Note that this change does not fix the bug reported.
........

Modified:
    branches/relax_disp/   (props changed)
    branches/relax_disp/test_suite/unit_tests/package_checking.py

Propchange: branches/relax_disp/
------------------------------------------------------------------------------

(Continue reading)

edward | 17 May 2013 10:47

r19695 - /trunk/test_suite/unit_tests/package_checking.py

Author: bugman
Date: Fri May 17 10:47:20 2013
New Revision: 19695

URL: http://svn.gna.org/viewcvs/relax?rev=19695&view=rev
Log:
Fix for the package checking as part of the unit tests.

This was identified from the bug report #20820 (https://gna.org/bugs/?20820) submitted by Troels E.
Linnet (https://gna.org/users/tlinnet).

The problem was that on some systems, the full path is required for checking the presence of the
directories which are the sub-packages of the main package being checked.  The result was that 
checking for the package in the __all__ list was skipped.

Note that this change does not fix the bug reported.

Modified:
    trunk/test_suite/unit_tests/package_checking.py

Modified: trunk/test_suite/unit_tests/package_checking.py
URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/package_checking.py?rev=19695&r1=19694&r2=19695&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/package_checking.py (original)
+++ trunk/test_suite/unit_tests/package_checking.py Fri May 17 10:47:20 2013
 <at>  <at>  -25,6 +25,7  <at>  <at> 
 from re import search

 # relax module imports.
+from status import Status; status = Status()

(Continue reading)

edward | 16 May 2013 19:26

r19694 - in /branches/relax_disp/specific_analyses/relax_disp: init.py parameters.py

Author: bugman
Date: Thu May 16 19:26:25 2013
New Revision: 19694

URL: http://svn.gna.org/viewcvs/relax?rev=19694&view=rev
Log:
A number of fixes to partly enable Monte Carlo simulations for the non 'R2eff' dispersion models.

Modified:
    branches/relax_disp/specific_analyses/relax_disp/__init__.py
    branches/relax_disp/specific_analyses/relax_disp/parameters.py

Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19694&r1=19693&r2=19694&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Thu May 16 19:26:25 2013
 <at>  <at>  -55,7 +55,7  <at>  <at> 
 from pipe_control.result_files import add_result_file
 from specific_analyses.api_base import API_base
 from specific_analyses.api_common import API_common
-from specific_analyses.relax_disp.disp_data import average_intensity, find_intensity_keys,
loop_frq, loop_frq_point, loop_frq_point_key, loop_frq_point_time, loop_point, loop_time,
relax_time, return_cpmg_frqs, return_key_from_disp_point_index, return_param_key_from_data,
return_r2eff_arrays, return_spin_lock_nu1
+from specific_analyses.relax_disp.disp_data import average_intensity, find_intensity_keys,
loop_frq, loop_frq_point, loop_frq_point_key, loop_frq_point_time, loop_point, loop_time,
relax_time, return_cpmg_frqs, return_index_from_disp_point, return_index_from_frq,
return_key_from_disp_point_index, return_param_key_from_data, return_r2eff_arrays, return_spin_lock_nu1
 from specific_analyses.relax_disp.parameters import assemble_param_vector,

(Continue reading)

edward | 16 May 2013 18:35

r19693 - in /branches/relax_disp/specific_analyses/relax_disp: init.py disp_data.py parameters.py

Author: bugman
Date: Thu May 16 18:35:52 2013
New Revision: 19693

URL: http://svn.gna.org/viewcvs/relax?rev=19693&view=rev
Log:
Major redesign of the relaxation dispersion data model in the relax data store.

The data model now revolves around the three concepts of the spectrometer frequency, the dispersion
points, and the relaxation times.  Peak intensity data is now handled through averaging using the
new specific_analyses.relax_disp.disp_data.average_intensity() function.  R2eff/R1rho values are now
referenced by a key generated from the spectrometer frequency and nu_CPMG frequency or nu1 spin-lock
field strength.  All of the specific_analyses.relax_disp package has been standardised around these
concepts.  This simplifies all of the modules of the package and removes a large number of latent
bugs.

Modified:
    branches/relax_disp/specific_analyses/relax_disp/__init__.py
    branches/relax_disp/specific_analyses/relax_disp/disp_data.py
    branches/relax_disp/specific_analyses/relax_disp/parameters.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19693&r1=19692&r2=19693&view=diff

Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=19693&r1=19692&r2=19693&view=diff

Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py

(Continue reading)

edward | 15 May 2013 18:23

r19692 - in /branches/relax_disp: ./ compat.py

Author: bugman
Date: Wed May 15 18:23:11 2013
New Revision: 19692

URL: http://svn.gna.org/viewcvs/relax?rev=19692&view=rev
Log:
Merged revisions 19691 via svnmerge from 
svn+ssh://bugman@.../svn/relax/trunk

........
  r19691 | bugman | 2013-05-15 18:19:46 +0200 (Wed, 15 May 2013) | 3 lines

  Epydoc docstring fixes for the compat module.
........

Modified:
    branches/relax_disp/   (props changed)
    branches/relax_disp/compat.py

Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed May 15 18:23:11 2013
 <at>  <at>  -1,1 +1,1  <at>  <at> 
-/trunk:1-19688
+/trunk:1-19691

Modified: branches/relax_disp/compat.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/compat.py?rev=19692&r1=19691&r2=19692&view=diff
==============================================================================

(Continue reading)

edward | 15 May 2013 18:19

r19691 - /trunk/compat.py

Author: bugman
Date: Wed May 15 18:19:46 2013
New Revision: 19691

URL: http://svn.gna.org/viewcvs/relax?rev=19691&view=rev
Log:
Epydoc docstring fixes for the compat module.

Modified:
    trunk/compat.py

Modified: trunk/compat.py
URL: http://svn.gna.org/viewcvs/relax/trunk/compat.py?rev=19691&r1=19690&r2=19691&view=diff
==============================================================================
--- trunk/compat.py (original)
+++ trunk/compat.py Wed May 15 18:19:46 2013
 <at>  <at>  -107,7 +107,7  <at>  <at> 
      <at> param file:    The file path to open.
      <at> type file:     str
      <at> keyword mode:  The mode to open the file with.  Only the values of 'r' and 'w' for reading and writing
respectively are supported.
-     <at> type model:    str
+     <at> type mode:     str
      <at> return:        The bzip2 file object.
      <at> rtype:         file object
     """
 <at>  <at>  -161,7 +161,7  <at>  <at> 
      <at> param file:    The file path to open.
      <at> type file:     str
      <at> keyword mode:  The mode to open the file with.  Only the values of 'r' and 'w' for reading and writing

(Continue reading)

edward | 15 May 2013 17:57

r19690 - /branches/relax_disp/specific_analyses/relax_disp/init.py

Author: bugman
Date: Wed May 15 17:57:18 2013
New Revision: 19690

URL: http://svn.gna.org/viewcvs/relax?rev=19690&view=rev
Log:
Basic fix for the _back_calc_r2eff() relaxation dispersion method.

A variable was misnamed.

Modified:
    branches/relax_disp/specific_analyses/relax_disp/__init__.py

Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19690&r1=19689&r2=19690&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Wed May 15 17:57:18 2013
 <at>  <at>  -140,7 +140,7  <at>  <at> 
         results = {}
         for frq_index in range(field_count):
             for point_index in range(cdp.dispersion_points):
-                key = disp_point_key_from_index(i)
+                key = disp_point_key_from_index(point_index)
                 results[key] = model.back_calc[0, 0, point_index]

         # Return the back calculated R2eff values.

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r19700 - in /branches/relax_disp/test_suite/shared_data/dispersion/Han (17 May 2013)
r19699 - in /branches/relax_disp/test_suite/shared_data/dispersion/Han (17 May 2013)
r19698 - in /branches/relax_disp/test_suite/shared_data/dispersion/Han (17 May 2013)
r19697 - /branches/relax_disp/specific_analyses/relax_disp/parameters. (17 May 2013)
r19696 - in /branches/relax_disp: ./ test_suite/unit_tests/package_che (17 May 2013)
r19695 - /trunk/test_suite/unit_tests/package_checking.py (17 May 2013)
r19694 - in /branches/relax_disp/specific_analyses/relax_disp: __init_ (16 May 2013)
r19693 - in /branches/relax_disp/specific_analyses/relax_disp: __init_ (16 May 2013)
r19692 - in /branches/relax_disp: ./ compat.py (15 May 2013)
r19691 - /trunk/compat.py (15 May 2013)
r19690 - /branches/relax_disp/specific_analyses/relax_disp/__init__.py (15 May 2013)
r19689 - in /branches/relax_disp: ./ specific_analyses/ specific_analy (15 May 2013)
r19688 - in /trunk/specific_analyses: ./ consistency_tests/ frame_orde (15 May 2013)
r19687 - /branches/relax_disp/specific_analyses/relax_disp/parameters. (15 May 2013)
r19686 - /branches/relax_disp/specific_analyses/relax_disp/__init__.py (15 May 2013)
r19685 - /branches/relax_disp/test_suite/system_tests/relax_disp.py (15 May 2013)
r19684 - in /branches/relax_disp: ./ test_suite/system_tests/scripts/n (15 May 2013)
r19683 - /trunk/test_suite/system_tests/scripts/n_state_model/paramag_ (15 May 2013)
r19682 - /website/windows_devel.html (14 May 2013)
r19681 - /website/windows_devel.html (13 May 2013)
r19680 - /website/windows_devel.html (13 May 2013)

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