Author: semor
Date: Sun May 10 19:31:20 2009
New Revision: 9047
URL: http://svn.gna.org/viewcvs/relax?rev=9047&view=rev
Log:
Merged revisions 9015-9017,9019-9024,9028-9040,9042-9043 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
................
r9015 | bugman | 2009-04-27 09:26:25 -0400 (Mon, 27 Apr 2009) | 5 lines
Bug fix.
The PyMOL code was failing because of the new design of the structural data
object.
................
r9016 | bugman | 2009-04-28 07:47:51 -0400 (Tue, 28 Apr 2009) | 3 lines
Added a catch for bug #13442 (https://gna.org/bugs/index.php?13442) to the
test suite.
................
r9017 | bugman | 2009-04-28 08:02:02 -0400 (Tue, 28 Apr 2009) | 6 lines
Fix for bug #13442 (https://gna.org/bugs/index.php?13442).
The problem was that global minimisation objects were being accessed when
the do not exist. These
are now skipped.
................
r9019 | bugman | 2009-04-28 08:05:30 -0400 (Tue, 28 Apr 2009) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-8161" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe
................
r9020 | bugman | 2009-04-28 08:28:05 -0400 (Tue, 28 Apr 2009) | 321 lines
Merged revisions
8162-8179,8181-8182,8643-8655,8657-8668,8671-8672,8674,8677,8679-8680,8689-8695,8700-8701,8710-8713,8716,9005-9009,9013
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe
........
r8162 | bugman | 2008-12-08 16:41:32 +0100 (Mon, 08 Dec 2008) | 5 lines
Fix for the noe.read_constraints() user function.
The noe object is called noe_obj.
........
r8163 | bugman | 2008-12-08 16:46:53 +0100 (Mon, 08 Dec 2008) | 7 lines
The noe.read_constraints() user function now calls
generic_fns.noesy.read_constraints().
The noe user functions need not all point to the specific NOE object!
Maybe later the steady-state
NOE can be separated from the NOESY, but for now it isn't too illogical
for both to be in the same
user function class.
........
r8164 | bugman | 2008-12-08 16:48:34 +0100 (Mon, 08 Dec 2008) | 3 lines
Created an empty module for NOESY data.
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r8165 | bugman | 2008-12-09 10:30:36 +0100 (Tue, 09 Dec 2008) | 3 lines
Wrote a stub function generic_fns.noesy.read_constraints().
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r8166 | bugman | 2008-12-09 10:37:16 +0100 (Tue, 09 Dec 2008) | 3 lines
Added a directory to the test-suite for holding NOE restraint data.
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r8167 | bugman | 2008-12-09 10:39:00 +0100 (Tue, 09 Dec 2008) | 5 lines
Added an RNA H-bond Xplor restraint file.
This comes from http://bass.chem.yale.edu/labdocs/packages/xplor.html.
........
r8168 | bugman | 2008-12-09 10:45:58 +0100 (Tue, 09 Dec 2008) | 5 lines
Added the system test framework for NOE restraint reading tests.
This includes one test for the reading of RNA H-bond restraints from an
Xplor formatted input file.
........
r8169 | bugman | 2008-12-09 10:47:29 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed 'constraints' to 'restraints' for the NOEs.
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r8170 | bugman | 2008-12-09 11:04:24 +0100 (Tue, 09 Dec 2008) | 3 lines
The RNA sequence of the noe_rna_hbond.dat file is now generated through a
new class method.
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r8171 | bugman | 2008-12-09 11:06:01 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed all the noe.read_constraints() references in the unit tests to
noe.read_restraints().
........
r8172 | bugman | 2008-12-09 13:31:47 +0100 (Tue, 09 Dec 2008) | 5 lines
Completed the test_read_xplor_rna() system test.
Checks for the restraint list have now been added.
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r8173 | bugman | 2008-12-09 13:32:57 +0100 (Tue, 09 Dec 2008) | 3 lines
Activated the Noe_restraints system test framework.
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r8174 | bugman | 2008-12-09 13:33:19 +0100 (Tue, 09 Dec 2008) | 3 lines
Bug fix in the rna_seq() method.
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r8175 | bugman | 2008-12-09 13:36:17 +0100 (Tue, 09 Dec 2008) | 3 lines
Another bug fix for the rna_seq() sequence generation method.
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r8176 | bugman | 2008-12-09 13:49:38 +0100 (Tue, 09 Dec 2008) | 3 lines
Final fixes for the rna_seq() sequence generation method.
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r8177 | bugman | 2008-12-09 13:50:30 +0100 (Tue, 09 Dec 2008) | 3 lines
Fix for the call to noe.read_restraints() in test_read_xplor_rna().
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r8178 | bugman | 2008-12-09 13:57:32 +0100 (Tue, 09 Dec 2008) | 3 lines
Removed the non-existent frq arg and a docstring clarification about the
relax formatted file.
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r8179 | bugman | 2008-12-09 14:02:53 +0100 (Tue, 09 Dec 2008) | 3 lines
Missing import!
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r8181 | bugman | 2008-12-10 14:30:44 +0100 (Wed, 10 Dec 2008) | 3 lines
Added a missing import.
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r8182 | bugman | 2008-12-10 15:18:38 +0100 (Wed, 10 Dec 2008) | 3 lines
Added some more code to the read_restraints() function.
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r8643 | bugman | 2009-01-26 11:52:11 +0100 (Mon, 26 Jan 2009) | 3 lines
Wrote the __file_format() function for determining the NOE restraint file
format.
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r8644 | bugman | 2009-01-26 13:30:06 +0100 (Mon, 26 Jan 2009) | 3 lines
The non-implemented function generic_fns.xplor.parse_noe_restraints() is
now being called.
........
r8645 | bugman | 2009-01-26 13:44:06 +0100 (Mon, 26 Jan 2009) | 3 lines
Reverted to calling file.readlines() rather than file.read().
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r8646 | bugman | 2009-01-26 15:01:10 +0100 (Mon, 26 Jan 2009) | 6 lines
Created the Xplor module for handling Xplor formatted files.
The function parse_noe_restraints() has been added to parse the NOE
restraints. The function
strip_comments() has been written to remove Xplor comments from the input
data.
........
r8647 | bugman | 2009-01-26 15:24:53 +0100 (Mon, 26 Jan 2009) | 3 lines
Created __convert_to_id() to convert from Xplor atom string to relax atom
id.
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r8648 | bugman | 2009-01-26 15:31:05 +0100 (Mon, 26 Jan 2009) | 3 lines
Added checks to make sure spin containers corresponding to the Xplor atom
strings exist.
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r8649 | bugman | 2009-01-26 16:26:45 +0100 (Mon, 26 Jan 2009) | 3 lines
Typo fix. 'H4' should have been 'N4'!
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r8650 | bugman | 2009-01-26 16:32:49 +0100 (Mon, 26 Jan 2009) | 3 lines
The NOE restraints are now stored in the current data pipe.
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r8651 | bugman | 2009-01-26 16:39:22 +0100 (Mon, 26 Jan 2009) | 3 lines
Fixes for the test_read_xplor_rna() system test.
........
r8652 | bugman | 2009-01-26 16:40:32 +0100 (Mon, 26 Jan 2009) | 5 lines
Modified the NOE restraint list so that some restraints are spread across
2 lines.
This should test the Xplor parsing code better.
........
r8653 | bugman | 2009-01-26 16:42:12 +0100 (Mon, 26 Jan 2009) | 5 lines
Bug fix for the parse_noe_restraints() function.
Xplor restraints spread across 2 lines are now properly handled.
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r8654 | bugman | 2009-01-26 16:43:23 +0100 (Mon, 26 Jan 2009) | 3 lines
Added a few comments to test the Xplor parsing even more.
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r8655 | bugman | 2009-01-26 18:44:13 +0100 (Mon, 26 Jan 2009) | 3 lines
Shifted the checks of the atom id strings from the Xplor parser to the
NOE restraint reading fn.
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r8657 | bugman | 2009-01-27 09:35:53 +0100 (Tue, 27 Jan 2009) | 3 lines
Missing RelaxError import.
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r8658 | bugman | 2009-01-27 09:44:38 +0100 (Tue, 27 Jan 2009) | 3 lines
Added some test NOEs, in a generic formatted file, for phthalic acid and
testing the NOE reading.
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r8659 | bugman | 2009-01-27 10:01:41 +0100 (Tue, 27 Jan 2009) | 3 lines
Created a system test for the reading of a generically formatted NOE
restraint file.
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r8660 | bugman | 2009-01-27 10:15:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed an unused import.
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r8661 | bugman | 2009-01-27 10:16:04 +0100 (Tue, 27 Jan 2009) | 3 lines
The generically formatted NOE restraint file is now being parsed.
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r8662 | bugman | 2009-01-27 11:10:45 +0100 (Tue, 27 Jan 2009) | 3 lines
Modified the phthalic acid NOE restraint reading test to include
pseudo-atoms.
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r8663 | bugman | 2009-01-27 13:45:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed the '@' from the pseudo-atom spin names.
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r8664 | bugman | 2009-01-27 13:47:35 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote a unit test for the creation of pseudo-atom spin containers.
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r8665 | bugman | 2009-01-27 13:55:57 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote 5 arg unit tests for the spin.create_pseudo() user function.
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r8666 | bugman | 2009-01-27 14:00:37 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the interface for the spin.create_pseudo() user function.
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r8667 | bugman | 2009-01-27 14:03:18 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the arg unit tests of spin.create_pseudo().
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r8668 | bugman | 2009-01-27 14:06:13 +0100 (Tue, 27 Jan 2009) | 3 lines
Imported the non-existant create_pseudo_spin() function.
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r8671 | bugman | 2009-01-27 16:14:22 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the create_pseudo_spin() and __linear_ave() functions for
pseudo-atom support.
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r8672 | bugman | 2009-01-27 16:17:07 +0100 (Tue, 27 Jan 2009) | 5 lines
Fix for the phthalic acid NOE restraint reading system test.
Pseudo-atom creation was not correctly called.
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r8674 | bugman | 2009-01-27 16:27:54 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the create_pseudo_spin() and __linear_ave() functions.
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r8677 | bugman | 2009-01-27 16:41:23 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the 2 test_create_pseudo_spin() unit tests.
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r8679 | bugman | 2009-01-27 16:49:58 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the test_create_pseudo_spin() unit test. The atomic positions
are now set.
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r8680 | bugman | 2009-01-27 16:51:47 +0100 (Tue, 27 Jan 2009) | 3 lines
The __linear_ave() now handles the coordinates as numpy arrays.
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r8689 | bugman | 2009-01-28 11:24:04 +0100 (Wed, 28 Jan 2009) | 3 lines
Added some more checks for the test_create_pseudo_spin() unit test.
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r8690 | bugman | 2009-01-28 11:30:24 +0100 (Wed, 28 Jan 2009) | 3 lines
Wrote a second unit test for the creation of a pseudo-spin.
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r8691 | bugman | 2009-01-28 11:38:57 +0100 (Wed, 28 Jan 2009) | 3 lines
Modified the checks for the pseudo-spin creation unit tests.
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r8692 | bugman | 2009-01-28 11:40:14 +0100 (Wed, 28 Jan 2009) | 5 lines
The pseudo-spin name and number is now stored in the member spin
containers.
This gives a mapping between from the spin to the pseudo-spin.
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r8693 | bugman | 2009-01-28 11:40:50 +0100 (Wed, 28 Jan 2009) | 3 lines
Fixes for test_create_pseudo_spin() and test_create_pseudo_spin2().
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r8694 | bugman | 2009-01-28 11:41:27 +0100 (Wed, 28 Jan 2009) | 3 lines
One more fix for test_create_pseudo_spin().
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r8695 | bugman | 2009-01-28 11:42:32 +0100 (Wed, 28 Jan 2009) | 3 lines
The members list is now stored in the pseudo-spin to map this to the
respective spin containers.
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r8700 | bugman | 2009-01-29 09:42:21 +0100 (Thu, 29 Jan 2009) | 3 lines
Added a call to calc() to test the quadratic potential calculation.
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r8701 | bugman | 2009-01-29 16:40:07 +0100 (Thu, 29 Jan 2009) | 5 lines
Created a module for calculating different optimisation/energy potentials.
The function quad_pot() has been written to provide a flat-bottom
potential.
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r8710 | bugman | 2009-02-02 10:44:48 +0100 (Mon, 02 Feb 2009) | 3 lines
Added tests for the existence of the current data pipe.
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r8711 | bugman | 2009-02-02 10:49:06 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified the RelaxNoModelError print out to be more informative,
especially for the N-state model.
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r8712 | bugman | 2009-02-02 10:51:17 +0100 (Mon, 02 Feb 2009) | 3 lines
Added the start of the calculate() method.
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r8713 | bugman | 2009-02-02 10:51:45 +0100 (Mon, 02 Feb 2009) | 3 lines
The N-state model is now selected in the NOESY system test.
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r8716 | bugman | 2009-02-02 11:05:21 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified __base_data_types() to include NOE restraints.
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r9005 | bugman | 2009-04-09 19:33:13 +0200 (Thu, 09 Apr 2009) | 3 lines
Fixed the calls to generic_fns.mol_res_spin.spin.create() function.
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r9006 | bugman | 2009-04-09 19:46:04 +0200 (Thu, 09 Apr 2009) | 5 lines
Fix for the rna_seq() method.
The create_residue() and create_molecule() functions were being
incorrectly called.
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r9007 | bugman | 2009-04-10 20:43:00 +0200 (Fri, 10 Apr 2009) | 5 lines
Added the calc_ave_dist() method.
This doesn't work yet and has been cut and paste from an external relax
script.
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r9008 | bugman | 2009-04-15 11:46:03 +0200 (Wed, 15 Apr 2009) | 3 lines
Completed the calculate() and calc_ave_dist() methods for the dynamically
averaged NOE analysis.
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r9009 | bugman | 2009-04-15 14:04:02 +0200 (Wed, 15 Apr 2009) | 3 lines
Bug fix in the calc_ave_dist() method for multiple models.
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r9013 | bugman | 2009-04-15 17:06:54 +0200 (Wed, 15 Apr 2009) | 5 lines
Bug fix for the calc_ave_dist() method.
The negative of the exponential was being used!
........
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r9021 | bugman | 2009-04-28 09:02:54 -0400 (Tue, 28 Apr 2009) | 3 lines
Fixed the testing of the Monte Carlo simulations.
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r9022 | bugman | 2009-04-28 09:03:39 -0400 (Tue, 28 Apr 2009) | 5 lines
Bug fix.
The minimisation statistics are no longer reset by the Monte Carlo
simulation setup.
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r9023 | bugman | 2009-04-28 11:50:25 -0400 (Tue, 28 Apr 2009) | 6 lines
The centre() function can now handle pseudoatoms.
Positional information is taken from the mol, res, spin data structure
rather than the structural
object, hence pseudoatoms can be supported.
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r9024 | bugman | 2009-04-28 11:52:06 -0400 (Tue, 28 Apr 2009) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/ave_noe
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r9028 | bugman | 2009-04-28 12:06:17 -0400 (Tue, 28 Apr 2009) | 3 lines
Fix for the __assemble_scaling_matrix() method for the 'fixed' N-state
model.
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r9029 | bugman | 2009-04-28 13:34:45 -0400 (Tue, 28 Apr 2009) | 5 lines
Fix for the 'fixed' N-state model.
When constraints are automatically turned off for this, the minimisation
algorithm should as change.
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r9030 | bugman | 2009-04-28 13:45:17 -0400 (Tue, 28 Apr 2009) | 6 lines
Fixed a bug introduced at r9029.
The removal of the 'Method of Multipliers' algorithm with automatic
constraint removal didn't take
the grid search into account.
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r9031 | bugman | 2009-04-29 04:41:43 -0400 (Wed, 29 Apr 2009) | 6 lines
Fixed a bug introduced at r9023.
The spin position was being assumed to be a list of numpy arrays, but in
some cases it was simply a
numpy array.
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r9032 | bugman | 2009-04-29 04:57:31 -0400 (Wed, 29 Apr 2009) | 3 lines
The lanthanide atoms are now loaded into the relax data store for the
lactose N-state model test.
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r9033 | bugman | 2009-04-29 05:01:49 -0400 (Wed, 29 Apr 2009) | 5 lines
Some more fixes for the centre() function.
This should now be fully debugged!
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r9034 | bugman | 2009-04-29 05:10:20 -0400 (Wed, 29 Apr 2009) | 3 lines
Added the ave_pos flag to the pcs.centre() user function.
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r9035 | bugman | 2009-04-29 05:23:36 -0400 (Wed, 29 Apr 2009) | 3 lines
Added support for multiple paramagnetic centre extraction to the centre()
function.
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r9036 | bugman | 2009-05-06 04:50:56 -0400 (Wed, 06 May 2009) | 3 lines
Added an Xplor NOE restraint file fragment with a methyl group.
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r9037 | bugman | 2009-05-06 04:55:04 -0400 (Wed, 06 May 2009) | 3 lines
Added a system test for the reading of the Xplor pseudoatom data.
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r9038 | bugman | 2009-05-06 07:52:18 -0400 (Wed, 06 May 2009) | 3 lines
Fixes for the NOE restraint system tests.
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r9039 | bugman | 2009-05-06 10:50:13 -0400 (Wed, 06 May 2009) | 3 lines
Added pseudoatom support to the parse_noe_restraints() function.
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r9040 | bugman | 2009-05-06 11:03:00 -0400 (Wed, 06 May 2009) | 6 lines
Rewrote how the Xplor NOE restraints are read.
Two new functions, first_parse() and second_parse() have been written to
first extract all assign
statements and then handle pseudoatoms.
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r9042 | bugman | 2009-05-09 12:10:07 -0400 (Sat, 09 May 2009) | 5 lines
Bug fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149()
system test.
This is solely for Python 2.6.
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r9043 | bugman | 2009-05-09 12:22:35 -0400 (Sat, 09 May 2009) | 5 lines
Python 2.6 bug fix for the RelaxWarnings format() function.
The warn.formatwarning() function this replaces has a new keyword arg.
................
Added:
branches/relax_disp/generic_fns/noesy.py
- copied unchanged from r9043, 1.3/generic_fns/noesy.py
branches/relax_disp/generic_fns/xplor.py
- copied unchanged from r9043, 1.3/generic_fns/xplor.py
branches/relax_disp/maths_fns/potential.py
- copied unchanged from r9043, 1.3/maths_fns/potential.py
branches/relax_disp/test_suite/shared_data/noe_restraints/
- copied from r9043, 1.3/test_suite/shared_data/noe_restraints/
branches/relax_disp/test_suite/system_tests/noe_restraints.py
- copied unchanged from r9043,
1.3/test_suite/system_tests/noe_restraints.py
branches/relax_disp/test_suite/system_tests/scripts/phthalic_acid_noes.py
- copied unchanged from r9043,
1.3/test_suite/system_tests/scripts/phthalic_acid_noes.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/generic_fns/minimise.py
branches/relax_disp/generic_fns/mol_res_spin.py
branches/relax_disp/generic_fns/pcs.py
branches/relax_disp/generic_fns/pymol.py
branches/relax_disp/prompt/noe.py
branches/relax_disp/prompt/pcs.py
branches/relax_disp/prompt/spin.py
branches/relax_disp/relax_warnings.py
branches/relax_disp/specific_fns/model_free/main.py
branches/relax_disp/specific_fns/model_free/mf_minimise.py
branches/relax_disp/specific_fns/n_state_model.py
branches/relax_disp/test_suite/system_tests/__init__.py
branches/relax_disp/test_suite/system_tests/model_free.py
branches/relax_disp/test_suite/system_tests/scripts/lactose_n_state.py
branches/relax_disp/test_suite/unit_tests/_generic_fns/spin.py
branches/relax_disp/test_suite/unit_tests/_prompt/test_noe.py
branches/relax_disp/test_suite/unit_tests/_prompt/test_spin.py
branches/relax_disp/test_suite/unit_tests/spin_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/minimise.py?rev=9047&r1=9046&r2=9047&view=diff
[... 51 lines stripped ...]
r9047 - in /branches/relax_disp: ./ generic_fns/ maths_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/shared...