Author: bugman
Date: Tue Jul 8 16:05:25 2008
New Revision: 6836
URL: http://svn.gna.org/viewcvs/relax?rev=6836&view=rev
Log:
Merged revisions 6742-6835 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r6742 | bugman | 2008-07-05 13:42:13 +0200 (Sat, 05 Jul 2008) | 6 lines
Module docsting updates in the generic_fns package.
All missing module docstrings were created, the current ones modified, and
the copyright notices
updated.
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r6743 | bugman | 2008-07-05 14:47:44 +0200 (Sat, 05 Jul 2008) | 7 lines
Expanded the OMP model-free optimisation system test.
The initial round of spherical diffusion optimisation (removal of tm and
diffusion tensor opt) is
now tested. The first round of normal optimisation is also implemented
with the optimisation of the
model-free models and model selection.
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r6744 | bugman | 2008-07-05 14:48:27 +0200 (Sat, 05 Jul 2008) | 3 lines
Fix for the pipe.copy() user function print out.
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r6745 | bugman | 2008-07-05 15:48:21 +0200 (Sat, 05 Jul 2008) | 3 lines
Converted the model-free remove_tm() method to the new design.
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r6746 | bugman | 2008-07-05 15:50:41 +0200 (Sat, 05 Jul 2008) | 3 lines
Converted the fix() user function interface to the new design.
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r6747 | bugman | 2008-07-05 15:52:00 +0200 (Sat, 05 Jul 2008) | 3 lines
Converted the fix() class method to a module function.
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r6748 | bugman | 2008-07-05 15:55:35 +0200 (Sat, 05 Jul 2008) | 3 lines
Fixed the fix() user function docstring.
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r6749 | bugman | 2008-07-05 16:01:52 +0200 (Sat, 05 Jul 2008) | 3 lines
Converted the fix() function to the new design.
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r6750 | bugman | 2008-07-05 16:02:29 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the omp model-free optimisation system test.
The fix() user function is properly called.
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r6751 | bugman | 2008-07-05 16:03:50 +0200 (Sat, 05 Jul 2008) | 3 lines
Renamed run to data pipe in the model selection function.
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r6752 | bugman | 2008-07-05 16:07:52 +0200 (Sat, 05 Jul 2008) | 3 lines
Added some missing imports.
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r6753 | bugman | 2008-07-05 16:13:11 +0200 (Sat, 05 Jul 2008) | 3 lines
Added the modified OMP PDB file 1F35 with only H and N atoms present and
created through Molmol.
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r6754 | bugman | 2008-07-05 16:14:21 +0200 (Sat, 05 Jul 2008) | 3 lines
Added a missing import.
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r6755 | bugman | 2008-07-05 16:15:55 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the assemble_scaling_matrix() method.
The current data pipe is now aliased as required.
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r6756 | bugman | 2008-07-05 16:18:18 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the grid_search_config_diff() method and the call to it.
The current data pipe is aliased, and the verbosity flag is not sent into
the method.
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r6757 | bugman | 2008-07-05 16:19:25 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for grid_search_config_diff().
The diffusion tensor is located in 'cdp.diff_tensor'.
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r6758 | bugman | 2008-07-05 16:20:57 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the OMP model-free optimisation system test.
The MF_MODELS variable now exists.
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r6759 | bugman | 2008-07-05 16:33:56 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the OMP model-free optimisation system test.
Switching between pipes was not occurring, so the diffusion tensor appeared
to be missing.
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r6760 | bugman | 2008-07-05 16:50:29 +0200 (Sat, 05 Jul 2008) | 3 lines
Docstring fix in the base API write_pdb() method for epydoc.
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r6761 | bugman | 2008-07-05 16:53:04 +0200 (Sat, 05 Jul 2008) | 3 lines
Removed an out of place double quote.
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r6762 | bugman | 2008-07-05 19:03:36 +0200 (Sat, 05 Jul 2008) | 5 lines
Fixes for the overfit_deselect() method.
The diffusion tensor object is now correctly referenced and the params
variable can be None.
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r6763 | bugman | 2008-07-05 19:23:17 +0200 (Sat, 05 Jul 2008) | 3 lines
Fix for the fix() user function call in the full_analysis.py script.
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r6764 | bugman | 2008-07-05 19:29:14 +0200 (Sat, 05 Jul 2008) | 6 lines
Fix for the model_setup() method.
The diffusion tensor was incorrectly referenced and the model, parameters,
and equation were not
always being set.
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r6765 | bugman | 2008-07-05 20:25:15 +0200 (Sat, 05 Jul 2008) | 3 lines
Removed a useless check for models of zero length.
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r6766 | bugman | 2008-07-05 20:25:46 +0200 (Sat, 05 Jul 2008) | 3 lines
Added a few additional comments.
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r6767 | bugman | 2008-07-05 20:35:36 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the final data pipe.
This is created by model selection, so pipe.create() doesn't need to be
called.
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r6768 | bugman | 2008-07-05 20:38:09 +0200 (Sat, 05 Jul 2008) | 5 lines
Fix for the OMP model-free optimisation system test.
The 'aic' data pipe already exists, so now it is deleted prior to model
selection.
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r6769 | bugman | 2008-07-05 23:16:40 +0200 (Sat, 05 Jul 2008) | 5 lines
Fixes for the duplicate_data() method.
The diffusion tensor object now has its sub-objects compared.
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r6770 | bugman | 2008-07-05 23:25:39 +0200 (Sat, 05 Jul 2008) | 5 lines
Another fix for the duplicate_data() method.
The diffusion tensor object was being copied from the source pipe back to
the source pipe!
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r6771 | bugman | 2008-07-05 23:36:16 +0200 (Sat, 05 Jul 2008) | 3 lines
Fix for the full_analysis.py script. The references to the diffusion
tensor object were incorrect.
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r6772 | bugman | 2008-07-05 23:50:05 +0200 (Sat, 05 Jul 2008) | 6 lines
Fixes for the model_selection() method of the full_analysis.py script.
The model selection pipe must be deleted each time for the automatic
CONV_LOOP looping to be
possible.
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r6773 | bugman | 2008-07-06 00:39:32 +0200 (Sun, 06 Jul 2008) | 3 lines
Added the reset_min_stats() method to reset all minimisation stats prior to
optimisation.
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r6774 | bugman | 2008-07-06 01:35:04 +0200 (Sun, 06 Jul 2008) | 5 lines
Modified the XML results files to store higher precision versions of the
floats.
The float is stored as an IEEE-754 byte array in the XML attribute
ieee_754_byte_array.
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r6775 | bugman | 2008-07-06 01:54:56 +0200 (Sun, 06 Jul 2008) | 3 lines
The IEEE-754 byte arrays are now restored from the results files, giving
full precision.
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r6776 | bugman | 2008-07-06 02:05:53 +0200 (Sun, 06 Jul 2008) | 7 lines
Modified the convergence tests in the full_analysis.py script to print the
IEEE-754 byte array.
This representation is platform and float type (float vs. numpy.float64 vs.
Numeric.Float64, etc.)
independent. Even if the values evaluate to being equal, the python print
out can be different.
The IEEE-754 float byte array representation is independent of this
insanity.
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r6777 | bugman | 2008-07-06 02:07:50 +0200 (Sun, 06 Jul 2008) | 5 lines
Fix for the convergence tests in full_analysis.py.
The spin name can now be absent.
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r6778 | bugman | 2008-07-06 02:14:36 +0200 (Sun, 06 Jul 2008) | 3 lines
The spin ID is now printed in the convergence tests, rather than the spin
number and name.
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r6779 | bugman | 2008-07-06 02:15:09 +0200 (Sun, 06 Jul 2008) | 3 lines
Better formatting of the chi2 comparison print out.
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r6780 | bugman | 2008-07-06 02:17:02 +0200 (Sun, 06 Jul 2008) | 3 lines
Added a missing import.
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r6781 | bugman | 2008-07-06 02:24:35 +0200 (Sun, 06 Jul 2008) | 3 lines
Created a relax script to regenerate final_results_trunc_1.3.bz2 from
final_results_trunc_1.2.bz2.
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r6782 | bugman | 2008-07-06 02:25:10 +0200 (Sun, 06 Jul 2008) | 3 lines
Updated the results file for the new XML output with IEEE-754 byte arrays.
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r6783 | bugman | 2008-07-06 02:29:13 +0200 (Sun, 06 Jul 2008) | 3 lines
A few fixes for the 'final' run of the full_analysis.py script.
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r6784 | semor | 2008-07-06 18:52:50 +0200 (Sun, 06 Jul 2008) | 3 lines
Converted the output file to 'devnull'.
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r6785 | bugman | 2008-07-07 08:24:59 +0200 (Mon, 07 Jul 2008) | 3 lines
Fix for optimisation requiring the presence of structural data.
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r6786 | bugman | 2008-07-07 11:54:03 +0200 (Mon, 07 Jul 2008) | 3 lines
Redesign of the structure.vectors() user function to allow more flexibility
with multiple structures.
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r6787 | bugman | 2008-07-07 13:52:16 +0200 (Mon, 07 Jul 2008) | 3 lines
Started to redesign the vectors() function.
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r6788 | bugman | 2008-07-07 13:53:47 +0200 (Mon, 07 Jul 2008) | 3 lines
Renamed the structural API method num_models() to num_structures().
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r6789 | bugman | 2008-07-07 13:56:17 +0200 (Mon, 07 Jul 2008) | 3 lines
Improved the vectors() function print out.
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r6790 | bugman | 2008-07-07 14:05:52 +0200 (Mon, 07 Jul 2008) | 3 lines
Finished modifying the vectors() method to handle bond vectors more
flexibly.
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r6791 | bugman | 2008-07-07 14:27:55 +0200 (Mon, 07 Jul 2008) | 3 lines
Renamed the structural object method bond_vectors() model arg to
struct_index.
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r6792 | bugman | 2008-07-07 14:29:07 +0200 (Mon, 07 Jul 2008) | 3 lines
Fixed the call to the __molecule_loop() method from bond_vectors().
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r6793 | bugman | 2008-07-07 14:31:01 +0200 (Mon, 07 Jul 2008) | 3 lines
Fixed the call to the __residue_loop() method from bond_vectors().
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r6794 | bugman | 2008-07-07 14:35:59 +0200 (Mon, 07 Jul 2008) | 3 lines
Fix for the proton arg test of the structure.vectors() user function - it's
now the attached arg.
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r6795 | bugman | 2008-07-07 14:42:56 +0200 (Mon, 07 Jul 2008) | 3 lines
Wrote 4 arg unit tests for the structure.vectors() user function.
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r6796 | bugman | 2008-07-07 15:01:01 +0200 (Mon, 07 Jul 2008) | 3 lines
Fixed two calls to structure.vectors() in the system tests.
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r6797 | bugman | 2008-07-07 15:19:06 +0200 (Mon, 07 Jul 2008) | 3 lines
Fixes for the ellipsoid_frame() function.
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r6798 | bugman | 2008-07-07 15:20:59 +0200 (Mon, 07 Jul 2008) | 3 lines
Reverted all bond_vector references to xh_vector.
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r6799 | bugman | 2008-07-07 15:28:48 +0200 (Mon, 07 Jul 2008) | 3 lines
Spun out the wildcard_match() function into a new module for relax regular
expression.
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r6800 | bugman | 2008-07-07 15:31:24 +0200 (Mon, 07 Jul 2008) | 5 lines
Fixed all calls to generic_fns.mol_res_spin.wildcard_match().
The function is now called generic_fns.relax_re.search().
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r6801 | bugman | 2008-07-07 15:36:04 +0200 (Mon, 07 Jul 2008) | 3 lines
Added code to vectors() to determine if the attached atom is a proton or
not.
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r6802 | bugman | 2008-07-07 15:38:16 +0200 (Mon, 07 Jul 2008) | 5 lines
Fix for the generic_fns.relax_re.search() function.
The re.search() function was clashing with the relax_re.search() function.
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r6803 | bugman | 2008-07-07 15:39:20 +0200 (Mon, 07 Jul 2008) | 3 lines
Rearrangement of the header line print out.
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r6804 | bugman | 2008-07-07 15:41:36 +0200 (Mon, 07 Jul 2008) | 3 lines
Fixed the setting up of the bond vector inside the SpinContainer.
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r6805 | bugman | 2008-07-07 20:22:42 +0200 (Mon, 07 Jul 2008) | 3 lines
Incomplete fixes for the __find_bonded_atom() method.
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r6806 | bugman | 2008-07-07 21:31:11 +0200 (Mon, 07 Jul 2008) | 3 lines
Fix for the atom matching statement in the __find_bonded_atom() method.
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r6807 | bugman | 2008-07-07 21:37:47 +0200 (Mon, 07 Jul 2008) | 5 lines
Fix for the Scientific PDB structural object atom_loop() method.
Empty molecule, residue, and spin names and numbers are now replaced with
None before being returned.
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r6808 | bugman | 2008-07-07 21:39:33 +0200 (Mon, 07 Jul 2008) | 3 lines
Small fix for one of the tests in vectors().
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r6809 | bugman | 2008-07-07 22:24:34 +0200 (Mon, 07 Jul 2008) | 3 lines
Another fix for the __find_bonded_atom() Scientific PDB object method.
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r6810 | bugman | 2008-07-07 22:26:26 +0200 (Mon, 07 Jul 2008) | 5 lines
Some fixes for the test_angles() system test.
'attached_proton' is now called 'attached_atom'.
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r6811 | bugman | 2008-07-07 22:31:18 +0200 (Mon, 07 Jul 2008) | 5 lines
Removed some code checking for deselected molecules and residues.
Only spins can be selected and deselected (one molecule at a time maybe,
but still just the spins)!
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r6812 | bugman | 2008-07-07 22:44:53 +0200 (Mon, 07 Jul 2008) | 3 lines
Added a unit test for the generic_fns.relax_re.search() function.
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r6813 | bugman | 2008-07-07 22:58:23 +0200 (Mon, 07 Jul 2008) | 3 lines
Swapped the generic_fns.relax_re.search() arg order, and fixed all calls to
it.
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r6814 | semor | 2008-07-07 23:46:52 +0200 (Mon, 07 Jul 2008) | 7 lines
Switched from os.devnull to devnull within relax_io.open_write_file().
This is as proposed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-07/msg00021.html (Message ID:
7f080ed10807061152i2a101224p5c5d710d6a92ee@xxxxxxxxxxxxxx)
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r6815 | semor | 2008-07-08 00:24:29 +0200 (Tue, 08 Jul 2008) | 3 lines
Correction for the structure.atom_add() function calls to match the
variables needed.
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r6816 | semor | 2008-07-08 00:31:15 +0200 (Tue, 08 Jul 2008) | 3 lines
Corrections for the atom_connect() function calls to match the needed
variables.
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r6817 | semor | 2008-07-08 00:36:46 +0200 (Tue, 08 Jul 2008) | 3 lines
Changed calls to write_pdb_file() to its actual name: write_pdb().
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r6818 | bugman | 2008-07-08 01:15:32 +0200 (Tue, 08 Jul 2008) | 5 lines
Added 2 new methods to the internal relax structural object.
These are __find_bonded_atom() and bond_vectors().
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r6819 | bugman | 2008-07-08 01:41:48 +0200 (Tue, 08 Jul 2008) | 6 lines
Modified the __find_bonded_atom() and bond_vectors() methods to return more
data.
This additional data is the name of the attached atom and any warnings when
trying to find the
attached atom.
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r6820 | bugman | 2008-07-08 01:46:47 +0200 (Tue, 08 Jul 2008) | 3 lines
Modified vectors() to use the new data returned by
cdp.structure.bond_vectors().
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r6821 | bugman | 2008-07-08 01:51:56 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the bond_vectors() method - the spin.attached_atom variable is
correctly set.
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r6822 | bugman | 2008-07-08 02:00:59 +0200 (Tue, 08 Jul 2008) | 3 lines
Modified the print out during the extraction of bond vectors.
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r6823 | bugman | 2008-07-08 02:04:51 +0200 (Tue, 08 Jul 2008) | 3 lines
Added the missing return_name and return_warnings args to the structural
API bond_vectors() method.
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r6824 | bugman | 2008-07-08 02:06:29 +0200 (Tue, 08 Jul 2008) | 3 lines
Added the missing return_name and return_warnings args to the Scientific
PDB bond_vectors() method.
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r6825 | bugman | 2008-07-08 02:09:02 +0200 (Tue, 08 Jul 2008) | 3 lines
Small print out fix.
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r6826 | bugman | 2008-07-08 02:18:10 +0200 (Tue, 08 Jul 2008) | 3 lines
Brought the Scientific PDB structural object into line with the structural
API.
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r6827 | bugman | 2008-07-08 02:22:30 +0200 (Tue, 08 Jul 2008) | 3 lines
Improved the extracted bond vector print out to show the atom names of the
vector.
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r6828 | bugman | 2008-07-08 02:28:37 +0200 (Tue, 08 Jul 2008) | 5 lines
Fix for the extraction of bond vectors.
When all vectors are asked for, now all vectors are placed into the spin
container.
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r6829 | bugman | 2008-07-08 02:38:34 +0200 (Tue, 08 Jul 2008) | 3 lines
Fixed the calls to the structure.vectors() user function.
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r6830 | bugman | 2008-07-08 02:44:54 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the vectors() function. The spin name or number check now
correctly works.
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r6831 | bugman | 2008-07-08 02:47:15 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the check of pre-existing bond vectors.
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r6832 | bugman | 2008-07-08 02:51:39 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the bond_vectors() method, some variables needed to be initialised
to None.
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r6833 | bugman | 2008-07-08 02:59:03 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the bond_vectors() method, some variables needed to be initialised
to None.
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r6834 | semor | 2008-07-08 06:42:46 +0200 (Tue, 08 Jul 2008) | 3 lines
Corrected a typo introduced in r6815.
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r6835 | semor | 2008-07-08 07:06:37 +0200 (Tue, 08 Jul 2008) | 5 lines
Added a script to test jw_mapping.
This one is based on the same code for testing the consistency testing code.
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Added:
branches/rdc_analysis/generic_fns/relax_re.py
- copied unchanged from r6835, 1.3/generic_fns/relax_re.py
branches/rdc_analysis/test_suite/shared_data/model_free/OMP/generate_final_results_trunc_1.3.py
- copied unchanged from r6835,
1.3/test_suite/shared_data/model_free/OMP/generate_final_results_trunc_1.3.py
branches/rdc_analysis/test_suite/shared_data/structures/1F35_N_H_molmol.pdb
- copied unchanged from r6835,
1.3/test_suite/shared_data/structures/1F35_N_H_molmol.pdb
branches/rdc_analysis/test_suite/system_tests/scripts/jw_mapping.py
- copied unchanged from r6835,
1.3/test_suite/system_tests/scripts/jw_mapping.py
branches/rdc_analysis/test_suite/unit_tests/_generic_fns/test_relax_re.py
- copied unchanged from r6835,
1.3/test_suite/unit_tests/_generic_fns/test_relax_re.py
Modified:
branches/rdc_analysis/ (props changed)
branches/rdc_analysis/data/mol_res_spin.py
branches/rdc_analysis/data/relax_xml.py
branches/rdc_analysis/generic_fns/align_tensor.py
branches/rdc_analysis/generic_fns/angles.py
branches/rdc_analysis/generic_fns/dasha.py
branches/rdc_analysis/generic_fns/diffusion_tensor.py
branches/rdc_analysis/generic_fns/fix.py
branches/rdc_analysis/generic_fns/grace.py
branches/rdc_analysis/generic_fns/minimise.py
branches/rdc_analysis/generic_fns/model_selection.py
branches/rdc_analysis/generic_fns/mol_res_spin.py
branches/rdc_analysis/generic_fns/molmol.py
branches/rdc_analysis/generic_fns/palmer.py
branches/rdc_analysis/generic_fns/pipes.py
branches/rdc_analysis/generic_fns/pymol.py
branches/rdc_analysis/generic_fns/results.py
branches/rdc_analysis/generic_fns/selection.py
branches/rdc_analysis/generic_fns/sequence.py
branches/rdc_analysis/generic_fns/state.py
branches/rdc_analysis/generic_fns/structure/api_base.py
branches/rdc_analysis/generic_fns/structure/geometric.py
branches/rdc_analysis/generic_fns/structure/internal.py
branches/rdc_analysis/generic_fns/structure/main.py
branches/rdc_analysis/generic_fns/structure/mass.py
branches/rdc_analysis/generic_fns/structure/scientific.py
branches/rdc_analysis/generic_fns/value.py
branches/rdc_analysis/generic_fns/vmd.py
branches/rdc_analysis/prompt/fix.py
branches/rdc_analysis/prompt/pipe.py
branches/rdc_analysis/prompt/structure.py
branches/rdc_analysis/sample_scripts/full_analysis.py
branches/rdc_analysis/specific_fns/model_free/main.py
branches/rdc_analysis/specific_fns/model_free/mf_minimise.py
branches/rdc_analysis/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
branches/rdc_analysis/test_suite/system_tests/angles.py
branches/rdc_analysis/test_suite/system_tests/diffusion_tensor.py
[... 131 lines stripped ...]
r6836 - in /branches/rdc_analysis: ./ data/ generic_fns/ generic_fns/structure/ prompt/ sample_scripts/ specific_fns/model_f...