Author: bugman
Date: Tue Feb 23 19:18:47 2010
New Revision: 10871
URL: http://svn.gna.org/viewcvs/relax?rev=10871&view=rev
Log:
Merged revisions
10766-10789,10794-10829,10838,10841-10842,10845-10860,10862,10865 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r10766 | bugman | 2010-02-19 11:09:06 +0100 (Fri, 19 Feb 2010) | 3 lines
Converted write_multi_header() to write_xy_header() and simplified the args
by expecting [X, Y] pairs.
........
r10767 | bugman | 2010-02-19 11:43:22 +0100 (Fri, 19 Feb 2010) | 6 lines
Clean up of write_xy_header().
Labels are now not overwritten if supplied, all file.write() operations are
collected together, and
the X and Y-axis settings have been merged.
........
r10768 | bugman | 2010-02-19 11:46:25 +0100 (Fri, 19 Feb 2010) | 3 lines
write_xy_header() now has a sets arg for specifying the number of data sets
in the graph G0.
........
r10769 | bugman | 2010-02-19 14:11:57 +0100 (Fri, 19 Feb 2010) | 7 lines
More changes to write_xy_header().
The return_units() and return_grace_string() analysis specific methods are
no longer passed in as
args but are set up in the method itself. Many simplifications have been
made. And now spin data
has been made axis independent - it can be X or Y data.
........
r10770 | bugman | 2010-02-19 14:43:19 +0100 (Fri, 19 Feb 2010) | 3 lines
Bug fix for write_xy_header(), a statement typo was stopping relax from
running.
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r10771 | bugman | 2010-02-19 14:46:26 +0100 (Fri, 19 Feb 2010) | 3 lines
Added symbol formatting to the individual graph sets in write_xy_header().
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r10772 | bugman | 2010-02-19 14:47:42 +0100 (Fri, 19 Feb 2010) | 5 lines
Deletion of the write_header() function.
This is now redundant due to the improvements in write_xy_header().
........
r10773 | bugman | 2010-02-19 14:51:15 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the call to write_xy_header().
This is now independent of the number of data sets, and is called correctly.
........
r10774 | bugman | 2010-02-19 14:54:39 +0100 (Fri, 19 Feb 2010) | 3 lines
Added the axis_min and axis_max args to write_xy_header() for specifying
the graph ranges.
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r10775 | bugman | 2010-02-19 14:56:10 +0100 (Fri, 19 Feb 2010) | 5 lines
Typo fix in write_xy_header().
axis_label should have been axis_labels!
........
r10776 | bugman | 2010-02-19 15:09:10 +0100 (Fri, 19 Feb 2010) | 5 lines
Spin ids are no longer passed into write_xy_header().
Instead the new args seq_type and set_names are passed in.
........
r10777 | bugman | 2010-02-19 15:13:32 +0100 (Fri, 19 Feb 2010) | 3 lines
Fix for the counting of the number of graph sets.
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r10778 | bugman | 2010-02-19 15:33:40 +0100 (Fri, 19 Feb 2010) | 5 lines
Shifted to using write_xy_data().
This was the write_multi_data() function, and write_data() function has
been deleted.
........
r10779 | bugman | 2010-02-19 15:52:28 +0100 (Fri, 19 Feb 2010) | 7 lines
Changed the format of the data arg to write_xy_data().
This is a huge simplification and makes the function more usable for any
type of data thrown at it.
The structure is now expected to be a 4D list/array corresponding to Gx,
Sx, data point, data point
info.
........
r10780 | bugman | 2010-02-19 17:03:42 +0100 (Fri, 19 Feb 2010) | 7 lines
Redesign of get_data() and deletion of determine_graph_type().
get_data() determines the graph type in a few lines of code, so
determine_graph_type() is not
necessary. get_data() now returns the 4D grace graph data structure, the
labels for the data sets,
and the graph_type.
........
r10781 | bugman | 2010-02-19 17:08:23 +0100 (Fri, 19 Feb 2010) | 3 lines
Clean up of the write() function for the new get_data() design.
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r10782 | bugman | 2010-02-19 18:18:44 +0100 (Fri, 19 Feb 2010) | 3 lines
Fixes for get_data() for when the analysis specific return_value() fn
returns a list of values!
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r10783 | bugman | 2010-02-19 18:22:23 +0100 (Fri, 19 Feb 2010) | 3 lines
Fix for the graph type determination in get_data().
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r10784 | bugman | 2010-02-19 18:23:34 +0100 (Fri, 19 Feb 2010) | 3 lines
Removed the linestyle setting in write_xy_header() that made the line
invisible.
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r10785 | bugman | 2010-02-19 18:35:57 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the write_xy_header() method.
The args are now explicitly reset as they are lists and are persistent!
........
r10786 | bugman | 2010-02-19 18:37:59 +0100 (Fri, 19 Feb 2010) | 5 lines
Another fix for write_xy_header().
The "world xmax" and "world xmax" were being set as the minimums!
........
r10787 | bugman | 2010-02-19 18:40:42 +0100 (Fri, 19 Feb 2010) | 5 lines
Another fix for write_xy_header().
This time, "(normalised)" is not added to the X-axis label for normalised
plots.
........
r10788 | bugman | 2010-02-19 19:00:30 +0100 (Fri, 19 Feb 2010) | 5 lines
Fix for the test_bug_12670_12679() system test.
The Grace file lines are now not hardcoded!!!
........
r10789 | bugman | 2010-02-21 15:44:45 +0100 (Sun, 21 Feb 2010) | 5 lines
Bug fix for the test_R_to_axis_angle_180_complex() for MS Windows.
self.assertAlmostEquals() has to be used do to precision issues.
........
r10794 | bugman | 2010-02-22 10:13:04 +0100 (Mon, 22 Feb 2010) | 3 lines
Args after the flags -x, -u, -s are now considered to be the tests
performed and not a script.
........
r10795 | bugman | 2010-02-22 10:14:15 +0100 (Mon, 22 Feb 2010) | 3 lines
Test_suite_runner now has an __init__() method and stores the list of tests.
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r10796 | bugman | 2010-02-22 10:20:14 +0100 (Mon, 22 Feb 2010) | 3 lines
Finished the __init__() docstring and passed the tests arg into the system
tests.
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r10797 | bugman | 2010-02-22 10:22:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Passed self.tests into the run() method instead of the class __init__()
method.
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r10798 | bugman | 2010-02-22 10:32:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Individual system tests can now be executed through the relax test suite.
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r10799 | bugman | 2010-02-22 10:33:34 +0100 (Mon, 22 Feb 2010) | 3 lines
The tests list is now optional.
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r10800 | bugman | 2010-02-22 10:39:03 +0100 (Mon, 22 Feb 2010) | 3 lines
The paper size of A4 can now be set in write_xy_header().
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r10801 | bugman | 2010-02-22 10:43:28 +0100 (Mon, 22 Feb 2010) | 5 lines
Changed the handling of the [None, None] format args.
These now default to None and are converted to [None, None] inside the
function.
........
r10802 | bugman | 2010-02-22 10:47:27 +0100 (Mon, 22 Feb 2010) | 3 lines
In write_xy_header(), the legend box can be now turned on or off and can
have its position set.
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r10803 | bugman | 2010-02-22 10:50:42 +0100 (Mon, 22 Feb 2010) | 3 lines
Set colours can now be specified in write_xy_header().
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r10804 | bugman | 2010-02-22 10:52:36 +0100 (Mon, 22 Feb 2010) | 3 lines
The symbols are now also coloured in write_xy_header().
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r10805 | bugman | 2010-02-22 11:00:12 +0100 (Mon, 22 Feb 2010) | 5 lines
Much finer control of the set appearance in write_xy_header().
The symbol style, sizes, and line linestyle can now all be specified.
........
r10806 | bugman | 2010-02-22 11:10:18 +0100 (Mon, 22 Feb 2010) | 5 lines
Fix for the colour setting in write_xy_header().
The arg is called set_colours, not colours!
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r10807 | bugman | 2010-02-22 11:15:09 +0100 (Mon, 22 Feb 2010) | 3 lines
The graph title and subtitle can be specified in write_xy_header().
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r10808 | bugman | 2010-02-22 11:18:28 +0100 (Mon, 22 Feb 2010) | 3 lines
Fix for write_xy_header(), axis limits are now set when the value is 0.
........
r10809 | bugman | 2010-02-22 11:21:03 +0100 (Mon, 22 Feb 2010) | 3 lines
The 'Spin ' text is now prepended to the legend only in get_data(), and not
write_xy_header().
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r10810 | bugman | 2010-02-22 11:23:04 +0100 (Mon, 22 Feb 2010) | 3 lines
The grace version of the write_xy_header() header is not output.
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r10811 | bugman | 2010-02-22 13:07:36 +0100 (Mon, 22 Feb 2010) | 3 lines
The graph view port size can now be changes and defaults to a larger value.
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r10812 | bugman | 2010-02-22 13:21:51 +0100 (Mon, 22 Feb 2010) | 3 lines
The symbol fill style can now be specified in write_xy_header().
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r10813 | bugman | 2010-02-22 13:26:50 +0100 (Mon, 22 Feb 2010) | 3 lines
The linewidth for all graph elements can now be set in write_xy_header().
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r10814 | bugman | 2010-02-22 13:38:09 +0100 (Mon, 22 Feb 2010) | 3 lines
The line type for each set can now be specified in write_xy_header().
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r10815 | bugman | 2010-02-22 13:39:46 +0100 (Mon, 22 Feb 2010) | 3 lines
Stereochem_analysis.grace_plots() now uses the new write_xy_header() &
write_xy_data() fns.
........
r10816 | bugman | 2010-02-22 14:31:21 +0100 (Mon, 22 Feb 2010) | 5 lines
The number of ensembles string is now more nicely formatted in the subtitle.
This is in Stereochem_analysis.grace_plots().
........
r10817 | bugman | 2010-02-22 15:10:11 +0100 (Mon, 22 Feb 2010) | 3 lines
Fix for the write_xy_header() function for when the data_type arg is not
supplied.
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r10818 | bugman | 2010-02-22 16:13:55 +0100 (Mon, 22 Feb 2010) | 3 lines
Added an NOE normalisation variable to the stereochem_analysis.py sample
script.
........
r10819 | bugman | 2010-02-22 16:19:10 +0100 (Mon, 22 Feb 2010) | 3 lines
Scaled NOE violation correlation plots (RDC Q vs. NOE Q) are now being
created.
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r10820 | bugman | 2010-02-22 16:20:45 +0100 (Mon, 22 Feb 2010) | 3 lines
The noe_norm arg is now accepted by the Stereochem_analysis class.
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r10821 | bugman | 2010-02-22 16:21:22 +0100 (Mon, 22 Feb 2010) | 3 lines
Whitespace fixes for the storage of all the Stereochem_analysis args.
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r10822 | bugman | 2010-02-22 16:36:13 +0100 (Mon, 22 Feb 2010) | 3 lines
Completed the Stereochem_analysis.__init__() docstring, adding all the
epydoc tags.
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r10823 | bugman | 2010-02-22 16:45:27 +0100 (Mon, 22 Feb 2010) | 3 lines
Fixed the x-axis label for the scaled Q-factor vs. Q-factor correlation
plot.
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r10824 | bugman | 2010-02-22 17:03:21 +0100 (Mon, 22 Feb 2010) | 3 lines
Changed the axis ranges for the RDC Q-factor vs. NOE Q-factor correlation
plot.
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r10825 | bugman | 2010-02-22 18:04:14 +0100 (Mon, 22 Feb 2010) | 6 lines
Added the -i or --info option to relax.
This causes all of the information about relax and Python to be printed by
calling
Info_box.print_sys_info(). This option will be useful for determining
issues with relax installs!
........
r10826 | bugman | 2010-02-22 18:10:52 +0100 (Mon, 22 Feb 2010) | 3 lines
Shifted the relax intro string (written to STDOUT) from the interpreter
module to the Info_box.
........
r10827 | bugman | 2010-02-22 18:17:12 +0100 (Mon, 22 Feb 2010) | 5 lines
Renamed Info_box.print_sys_info() to Info_box.sys_info().
The method now returns the info string, and this is printed later.
........
r10828 | bugman | 2010-02-22 18:19:09 +0100 (Mon, 22 Feb 2010) | 3 lines
Replaced the relax version line with the full relax intro when using the -i
cmdline flag.
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r10829 | bugman | 2010-02-22 19:59:57 +0100 (Mon, 22 Feb 2010) | 14 lines
The Info_box.package_info() has been added to provide package information.
This is show with the -i cmdline option. The following packages are
currently reported:
minfx
bmrblib
numpy
Numeric
ScientificPython
wxPython
mpi4py
scons
epydoc
........
r10838 | bugman | 2010-02-23 02:41:04 +0100 (Tue, 23 Feb 2010) | 3 lines
Fixes for the N_state_model.test_stereochem_analysis system test for the
new normalised NOE plots.
........
r10841 | bugman | 2010-02-23 02:52:08 +0100 (Tue, 23 Feb 2010) | 3 lines
Fix for the Info_box.package_info() method for when a package is not
installed.
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r10842 | bugman | 2010-02-23 02:55:39 +0100 (Tue, 23 Feb 2010) | 3 lines
Info_box.sys_info() no longer prints the computer's URL!
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r10845 | bugman | 2010-02-23 11:15:31 +0100 (Tue, 23 Feb 2010) | 5 lines
Added a 6th stage to the stereochemistry analysis script.
This is the ordering of all ensembles using a combined Q-factor.
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r10846 | bugman | 2010-02-23 11:18:32 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the stage number in the stereochemistry auto analysis.
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r10847 | bugman | 2010-02-23 11:43:47 +0100 (Tue, 23 Feb 2010) | 5 lines
Stage 6, the combined Q-factor and final ordering is now complete.
The combined_q() method was written to perform this last analysis.
........
r10848 | bugman | 2010-02-23 13:29:04 +0100 (Tue, 23 Feb 2010) | 5 lines
The modules are no longer deleted after import from dep_check.
This will allow dep_check to be used for extracting package information by
the Info_box.
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r10849 | bugman | 2010-02-23 13:44:08 +0100 (Tue, 23 Feb 2010) | 3 lines
Added checks for the bmrblib and Numeric packages.
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r10850 | bugman | 2010-02-23 13:49:32 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a specific import check for Scientific - the other checking the PDB
module import.
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r10851 | bugman | 2010-02-23 13:52:53 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the wx module.
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r10852 | bugman | 2010-02-23 13:54:49 +0100 (Tue, 23 Feb 2010) | 3 lines
Added a check for the mpi4py module.
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r10853 | bugman | 2010-02-23 13:55:24 +0100 (Tue, 23 Feb 2010) | 3 lines
Made the mpi4py import flag more consistent.
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r10854 | bugman | 2010-02-23 14:05:49 +0100 (Tue, 23 Feb 2010) | 3 lines
Added an import check for epydoc.
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r10855 | bugman | 2010-02-23 14:20:57 +0100 (Tue, 23 Feb 2010) | 3 lines
Imported os in the os.devnull import check, and deleted devnull.
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r10856 | bugman | 2010-02-23 14:23:45 +0100 (Tue, 23 Feb 2010) | 5 lines
Redesigned package_info() to remove the dependence on the pkg_resources
module.
This was a problem in many old python versions. The package info is now
presented in a table.
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r10857 | bugman | 2010-02-23 14:27:27 +0100 (Tue, 23 Feb 2010) | 3 lines
Added the relax C module compilation info.
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r10858 | bugman | 2010-02-23 14:28:33 +0100 (Tue, 23 Feb 2010) | 3 lines
The version-less modules now have an empty string for the version printed.
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r10859 | bugman | 2010-02-23 14:34:47 +0100 (Tue, 23 Feb 2010) | 6 lines
Made Info_box.sys_info() fault tolerant.
All the contents of the platform module are checked before added the text,
allowing for older python
versions.
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r10860 | bugman | 2010-02-23 16:06:48 +0100 (Tue, 23 Feb 2010) | 17 lines
A python 3.0 fix for the grace module.
The command used was:
2to3 -w \
> -f buffer \
> -f idioms \
> -f set_literal \
> -f ws_comma \
> -x except \
> -x import \
> -x imports \
> -x long \
> -x numliterals \
> -x xrange \
> relax .
........
r10862 | bugman | 2010-02-23 18:20:45 +0100 (Tue, 23 Feb 2010) | 5 lines
Converted the Info_box into a singleton.
This will allow for execution specific info to be placed in here and
accessed by all.
........
r10865 | bugman | 2010-02-23 18:31:03 +0100 (Tue, 23 Feb 2010) | 5 lines
The Info_box is now really a singleton - a bug in __new__() has been
eliminated.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/auto_analyses/stereochem_analysis.py
branches/bmrb/dep_check.py
branches/bmrb/generic_fns/grace.py
branches/bmrb/info.py
branches/bmrb/prompt/interpreter.py
branches/bmrb/relax
branches/bmrb/sample_scripts/stereochem_analysis.py
branches/bmrb/test_suite/system_tests/__init__.py
branches/bmrb/test_suite/system_tests/n_state_model.py
branches/bmrb/test_suite/system_tests/relax_fit.py
branches/bmrb/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
branches/bmrb/test_suite/test_suite_runner.py
branches/bmrb/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/auto_analyses/stereochem_analysis.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/dep_check.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/grace.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/info.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/interpreter.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/relax?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/sample_scripts/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/sample_scripts/stereochem_analysis.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/__init__.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/n_state_model.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/relax_fit.py?rev=10871&r1=10870&r2=10871&view=diff
Modified:
branches/bmrb/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py?rev=10871&r1=10870&r2=10871&view=diff
Modified: branches/bmrb/test_suite/test_suite_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/test_suite_runner.py?rev=10871&r1=10870&r2=10871&view=diff
Modified:
branches/bmrb/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py?rev=10871&r1=10870&r2=10871&view=diff
r10871 - in /branches/bmrb: ./ auto_analyses/ generic_fns/ prompt/ sample_scripts/ test_suite/ test_suite/system_tests/ test...