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@.../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@...>). The thread continues at
https://mail.gna.org/public/relax-users/2008-05/msg00000.html (Message-id:
<50dac1510bcb.510bcb50dac1@...>).
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@.../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@.../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
Fixed all the molecule_name unit tests.
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r6093 | bugman | 2008-05-04 15:04:35 +0200 (Sun, 04 May 2008) | 3 lines
Renamed 'rename' and 'renumber' to 'name' and 'number' in the residue user function class.
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r6094 | bugman | 2008-05-04 15:07:58 +0200 (Sun, 04 May 2008) | 3 lines
Renamed 'rename' to 'name' in the molecule user function class.
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r6095 | bugman | 2008-05-04 15:09:18 +0200 (Sun, 04 May 2008) | 3 lines
Fixes for the molecule.name() user function unit tests.
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r6096 | bugman | 2008-05-04 15:10:48 +0200 (Sun, 04 May 2008) | 3 lines
Fixes for the residue.name() and residue.number() user function unit tests.
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r6097 | bugman | 2008-05-04 15:13:10 +0200 (Sun, 04 May 2008) | 3 lines
Added the missing numbering functions.
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r6098 | bugman | 2008-05-04 15:14:35 +0200 (Sun, 04 May 2008) | 3 lines
Docstring fix.
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r6099 | bugman | 2008-05-04 15:49:31 +0200 (Sun, 04 May 2008) | 3 lines
Re-added tests for disallowed residue and spin selections.
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r6100 | bugman | 2008-05-04 15:53:46 +0200 (Sun, 04 May 2008) | 3 lines
Added the has_molecules(), has_residues(), and has_spins() methods to the Selection object.
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r6103 | bugman | 2008-05-04 16:00:16 +0200 (Sun, 04 May 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/mol_res_spin_module_rename
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r6104 | bugman | 2008-05-04 16:01:44 +0200 (Sun, 04 May 2008) | 5 lines
Updated the branch management section of the relax manual.
A commit instruction was missing.
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r6106 | bugman | 2008-05-04 20:46:04 +0200 (Sun, 04 May 2008) | 3 lines
Removed my name from the manual.
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r6110 | bugman | 2008-05-07 14:40:19 +0200 (Wed, 07 May 2008) | 3 lines
Updated all the deselect user functions to the new design (well, only the interface).
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r6111 | bugman | 2008-05-07 14:44:11 +0200 (Wed, 07 May 2008) | 3 lines
Added the infrastructure for the arg unit tests of the deselect user function class.
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r6112 | bugman | 2008-05-07 14:52:39 +0200 (Wed, 07 May 2008) | 3 lines
Added 9 arg unit tests for the deselect.read() user function.
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r6113 | bugman | 2008-05-07 14:54:33 +0200 (Wed, 07 May 2008) | 3 lines
Fixed the RelaxError imports.
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r6114 | bugman | 2008-05-07 14:56:28 +0200 (Wed, 07 May 2008) | 3 lines
Bug fix in the checking of the res_num_col arg.
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r6115 | bugman | 2008-05-07 14:58:45 +0200 (Wed, 07 May 2008) | 3 lines
Another bug fix in the checking of the res_num_col arg, this time in the relax_data.read() user fn.
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r6116 | bugman | 2008-05-07 15:04:51 +0200 (Wed, 07 May 2008) | 3 lines
Sorting of functions.
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r6117 | bugman | 2008-05-07 15:08:17 +0200 (Wed, 07 May 2008) | 3 lines
Added 2 arg unit tests for the deselect.spin() user function.
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r6118 | bugman | 2008-05-07 15:14:07 +0200 (Wed, 07 May 2008) | 3 lines
Docstring fix for the deselect.read() user function.
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r6119 | bugman | 2008-05-07 15:21:33 +0200 (Wed, 07 May 2008) | 3 lines
Added the spin_id arg to the deselect.reverse() user function.
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r6120 | bugman | 2008-05-07 15:22:47 +0200 (Wed, 07 May 2008) | 3 lines
Wrote the spin_id arg unit test for the deselect.reverse() user function.
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r6121 | bugman | 2008-05-07 15:29:54 +0200 (Wed, 07 May 2008) | 3 lines
Updated all the interfaces of the select user functions to the new relax design.
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r6122 | bugman | 2008-05-07 15:32:26 +0200 (Wed, 07 May 2008) | 3 lines
Added 12 arg unit tests for the select user functions.
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r6123 | bugman | 2008-05-07 15:34:52 +0200 (Wed, 07 May 2008) | 3 lines
Fixed all the RelaxError imports.
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r6124 | bugman | 2008-05-07 15:41:56 +0200 (Wed, 07 May 2008) | 3 lines
Wrote 2 unit tests for the boolean args of the select user functions.
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r6125 | bugman | 2008-05-07 15:54:40 +0200 (Wed, 07 May 2008) | 3 lines
Clean up of a ton of unused imports.
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r6126 | bugman | 2008-05-07 16:09:39 +0200 (Wed, 07 May 2008) | 3 lines
Converted the desel_all() function to the new relax design.
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r6127 | bugman | 2008-05-07 16:46:52 +0200 (Wed, 07 May 2008) | 3 lines
Updated the desel_read() function to the new relax design.
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r6128 | bugman | 2008-05-07 16:58:15 +0200 (Wed, 07 May 2008) | 3 lines
Created the new warning RelaxNoSpinWarning.
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r6129 | bugman | 2008-05-07 16:58:52 +0200 (Wed, 07 May 2008) | 3 lines
The desel_read() fn now uses RelaxNoSpinWarning.
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r6130 | bugman | 2008-05-07 17:00:28 +0200 (Wed, 07 May 2008) | 3 lines
Modifications to RelaxNoSpinWarning.
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r6131 | bugman | 2008-05-07 17:01:37 +0200 (Wed, 07 May 2008) | 3 lines
The generic_fns.intensity.read() fn now uses RelaxNoSpinWarning.
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r6132 | bugman | 2008-05-07 17:03:54 +0200 (Wed, 07 May 2008) | 3 lines
Bug fix in desel_read() - skip missing spins.
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r6133 | bugman | 2008-05-07 17:08:49 +0200 (Wed, 07 May 2008) | 3 lines
Updated the desel_spin() function to the new design.
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r6134 | bugman | 2008-05-07 17:11:30 +0200 (Wed, 07 May 2008) | 3 lines
Updates to the reverse() function.
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r6135 | bugman | 2008-05-07 17:13:57 +0200 (Wed, 07 May 2008) | 3 lines
Updated the sel_all() function to the new design.
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r6136 | bugman | 2008-05-07 17:19:51 +0200 (Wed, 07 May 2008) | 5 lines
Updates for RelaxNoPipeError and RelaxNoSequenceError.
The tests were added to reverse() and the RelaxErrors added to the epydoc text.
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r6137 | bugman | 2008-05-07 18:12:15 +0200 (Wed, 07 May 2008) | 3 lines
Wrote 2 unit tests for the boolean args of the select user functions.
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r6138 | bugman | 2008-05-07 18:13:52 +0200 (Wed, 07 May 2008) | 3 lines
Updated sel_read() to the new design.
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r6139 | bugman | 2008-05-07 18:16:55 +0200 (Wed, 07 May 2008) | 3 lines
Started to convert sel_spin() to the new design.
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r6140 | semor | 2008-05-09 18:08:16 +0200 (Fri, 09 May 2008) | 3 lines
Corrected a small error in a 'for' loop that prevented relax from working.
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r6141 | bugman | 2008-05-20 11:01:34 +0200 (Tue, 20 May 2008) | 3 lines
Started the conversion of the internal relax structural object to be independent of the PDB format.
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r6142 | bugman | 2008-05-20 11:02:11 +0200 (Tue, 20 May 2008) | 3 lines
Module rename.
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r6143 | bugman | 2008-05-20 11:04:02 +0200 (Tue, 20 May 2008) | 3 lines
Import fixes for the newly renamed generic_fns.structure.internal() module.
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r6144 | bugman | 2008-05-20 11:07:46 +0200 (Tue, 20 May 2008) | 3 lines
Copied the Scientific python unit tests for the internal relax structural object unit tests.
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r6145 | bugman | 2008-05-20 11:12:37 +0200 (Tue, 20 May 2008) | 3 lines
Updated the internal relax structural object unit tests to test this object.
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r6146 | bugman | 2008-05-20 11:15:15 +0200 (Tue, 20 May 2008) | 3 lines
Modified the unit tests to call Internal.load_pdb().
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r6147 | bugman | 2008-05-20 11:18:54 +0200 (Tue, 20 May 2008) | 5 lines
Changed a few method names in the API base class.
load_structures() is now load_pdb() and write_pdb_file() is now write_pdb().
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r6148 | bugman | 2008-05-20 11:21:11 +0200 (Tue, 20 May 2008) | 3 lines
Renamed load_structures() to load_pdb() in the Scientific python PDB structural object.
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r6149 | bugman | 2008-05-20 11:22:54 +0200 (Tue, 20 May 2008) | 3 lines
Updated the Scientific python PDB structural object unit tests to call load_pdb().
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r6150 | bugman | 2008-05-20 11:28:54 +0200 (Tue, 20 May 2008) | 3 lines
Renamed a call to load_structures() to load_pdb().
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r6151 | bugman | 2008-05-20 11:32:49 +0200 (Tue, 20 May 2008) | 3 lines
Removed a PDB reference in the __init__ docstring of the structural API base class.
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r6152 | bugman | 2008-05-20 11:46:56 +0200 (Tue, 20 May 2008) | 3 lines
Added 2 unit tests checking if the internal and Scientific structural objects conform to the API.
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r6153 | bugman | 2008-05-20 11:47:59 +0200 (Tue, 20 May 2008) | 3 lines
Added an identification string to the structural API base class.
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r6154 | bugman | 2008-05-20 11:59:04 +0200 (Tue, 20 May 2008) | 3 lines
Improvements to the structural API unit tests.
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r6155 | bugman | 2008-05-20 12:00:41 +0200 (Tue, 20 May 2008) | 3 lines
Renamed write_pdb_file() to write_pdb().
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r6156 | bugman | 2008-05-20 13:54:26 +0200 (Tue, 20 May 2008) | 3 lines
Fix for the RelaxImplementError message.
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r6157 | bugman | 2008-05-20 15:14:12 +0200 (Tue, 20 May 2008) | 3 lines
Added 2 unit tests for the args of the structural API methods.
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r6158 | bugman | 2008-05-20 15:38:44 +0200 (Tue, 20 May 2008) | 5 lines
Completely changed the design of the internal relax structural data object.
It is now a container holding arrays of structural information. This should speed this code up.
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r6159 | bugman | 2008-05-20 15:43:32 +0200 (Tue, 20 May 2008) | 3 lines
Docstring fix for the atom_connect() method.
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r6160 | bugman | 2008-05-20 15:44:03 +0200 (Tue, 20 May 2008) | 3 lines
Updated the API stub methods atom_add() and atom_connect().
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r6161 | bugman | 2008-05-20 15:46:14 +0200 (Tue, 20 May 2008) | 3 lines
Fix for the format_method unit test method.
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r6162 | bugman | 2008-05-20 15:50:43 +0200 (Tue, 20 May 2008) | 3 lines
Fixed the incomplete terminate() docstring.
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r6163 | bugman | 2008-05-20 15:51:16 +0200 (Tue, 20 May 2008) | 3 lines
Updated the structural API terminate() method.
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r6164 | bugman | 2008-05-20 16:05:20 +0200 (Tue, 20 May 2008) | 3 lines
Updated the __get_chemical_name() docstring.
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r6165 | bugman | 2008-05-20 16:06:58 +0200 (Tue, 20 May 2008) | 3 lines
Updated the load_pdb() docstring to be specific to PDB files.
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r6166 | bugman | 2008-05-20 16:17:15 +0200 (Tue, 20 May 2008) | 3 lines
Fixed all the function docstrings to be valid epytext.
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r6167 | bugman | 2008-05-20 18:41:57 +0200 (Tue, 20 May 2008) | 8 lines
Wrote the load_pdb() structural API method for the internal relax object.
This involved the addition of the following private methods:
__generate_object_from_pdb
__parse_models
__parse_pdb_record
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r6168 | bugman | 2008-05-20 18:46:40 +0200 (Tue, 20 May 2008) | 3 lines
Updated the atom_add() method to handle multiple models.
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r6169 | bugman | 2008-05-20 18:48:02 +0200 (Tue, 20 May 2008) | 3 lines
Updated the atom_connect() method to handle multiple models.
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r6170 | bugman | 2008-05-20 18:50:41 +0200 (Tue, 20 May 2008) | 3 lines
Updated the terminate() method to handle multiple models.
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r6171 | bugman | 2008-05-20 18:54:06 +0200 (Tue, 20 May 2008) | 3 lines
Updated the atom_add(), atom_connect(), and terminate() API base class methods for the model arg.
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r6172 | bugman | 2008-05-20 21:49:19 +0200 (Tue, 20 May 2008) | 3 lines
Fix for the unit test of Internal.load_pdb().
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r6173 | bugman | 2008-05-20 21:56:24 +0200 (Tue, 20 May 2008) | 5 lines
Fix for the initialisation of the Structure_container object.
The object variables were not being placed into self.
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r6174 | bugman | 2008-05-20 21:58:59 +0200 (Tue, 20 May 2008) | 3 lines
Fix by renaming of the Structure_container.__init__() method.
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r6175 | bugman | 2008-05-20 22:14:21 +0200 (Tue, 20 May 2008) | 3 lines
Wrote a unit test for the Internal.__parse_pdb_record() method.
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r6176 | bugman | 2008-05-20 22:30:56 +0200 (Tue, 20 May 2008) | 6 lines
Renamed __generate_object_from_pdb() to __fill_object_from_pdb() and changed its behaviour.
The method no longer returns a Structure_container instance but simply fills out the one
corresponding to the model.
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r6177 | bugman | 2008-05-20 22:32:24 +0200 (Tue, 20 May 2008) | 3 lines
The Structure_container.model variable is now initialised (to None).
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r6178 | bugman | 2008-05-20 22:35:22 +0200 (Tue, 20 May 2008) | 3 lines
Bug fix for the load_pdb() method, the Structure_container.model variable is now set.
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r6179 | bugman | 2008-05-20 22:52:42 +0200 (Tue, 20 May 2008) | 3 lines
Expanded the Internal.load_pdb() unit test to check all atomic information.
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r6180 | bugman | 2008-05-20 23:26:08 +0200 (Tue, 20 May 2008) | 3 lines
Wrote the atom_loop() method.
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r6181 | bugman | 2008-05-20 23:27:13 +0200 (Tue, 20 May 2008) | 3 lines
Deleted 6 unit tests for functions which will not be implemented yet.
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r6182 | bugman | 2008-05-20 23:41:34 +0200 (Tue, 20 May 2008) | 3 lines
Atom number are now stored in an array to allow for PDB files with missing atoms.
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r6183 | bugman | 2008-05-20 23:45:51 +0200 (Tue, 20 May 2008) | 3 lines
Fix for the atom_loop() method. The position is now returned as a numpy array.
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r6184 | bugman | 2008-05-20 23:47:35 +0200 (Tue, 20 May 2008) | 3 lines
Added the atom_num arg to the atom_add() structural API base class method.
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r6185 | bugman | 2008-05-21 11:46:02 +0200 (Wed, 21 May 2008) | 3 lines
Modified the structure.read_pdb() user function docstring to mention the new internal PDB parser.
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r6186 | bugman | 2008-05-21 11:53:16 +0200 (Wed, 21 May 2008) | 3 lines
Activated the internal relax PDB parser.
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r6187 | bugman | 2008-05-21 12:00:53 +0200 (Wed, 21 May 2008) | 3 lines
Updated the __all__ list.
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r6188 | bugman | 2008-05-21 21:30:56 +0200 (Wed, 21 May 2008) | 3 lines
Updated the select_model() method to the new design.
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r6189 | bugman | 2008-05-21 21:34:45 +0200 (Wed, 21 May 2008) | 3 lines
Updated the model_setup() method to the new design.
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r6190 | bugman | 2008-05-21 21:36:45 +0200 (Wed, 21 May 2008) | 3 lines
Updates to the data_init() method.
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r6191 | bugman | 2008-05-21 21:38:13 +0200 (Wed, 21 May 2008) | 3 lines
Fixes for the model_setup() method.
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r6192 | bugman | 2008-05-21 21:40:48 +0200 (Wed, 21 May 2008) | 3 lines
Updated the overfit_deselect() method to the new design.
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r6193 | bugman | 2008-05-21 21:42:25 +0200 (Wed, 21 May 2008) | 3 lines
Updates to the overfit_deselect() method.
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r6194 | bugman | 2008-05-21 21:46:19 +0200 (Wed, 21 May 2008) | 3 lines
Updated the grid_search() method to the new relax design.
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r6195 | bugman | 2008-05-21 22:00:23 +0200 (Wed, 21 May 2008) | 3 lines
Updated the minimise() method to the new relax design.
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r6196 | bugman | 2008-05-21 22:04:57 +0200 (Wed, 21 May 2008) | 3 lines
Updated the assemble_param_vector() method to the new relax design.
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r6197 | bugman | 2008-05-21 22:06:55 +0200 (Wed, 21 May 2008) | 3 lines
Docstring fix in the assemble_param_vector() method.
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r6198 | bugman | 2008-05-21 22:13:15 +0200 (Wed, 21 May 2008) | 3 lines
Updated the assemble_scaling_matrix() method to the new design.
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r6199 | bugman | 2008-05-21 22:20:04 +0200 (Wed, 21 May 2008) | 3 lines
Replaced a Numeric python dependence with the numpy equivalent.
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r6200 | bugman | 2008-05-21 22:33:16 +0200 (Wed, 21 May 2008) | 3 lines
Updated the grid_search_setup() to the new design.
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r6201 | bugman | 2008-05-21 22:36:57 +0200 (Wed, 21 May 2008) | 3 lines
Updated the linear_constraints() method to the new design.
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r6202 | bugman | 2008-05-21 22:41:26 +0200 (Wed, 21 May 2008) | 3 lines
A few fixes for the minimise() and grid_search_setup() methods.
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r6203 | bugman | 2008-05-21 22:45:03 +0200 (Wed, 21 May 2008) | 3 lines
Fix for the minimise() method - the func function is no longer overwritten by the chi2 value.
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r6204 | bugman | 2008-05-21 22:47:13 +0200 (Wed, 21 May 2008) | 3 lines
Docstring fix for the disassemble_param_vector() method.
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r6205 | bugman | 2008-05-21 22:49:31 +0200 (Wed, 21 May 2008) | 3 lines
Updated the disassemble_param_vector() method to the new design.
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r6206 | bugman | 2008-05-21 22:50:26 +0200 (Wed, 21 May 2008) | 3 lines
Fix for the relaxation curve fitting system test script.
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r6207 | bugman | 2008-05-21 22:56:11 +0200 (Wed, 21 May 2008) | 3 lines
Converted the __init__() method docstring into the class docstring.
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r6208 | bugman | 2008-05-21 22:57:08 +0200 (Wed, 21 May 2008) | 3 lines
Added a module docstring.
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r6209 | bugman | 2008-05-21 22:59:21 +0200 (Wed, 21 May 2008) | 3 lines
A few changes to tidy up the module.
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r6210 | bugman | 2008-05-21 23:01:08 +0200 (Wed, 21 May 2008) | 3 lines
Converted all class methods to module functions.
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r6211 | bugman | 2008-05-21 23:03:37 +0200 (Wed, 21 May 2008) | 3 lines
Removed an unused import.
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r6212 | bugman | 2008-05-21 23:09:11 +0200 (Wed, 21 May 2008) | 3 lines
Updated the create_data() function to the new design.
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r6213 | bugman | 2008-05-21 23:13:27 +0200 (Wed, 21 May 2008) | 3 lines
Updated the setup() function to the new design.
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r6214 | bugman | 2008-05-21 23:15:34 +0200 (Wed, 21 May 2008) | 3 lines
Fixed all specific function setups in the Monte Carlo sim module.
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r6215 | bugman | 2008-05-21 23:18:10 +0200 (Wed, 21 May 2008) | 3 lines
Converted the select_all_sims() function to the new design.
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r6216 | bugman | 2008-05-21 23:23:00 +0200 (Wed, 21 May 2008) | 3 lines
Updated the set_selected_sim() method to the new design.
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r6217 | bugman | 2008-05-21 23:26:52 +0200 (Wed, 21 May 2008) | 3 lines
Updated the set_selected_sim() method to the new relax design.
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r6218 | bugman | 2008-05-21 23:28:16 +0200 (Wed, 21 May 2008) | 3 lines
Spelling fix in the compilation error message.
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r6219 | bugman | 2008-05-21 23:28:52 +0200 (Wed, 21 May 2008) | 3 lines
Added a missing import.
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r6220 | bugman | 2008-05-21 23:32:06 +0200 (Wed, 21 May 2008) | 3 lines
Updated the create_mc_data() method to the new design.
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r6221 | bugman | 2008-05-21 23:38:26 +0200 (Wed, 21 May 2008) | 3 lines
Converted the back_calc() method to the new relax design.
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r6222 | bugman | 2008-05-21 23:41:06 +0200 (Wed, 21 May 2008) | 3 lines
Updated the return_data() and return_error() methods to the new relax design.
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r6223 | bugman | 2008-05-21 23:42:06 +0200 (Wed, 21 May 2008) | 3 lines
Fix for the return_error() method.
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r6224 | bugman | 2008-05-21 23:44:23 +0200 (Wed, 21 May 2008) | 3 lines
Updated the sim_pack_data() method to the new relax design.
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r6225 | bugman | 2008-05-21 23:46:37 +0200 (Wed, 21 May 2008) | 3 lines
Updated the initial_values() function to the new design.
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r6226 | bugman | 2008-05-21 23:53:45 +0200 (Wed, 21 May 2008) | 3 lines
Converted the sim_init_values() to the new relax design.
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r6227 | bugman | 2008-05-21 23:55:46 +0200 (Wed, 21 May 2008) | 3 lines
Updated the off() and on() functions to the new design.
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r6228 | bugman | 2008-05-22 00:02:56 +0200 (Thu, 22 May 2008) | 3 lines
Updated the error_analysis() function to the new design.
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r6229 | bugman | 2008-05-22 00:10:53 +0200 (Thu, 22 May 2008) | 3 lines
Updated the sim_return_selected() method to the new design.
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r6230 | bugman | 2008-05-22 00:16:08 +0200 (Thu, 22 May 2008) | 3 lines
Updated the sim_return_param() method to the new design.
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r6231 | bugman | 2008-05-22 00:20:47 +0200 (Thu, 22 May 2008) | 3 lines
Updated the set_error() method to the new design.
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r6232 | bugman | 2008-05-22 00:34:40 +0200 (Thu, 22 May 2008) | 3 lines
Cut most of the residues from the relaxation curve fitting system test to speed things up.
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r6233 | bugman | 2008-05-22 12:09:22 +0200 (Thu, 22 May 2008) | 3 lines
Fix for the system test of storing the S2 difference in a new data pipe.
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r6234 | bugman | 2008-05-22 12:10:49 +0200 (Thu, 22 May 2008) | 3 lines
Fix for the select.spin() user function.
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r6235 | bugman | 2008-05-22 12:20:23 +0200 (Thu, 22 May 2008) | 3 lines
Fixed the sel_spin() function.
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r6236 | bugman | 2008-05-22 12:24:13 +0200 (Thu, 22 May 2008) | 3 lines
Fixes for the sel_read() function.
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r6237 | bugman | 2008-05-22 12:25:26 +0200 (Thu, 22 May 2008) | 3 lines
Changed all selection flags to bools.
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r6238 | bugman | 2008-05-22 12:26:04 +0200 (Thu, 22 May 2008) | 3 lines
Another fix for the sel_read() function.
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r6239 | bugman | 2008-05-22 12:32:29 +0200 (Thu, 22 May 2008) | 3 lines
Added the boolean arg to the desel_spin() function.
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r6240 | bugman | 2008-05-22 14:16:43 +0200 (Thu, 22 May 2008) | 3 lines
Many updates and improvements to the spin selection and deselection functions.
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r6241 | bugman | 2008-05-22 14:18:36 +0200 (Thu, 22 May 2008) | 3 lines
Updated the epydoc fields in the docstring to include all error conditions.
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r6242 | bugman | 2008-05-22 14:21:14 +0200 (Thu, 22 May 2008) | 5 lines
Fixes for the system test of storing the S2 difference in a new data pipe.
The value.set() calls are now in the form of the new design.
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r6243 | bugman | 2008-05-22 14:40:02 +0200 (Thu, 22 May 2008) | 6 lines
Added a saved state containing Sparky peak heights.
This is will be used by the loading of peak heights system test. A script was also added to allow
the saved state to be regenerated when necessary.
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r6244 | bugman | 2008-05-22 14:41:12 +0200 (Thu, 22 May 2008) | 3 lines
Removed an old, incompatible saved state.
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r6245 | bugman | 2008-05-22 14:43:59 +0200 (Thu, 22 May 2008) | 3 lines
Updated the test_read_sparky system test to the new relax design.
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r6246 | bugman | 2008-05-22 15:05:21 +0200 (Thu, 22 May 2008) | 3 lines
Updated the state loading unit test to add additional data to the relax data store.
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r6247 | bugman | 2008-05-22 15:07:56 +0200 (Thu, 22 May 2008) | 5 lines
Split the state loading unit test into 2.
One tests the loading whereas the second checks the modification of a loaded state.
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r6248 | bugman | 2008-05-22 15:12:35 +0200 (Thu, 22 May 2008) | 3 lines
Wrote a unit test for the resetting of an unpickled and restored relax data storage singleton.
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