Author: bugman
Date: Thu May 22 15:32:20 2008
New Revision: 6250
URL: http://svn.gna.org/viewcvs/relax?rev=6250&view=rev
Log:
Merged revisions
5971,5973-6012,6015-6016,6018,6020-6023,6025-6033,6036-6041,6043-6044,6046-6055,6101-6104,6106,6110-6248
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r5971 | bugman | 2008-04-24 14:23:40 +0200 (Thu, 24 Apr 2008) | 3 lines
Rewrote the branches section of the development chapter to describe the use
of svnmerge.py.
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r5973 | bugman | 2008-04-24 15:47:39 +0200 (Thu, 24 Apr 2008) | 3 lines
Added a few single letter command line options for running the test-suite.
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r5974 | bugman | 2008-04-24 16:37:21 +0200 (Thu, 24 Apr 2008) | 6 lines
Converted the C modules to use numpy rather than Numeric.
This is going to require the use of numpy.get_include() to find the
location of the headers to
re-enable compilation.
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r5975 | bugman | 2008-04-24 16:41:54 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed the C module compilation by adding numpy.get_include() to the list of
C include flags.
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r5976 | bugman | 2008-04-24 16:50:20 +0200 (Thu, 24 Apr 2008) | 3 lines
Shifted the relaxation curve fitting script to the scripts directory.
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r5977 | bugman | 2008-04-24 16:51:43 +0200 (Thu, 24 Apr 2008) | 3 lines
Shifted the relaxation curve fitting data into the
'test_suite/shared_data/' directory.
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r5978 | bugman | 2008-04-24 16:53:08 +0200 (Thu, 24 Apr 2008) | 3 lines
Removed the call to state.save().
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r5979 | bugman | 2008-04-24 16:54:34 +0200 (Thu, 24 Apr 2008) | 3 lines
Converted the relaxation curve fitting script to the new relax design.
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r5980 | bugman | 2008-04-24 16:54:59 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed the data pipe creation.
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r5981 | bugman | 2008-04-24 16:56:05 +0200 (Thu, 24 Apr 2008) | 3 lines
Removed the commented out file writing user function.
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r5982 | bugman | 2008-04-24 17:14:07 +0200 (Thu, 24 Apr 2008) | 6 lines
Enabled the relaxation curve fitting system test.
This was done by writing a small method, test_curve_fitting(), which
executes the relax_fit.py
script.
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r5983 | bugman | 2008-04-24 17:20:18 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed the paths to the data files in the relaxation curve fitting script.
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r5984 | bugman | 2008-04-24 17:30:49 +0200 (Thu, 24 Apr 2008) | 3 lines
Converted the read() method to the new relax design.
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r5985 | bugman | 2008-04-24 17:31:36 +0200 (Thu, 24 Apr 2008) | 3 lines
Copyright notice update.
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r5986 | bugman | 2008-04-24 17:32:40 +0200 (Thu, 24 Apr 2008) | 3 lines
Added a module docstring.
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r5987 | bugman | 2008-04-24 17:33:56 +0200 (Thu, 24 Apr 2008) | 3 lines
Converted all class methods into module functions, and deleted the class.
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r5988 | bugman | 2008-04-24 17:53:20 +0200 (Thu, 24 Apr 2008) | 3 lines
Converted the read function to the new relax design.
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r5989 | bugman | 2008-04-24 17:55:21 +0200 (Thu, 24 Apr 2008) | 3 lines
Removed the call to the data_init() method.
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r5990 | bugman | 2008-04-24 17:57:14 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed the set up of the num_spectra global object.
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r5991 | bugman | 2008-04-24 17:59:42 +0200 (Thu, 24 Apr 2008) | 3 lines
Added a missing import.
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r5992 | bugman | 2008-04-24 18:00:43 +0200 (Thu, 24 Apr 2008) | 3 lines
Added another missing import.
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r5993 | bugman | 2008-04-24 18:05:24 +0200 (Thu, 24 Apr 2008) | 3 lines
Converted the number_of_header_lines() function to the new design.
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r5994 | bugman | 2008-04-24 18:20:43 +0200 (Thu, 24 Apr 2008) | 3 lines
The int_col arg is now being passed into all the required functions.
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r5995 | bugman | 2008-04-24 18:22:03 +0200 (Thu, 24 Apr 2008) | 3 lines
int_col is now passed into intensity_xeasy(), just in case.
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r5996 | bugman | 2008-04-24 18:39:33 +0200 (Thu, 24 Apr 2008) | 3 lines
Fixed a name clash between the intensity arg and intensity fn.
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r5997 | bugman | 2008-04-25 11:21:11 +0200 (Fri, 25 Apr 2008) | 3 lines
The curve fitting system test script now names the spins so they can be
matched to the assignments.
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r5998 | bugman | 2008-04-25 11:24:25 +0200 (Fri, 25 Apr 2008) | 3 lines
Renamed the rename() and renumber() fns to name() and number() respectively.
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r5999 | bugman | 2008-04-25 11:24:49 +0200 (Fri, 25 Apr 2008) | 3 lines
Copyright statement update.
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r6000 | bugman | 2008-04-25 11:29:34 +0200 (Fri, 25 Apr 2008) | 3 lines
Renamed the spin.rename() and spin.renumber() user fns to spin.name() and
spin.number().
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r6001 | bugman | 2008-04-25 11:31:45 +0200 (Fri, 25 Apr 2008) | 3 lines
The spin_id args to spin.name() and spin.number() can now be None to
identify all spins.
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r6002 | bugman | 2008-04-25 11:37:00 +0200 (Fri, 25 Apr 2008) | 3 lines
Fixes for all the unit tests of the spin naming an numbering functions.
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r6003 | bugman | 2008-04-25 11:37:56 +0200 (Fri, 25 Apr 2008) | 3 lines
Fixed the call to generic_fns.spin.name().
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r6004 | bugman | 2008-04-25 11:45:05 +0200 (Fri, 25 Apr 2008) | 3 lines
Simplified the name() and number() functions. They now handle complex spin
selections.
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r6005 | bugman | 2008-04-25 11:58:51 +0200 (Fri, 25 Apr 2008) | 3 lines
Updated the relaxation curve fitting system test script to call spin.name().
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r6006 | bugman | 2008-04-25 11:59:06 +0200 (Fri, 25 Apr 2008) | 3 lines
Updated the assign_function() method to the new relax design.
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r6007 | bugman | 2008-04-25 12:11:13 +0200 (Fri, 25 Apr 2008) | 3 lines
Converted the mean_and_error() method to the new relax design.
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r6008 | bugman | 2008-04-25 12:14:06 +0200 (Fri, 25 Apr 2008) | 3 lines
Added some missing imports and fixed an incorrectly named function call.
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r6009 | bugman | 2008-04-25 12:15:11 +0200 (Fri, 25 Apr 2008) | 5 lines
Fix for the mean_and_error() method.
The spin container was being referred to as 'data' rather than 'spin'.
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r6010 | bugman | 2008-04-25 12:30:40 +0200 (Fri, 25 Apr 2008) | 3 lines
Big spelling fix! Renamed all references to 'unselect' to 'deselect'.
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r6011 | bugman | 2008-04-25 12:31:19 +0200 (Fri, 25 Apr 2008) | 3 lines
Renamed the prompt.unselect module to prompt.deselect.
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r6012 | bugman | 2008-04-25 17:14:23 +0200 (Fri, 25 Apr 2008) | 7 lines
Improvements to the STDOUT and STDERR handling in the _RelaxTestResult
class.
Now STDOUT and STDERR are stored simultaneously within the same StringIO()
instance so that the
streams are merged into one. This means that the test suite tests print
out the messages as they
would appear on screen.
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r6015 | bugman | 2008-05-01 11:56:06 +0200 (Thu, 01 May 2008) | 3 lines
Spelling fixes: Renamed all references to 'unselect' to 'deselect' in the
manual.
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r6016 | bugman | 2008-05-01 12:03:26 +0200 (Thu, 01 May 2008) | 3 lines
One last renaming of 'Unselect' to 'Deselect'.
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r6018 | bugman | 2008-05-01 12:22:02 +0200 (Thu, 01 May 2008) | 3 lines
Added a section for PyMOL in the installation chapter.
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r6020 | bugman | 2008-05-01 12:52:26 +0200 (Thu, 01 May 2008) | 3 lines
Shifted the installation chapter from chapter 1 to chapter 2.
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r6021 | bugman | 2008-05-01 12:57:34 +0200 (Thu, 01 May 2008) | 3 lines
Converted the 'How to use relax' part from a chapter to a section.
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r6022 | bugman | 2008-05-01 13:00:12 +0200 (Thu, 01 May 2008) | 3 lines
Fixed the R1 and R2 in the abbreviation section.
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r6023 | bugman | 2008-05-01 14:11:53 +0200 (Thu, 01 May 2008) | 11 lines
Improvements and expansion of the introduction chapter.
These changes are in response to the email by Johnny Croy at
https://mail.gna.org/public/relax-users/2008-04/msg00028.html (Message-id:
<4E4F6DB4-5F27-4447-9EC9-6D2E9973A539@xxxxxxxxx>). The thread continues at
https://mail.gna.org/public/relax-users/2008-05/msg00000.html (Message-id:
<50dac1510bcb.510bcb50dac1@xxxxxxxxx>).
Most of this text comes from the relax website (http://nmr-relax.com).
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r6025 | bugman | 2008-05-01 14:17:27 +0200 (Thu, 01 May 2008) | 3 lines
Shortened the short title of the 'Model-free analysis using the diffusion
seeded paradigm' figure.
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r6026 | bugman | 2008-05-01 15:01:47 +0200 (Thu, 01 May 2008) | 3 lines
Updated the intro chapter to the new design.
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r6027 | bugman | 2008-05-01 15:16:09 +0200 (Thu, 01 May 2008) | 3 lines
Updated the NOE chapter of the relax manual to the new design.
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r6028 | bugman | 2008-05-01 15:17:52 +0200 (Thu, 01 May 2008) | 3 lines
Small fix for the NOE chapter. 'pipe.create' should have been written
rather than 'run.create'.
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r6029 | bugman | 2008-05-01 15:30:47 +0200 (Thu, 01 May 2008) | 3 lines
More updates to the noe.py sample script for the new relax design.
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r6030 | bugman | 2008-05-01 15:31:14 +0200 (Thu, 01 May 2008) | 3 lines
More updates for the relax_fit.py sample script for the new relax design.
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r6031 | bugman | 2008-05-01 15:42:07 +0200 (Thu, 01 May 2008) | 3 lines
Updated the relaxation curve fitting chapter to the new relax design.
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r6032 | bugman | 2008-05-01 16:35:25 +0200 (Thu, 01 May 2008) | 3 lines
Completed the relaxation curve fitting chapter of the relax manual.
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r6033 | bugman | 2008-05-01 16:39:50 +0200 (Thu, 01 May 2008) | 6 lines
Added a copyright statement to the model-free.py sample script.
The purpose of this is so the user knows who the author of the script was
and how ancient the script
is, as well as allowing the file to be redistributable.
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r6036 | bugman | 2008-05-01 16:43:01 +0200 (Thu, 01 May 2008) | 3 lines
Updated the model-free.py script to the new relax design.
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r6037 | bugman | 2008-05-01 16:45:25 +0200 (Thu, 01 May 2008) | 3 lines
The proton and heteronucleus types need to be set.
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r6038 | bugman | 2008-05-01 16:47:22 +0200 (Thu, 01 May 2008) | 3 lines
Removed the reference to 'run'.
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r6039 | bugman | 2008-05-01 16:47:54 +0200 (Thu, 01 May 2008) | 3 lines
Removed the call to the now non-existent 'nuclei()' user function.
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r6040 | bugman | 2008-05-01 16:49:23 +0200 (Thu, 01 May 2008) | 3 lines
Converted the model-free.py sample script presented in the model-free
chapter to the new design.
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r6041 | bugman | 2008-05-01 16:51:48 +0200 (Thu, 01 May 2008) | 6 lines
Added a copyright statement to the mf_multimodel.py sample script.
The purpose of this is so the user knows who the author of the script was
and how ancient the script
is, as well as allowing the file to be redistributable.
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r6043 | bugman | 2008-05-01 16:54:31 +0200 (Thu, 01 May 2008) | 3 lines
Updated the mf_multimodel.py sample script to the new relax design.
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r6044 | bugman | 2008-05-01 17:02:41 +0200 (Thu, 01 May 2008) | 6 lines
Added a copyright statement to the modsel.py sample script.
The purpose of this is so the user knows who the author of the script was
and how ancient the script
is, as well as allowing the file to be redistributable.
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r6046 | bugman | 2008-05-01 17:05:05 +0200 (Thu, 01 May 2008) | 3 lines
Updated the modsel.py script to the new relax design.
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r6047 | bugman | 2008-05-01 17:06:58 +0200 (Thu, 01 May 2008) | 3 lines
Updated the rest of the model-free chapter of the relax manual to the new
design.
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r6048 | bugman | 2008-05-01 17:08:46 +0200 (Thu, 01 May 2008) | 3 lines
Added the GPL to the index.
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r6049 | bugman | 2008-05-01 17:11:06 +0200 (Thu, 01 May 2008) | 3 lines
Changed all index entries of 'computer programs' to 'software'.
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r6050 | bugman | 2008-05-01 17:16:03 +0200 (Thu, 01 May 2008) | 3 lines
Removed a LaTeX file which was split into separate chapters long ago.
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r6051 | bugman | 2008-05-01 17:23:59 +0200 (Thu, 01 May 2008) | 3 lines
Updated the development chapter to the new relax design.
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r6052 | bugman | 2008-05-01 17:32:50 +0200 (Thu, 01 May 2008) | 3 lines
A few more updates to the development chapter for the new design.
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r6053 | bugman | 2008-05-01 17:34:57 +0200 (Thu, 01 May 2008) | 3 lines
Indexing fixes.
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r6054 | bugman | 2008-05-01 17:37:39 +0200 (Thu, 01 May 2008) | 3 lines
Fixed the indexing in the fetch_docstrings.py script.
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r6055 | bugman | 2008-05-01 17:40:31 +0200 (Thu, 01 May 2008) | 3 lines
Added automatic indexing for the model selection techniques.
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r6101 | bugman | 2008-05-04 15:56:58 +0200 (Sun, 04 May 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-6012" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/mol_res_spin_module_rename
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r6102 | bugman | 2008-05-04 15:59:34 +0200 (Sun, 04 May 2008) | 192 lines
Merged revisions 6013,6015-6068,6070-6101 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/mol_res_spin_module_rename
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r6013 | bugman | 2008-04-28 13:55:21 +0200 (Mon, 28 Apr 2008) | 3 lines
Created a temporary branch for some heavy duty module rearrangements.
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r6056 | bugman | 2008-05-02 19:16:06 +0200 (Fri, 02 May 2008) | 8 lines
Split up of the generic_fns.selection module.
All of the methods relating to the molecules, residues, and spins
(including the spin selection
string and associated functions and the spin selection object) have been
shifted into the
generic_fns.mol_res_spin module. The functions remaining in
generic_fns.selection are related to
purely the selection and deselection of spins.
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r6057 | bugman | 2008-05-04 11:34:42 +0200 (Sun, 04 May 2008) | 3 lines
Wrote a module docstring.
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r6058 | bugman | 2008-05-04 11:37:06 +0200 (Sun, 04 May 2008) | 5 lines
Renamed all the functions of the residue, molecule, and spin modules.
This is in preparation for merging into the generic_fns.mol_res_spin
module.
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r6059 | bugman | 2008-05-04 11:39:01 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the copy functions into generic_fns.mol_res_spin.
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r6060 | bugman | 2008-05-04 11:40:38 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the create functions into generic_fns.mol_res_spin.
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r6061 | bugman | 2008-05-04 11:41:39 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the delete functions into generic_fns.mol_res_spin.
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r6062 | bugman | 2008-05-04 11:43:00 +0200 (Sun, 04 May 2008) | 4 lines
Shifted all the display functions into generic_fns.mol_res_spin.
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r6063 | bugman | 2008-05-04 11:44:58 +0200 (Sun, 04 May 2008) | 3 lines
Renamed all the 'rename' and 'renumber' fns to 'name' and 'number'.
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r6064 | bugman | 2008-05-04 11:46:52 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the naming functions into generic_fns.mol_res_spin.
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r6065 | bugman | 2008-05-04 11:48:17 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the numbering functions into generic_fns.mol_res_spin.
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r6066 | bugman | 2008-05-04 11:54:18 +0200 (Sun, 04 May 2008) | 3 lines
Big simplifications to the molecule and residue naming functions.
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r6067 | bugman | 2008-05-04 11:56:33 +0200 (Sun, 04 May 2008) | 3 lines
Converted the number_residue() fn to the form of the number_spin() fn.
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r6068 | bugman | 2008-05-04 11:57:17 +0200 (Sun, 04 May 2008) | 3 lines
Removed the empty molecule, residue, and spin modules.
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r6070 | bugman | 2008-05-04 12:16:26 +0200 (Sun, 04 May 2008) | 3 lines
Fixed all the broken imports.
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r6071 | bugman | 2008-05-04 12:26:45 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the unit tests of test_selection to test_mol_spin_res, and
fixed the import and calls.
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r6072 | bugman | 2008-05-04 13:27:54 +0200 (Sun, 04 May 2008) | 3 lines
Updated the molecule, residue, and spin unit test base classes.
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r6073 | bugman | 2008-05-04 13:31:07 +0200 (Sun, 04 May 2008) | 3 lines
Shifted all the molecule, residue, and spin unit tests into
test_mol_spin_res.
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r6074 | bugman | 2008-05-04 13:32:11 +0200 (Sun, 04 May 2008) | 3 lines
Import fix.
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r6075 | bugman | 2008-05-04 13:34:23 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the molecule unit tests unique.
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r6076 | bugman | 2008-05-04 13:36:11 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the residue unit tests unique.
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r6077 | bugman | 2008-05-04 13:37:10 +0200 (Sun, 04 May 2008) | 3 lines
Made the names of the spin unit tests unique.
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r6078 | bugman | 2008-05-04 13:43:37 +0200 (Sun, 04 May 2008) | 3 lines
Set up some objects containing the molecule, residue, and spin fns of
generic_fns.mol_res_spin.
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r6079 | bugman | 2008-05-04 13:44:21 +0200 (Sun, 04 May 2008) | 3 lines
Fixed the naming of the test_mol_spin_res.py file.
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r6080 | bugman | 2008-05-04 13:51:18 +0200 (Sun, 04 May 2008) | 3 lines
Lots of unit test fixes.
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r6081 | bugman | 2008-05-04 14:07:18 +0200 (Sun, 04 May 2008) | 3 lines
A bit of code rearrangement as a test.
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r6082 | bugman | 2008-05-04 14:11:40 +0200 (Sun, 04 May 2008) | 3 lines
Renamed all the function calls.
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r6083 | bugman | 2008-05-04 14:13:00 +0200 (Sun, 04 May 2008) | 3 lines
Added a dummy molecule module for the unit tests.
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r6084 | bugman | 2008-05-04 14:18:57 +0200 (Sun, 04 May 2008) | 3 lines
Created more dummy modules.
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r6085 | bugman | 2008-05-04 14:24:44 +0200 (Sun, 04 May 2008) | 3 lines
Manually reverted r6073.
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r6086 | bugman | 2008-05-04 14:25:40 +0200 (Sun, 04 May 2008) | 3 lines
Removed the dummy modules.
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r6087 | bugman | 2008-05-04 14:27:31 +0200 (Sun, 04 May 2008) | 3 lines
Import of the dummy modules into the correct location.
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r6088 | bugman | 2008-05-04 14:29:27 +0200 (Sun, 04 May 2008) | 3 lines
Shifted the test_reverse unit test back into test_selection.py.
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r6089 | bugman | 2008-05-04 14:30:58 +0200 (Sun, 04 May 2008) | 3 lines
Added a missing import.
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r6090 | bugman | 2008-05-04 14:32:46 +0200 (Sun, 04 May 2008) | 3 lines
Removed a broken import.
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r6091 | bugman | 2008-05-04 14:54:44 +0200 (Sun, 04 May 2008) | 3 lines
Fixed all the residue_name and residue_number unit tests.
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r6092 | bugman | 2008-05-04 14:56:47 +0200 (Sun, 04 May 2008) | 3 lines
[... 1016 lines stripped ...]
r6250 - in /branches/multi_processor_merge: ./ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scr...