Author: bugman
Date: Thu Jan 13 14:34:06 2011
New Revision: 12326
URL: http://svn.gna.org/viewcvs/relax?rev=12326&view=rev
Log:
Merged revisions
11661,11663-11685,11688,11758,11801,11811-11812,11817,11820-11821,11826-11831,11837-11844,11848-11849,11854-11856,11858-11867,11873,11879,11886,11888,11890-11896,11900,11904-11915,11966-11967,12060,12063,12069-12070,12087-12090,12092-12155,12167-12168,12172-12179,12187,12202,12229-12274,12276-12320
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r11661 | bugman | 2010-10-25 10:10:42 +0200 (Mon, 25 Oct 2010) | 3 lines
Added 6 system tests for the spheroidal diffusion tensor.
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r11663 | bugman | 2010-11-16 18:07:43 +0100 (Tue, 16 Nov 2010) | 5 lines
Fix for the relatively unused calc_tensor_diag() for oblate tensors.
The eigenvalues were incorrectly ordered for oblate spheroids.
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r11664 | bugman | 2010-11-17 15:04:52 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for a failing diffusion tensor unit test.
This was testing an unused element of the diffusion tensor data structure
incorrectly.
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r11665 | bugman | 2010-11-17 16:03:54 +0100 (Wed, 17 Nov 2010) | 5 lines
The rotation matrix for the spheroidal diffusion tensors is now correctly
generated.
Again this is a fix for currently unused code (it will be used for BMRB
support though).
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r11666 | bugman | 2010-11-17 16:15:35 +0100 (Wed, 17 Nov 2010) | 5 lines
Fixes for the diffusion tensor system tests.
The spheroidal tensors are now correctly checked.
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r11667 | bugman | 2010-11-17 16:15:57 +0100 (Wed, 17 Nov 2010) | 3 lines
Removed some debugging code.
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r11668 | bugman | 2010-11-17 16:45:32 +0100 (Wed, 17 Nov 2010) | 3 lines
Some rotation matrix check fixes for the diffusion tensor unit tests.
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r11669 | bugman | 2010-11-17 16:48:20 +0100 (Wed, 17 Nov 2010) | 3 lines
Dpar_unit is no longer passed into calc_rotation() for spheroidal
diffusion, as it is not needed.
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r11670 | bugman | 2010-11-17 17:01:24 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the updating of the rotation and tensor MC sim objects for the
spheroidal diffusion.
This problem was only recently introduced.
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r11671 | bugman | 2010-11-17 17:05:46 +0100 (Wed, 17 Nov 2010) | 3 lines
Similar fix as in r11670, but for setting MC sim data.
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r11672 | bugman | 2010-11-17 17:18:29 +0100 (Wed, 17 Nov 2010) | 3 lines
Some more fixes for handling the diffusion tensor data structure
'spheroid_type' variable properly.
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r11673 | bugman | 2010-11-17 19:14:57 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the creation of the oblate spheroid geometric object PDB file.
The x and z axes need to be swapped now for the oblate tensor.
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r11674 | bugman | 2010-11-17 19:23:43 +0100 (Wed, 17 Nov 2010) | 6 lines
For some reason, the diffusion tensor PDB file for the oblate tensor now
has a slight rotation.
This rotation is about the unique axis of the tensor, so this gives a
different PDB file, but the
representation is the same.
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r11675 | bugman | 2010-11-18 13:42:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Some small cosmetic changes to the spheroid diffusion tensor system tests.
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r11676 | bugman | 2010-11-18 13:51:23 +0100 (Thu, 18 Nov 2010) | 3 lines
The hardcoded variables in get_spheroid() are now keyword args.
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r11677 | bugman | 2010-11-18 14:03:01 +0100 (Thu, 18 Nov 2010) | 3 lines
Added 6 system tests for the initialisation of the prolate spheroid
diffusion tensor.
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r11678 | bugman | 2010-11-18 16:52:49 +0100 (Thu, 18 Nov 2010) | 6 lines
Fix for the spheroid diffusion tensors for a recently introduced bug.
The oblate and prolate check was failing as the 'spheroid_type' variable
was set to None after a
call to diffusion_tensor.init(). 'spheroid_type' is now automatically
updated if Da is changed.
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r11679 | bugman | 2010-11-18 17:08:23 +0100 (Thu, 18 Nov 2010) | 5 lines
The tensor is first twisted before rotating to PDB frame in the spheroid
diffusion tensor system tests.
The twisting rotation was not being correctly performed.
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r11680 | bugman | 2010-11-18 17:25:40 +0100 (Thu, 18 Nov 2010) | 5 lines
Renamed test_init_spheroid_as_ellipsoid() to
test_init_prolate_spheroid_as_ellipsoid().
The print outs of the system test have been slightly improved.
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r11681 | bugman | 2010-11-18 17:38:09 +0100 (Thu, 18 Nov 2010) | 3 lines
Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid
checks into a separate method.
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r11682 | bugman | 2010-11-18 18:20:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Added a new system test test_init_oblate_spheroid_as_ellipsoid().
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r11683 | bugman | 2010-11-18 18:25:51 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2
eigenvalues are the same.
This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into
diffusion_tensor.init().
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r11684 | bugman | 2010-11-18 18:29:29 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy,
Dxz, Dyz).
The eigenvalues were being converted to ints!
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r11685 | bugman | 2010-11-18 18:53:39 +0100 (Thu, 18 Nov 2010) | 6 lines
Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal
diffusion parameters.
The numpy eigenvalue decomposition has been replaced by SVD as the
eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The
test suite now passes fully.
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r11688 | bugman | 2010-11-19 14:46:34 +0100 (Fri, 19 Nov 2010) | 3 lines
Improved the diffusion tensor print out.
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r11758 | bugman | 2010-12-10 16:27:22 +0100 (Fri, 10 Dec 2010) | 3 lines
The molecule type can now be specified.
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r11801 | bugman | 2010-12-13 23:51:44 +0100 (Mon, 13 Dec 2010) | 5 lines
The molecule_loop() and residue_loop() methods now accept the return_id
flag.
The molecule or residue ID strings are now returned when requested.
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r11811 | bugman | 2010-12-14 11:11:03 +0100 (Tue, 14 Dec 2010) | 8 lines
Added a system test for bug #17276.
This bug (https://gna.org/bugs/index.php?17276) was reported by Leanne
Minall <lm7902 att bristol
dot ac dott uk>.
The test passes though as the problem is not in this test data.
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r11812 | bugman | 2010-12-14 11:23:31 +0100 (Tue, 14 Dec 2010) | 3 lines
Bug #17276 is now triggered in the system test.
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r11817 | bugman | 2010-12-14 18:22:33 +0100 (Tue, 14 Dec 2010) | 6 lines
Removed some checks in the generic_fns.mol_res_spin.molecule_loop()
function which was triggering bugs.
The old checking code is of no use, as all types of molecule IDs should be
accepted! This only
recently became an issue for some unknown reason?!?!
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r11820 | bugman | 2010-12-14 23:47:05 +0100 (Tue, 14 Dec 2010) | 7 lines
An execution lock has been added to the status object.
This allows parts of relax to prevent others from running, which is
especially useful in certain
UIs. A special Exec_lock class object has been created to simulate a
proper threading.Lock object,
but with certain additional features.
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r11821 | bugman | 2010-12-14 23:47:33 +0100 (Tue, 14 Dec 2010) | 3 lines
All of the auto-analyses now lock relax's execution while they are in
operation.
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r11826 | bugman | 2010-12-15 01:33:13 +0100 (Wed, 15 Dec 2010) | 5 lines
The Mf.bug_14941_local_tm_global_selection system test now prints out some
status info.
This is to test the status container.
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r11827 | bugman | 2010-12-15 01:35:28 +0100 (Wed, 15 Dec 2010) | 5 lines
Fixes for the status object by renaming __init__() to setup() and calling
it only once.
The object was not acting as a singleton because of the presence of
__init__(). This is now fixed.
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r11828 | bugman | 2010-12-15 01:36:05 +0100 (Wed, 15 Dec 2010) | 3 lines
The status object is being initialised and setup before execution of the
main relax class.
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r11829 | bugman | 2010-12-15 01:36:48 +0100 (Wed, 15 Dec 2010) | 3 lines
The status object is not being initialised on import, to allow controlled
setup upon start up.
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r11830 | bugman | 2010-12-15 01:45:19 +0100 (Wed, 15 Dec 2010) | 6 lines
Security fix - execfile() is no longer used to run relax scripts.
Instead a custom function exec_script() is being used to call
runpy.run_module(). exec_script()
also locks and releases the relax execution lock before and after operation.
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r11831 | bugman | 2010-12-15 09:41:27 +0100 (Wed, 15 Dec 2010) | 3 lines
The execution lock is released by the interpreter in all Error situations.
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r11837 | bugman | 2010-12-16 11:52:56 +0100 (Thu, 16 Dec 2010) | 6 lines
The debugging flag now disables the execution locking mechanism.
The acquire() and release() calls are also recorded in the 'lock.log' file
to help with lock
debugging.
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r11838 | bugman | 2010-12-16 11:53:51 +0100 (Thu, 16 Dec 2010) | 3 lines
Missing module import.
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r11839 | bugman | 2010-12-16 11:56:02 +0100 (Thu, 16 Dec 2010) | 3 lines
Shifted the initialisation of the status object to be after the
__main__.debug initialisation.
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r11840 | bugman | 2010-12-16 12:17:36 +0100 (Thu, 16 Dec 2010) | 5 lines
The system and unit tests are placing their names into the status object.
This will be used for debugging.
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r11841 | bugman | 2010-12-16 12:18:14 +0100 (Thu, 16 Dec 2010) | 3 lines
The unit/system test name is being placed into the locking log when
debugging.
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r11842 | bugman | 2010-12-16 12:37:36 +0100 (Thu, 16 Dec 2010) | 3 lines
The execution lock mechanism no longer blocks scripts from running within
scripts.
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r11843 | bugman | 2010-12-16 12:49:07 +0100 (Thu, 16 Dec 2010) | 3 lines
Nested scripts no longer acquire the execution lock.
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r11844 | bugman | 2010-12-16 15:19:14 +0100 (Thu, 16 Dec 2010) | 5 lines
Better locking support for nested scripts.
The execution lock directly handles the locking of the nesting of scripts.
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r11848 | bugman | 2010-12-17 10:19:50 +0100 (Fri, 17 Dec 2010) | 3 lines
The 'scons clean' target now removes temporary relax save files.
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r11849 | bugman | 2010-12-17 10:36:56 +0100 (Fri, 17 Dec 2010) | 3 lines
Improved execution locking with support for auto analysis and script
launching from within a script.
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r11854 | bugman | 2010-12-17 12:05:30 +0100 (Fri, 17 Dec 2010) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-11813" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_list_handling
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r11855 | bugman | 2010-12-17 12:10:03 +0100 (Fri, 17 Dec 2010) | 58 lines
Merged revisions 11815-11816,11819,11832-11835,11847,11850-11853 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_list_handling
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r11815 | bugman | 2010-12-14 17:51:09 +0100 (Tue, 14 Dec 2010) | 3 lines
Modified the bug_17276 system test data so that there is some noise
simulated.
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r11816 | bugman | 2010-12-14 17:52:06 +0100 (Tue, 14 Dec 2010) | 3 lines
Peak intensity data is now stored as a dictionary with the spectrum_id
arg as keys.
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r11819 | bugman | 2010-12-14 19:02:59 +0100 (Tue, 14 Dec 2010) | 5 lines
Fix for the Relax_fit.test_read_sparky system test.
This was solely a problem within the test and its data.
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r11832 | bugman | 2010-12-15 12:17:28 +0100 (Wed, 15 Dec 2010) | 3 lines
Switched __errors_repl() to use dictionaries rather than lists.
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r11833 | bugman | 2010-12-15 18:33:22 +0100 (Wed, 15 Dec 2010) | 3 lines
Converted the specific relaxation curve fitting code to use the
dictionary data structures.
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r11834 | bugman | 2010-12-15 18:33:44 +0100 (Wed, 15 Dec 2010) | 3 lines
The Monte Carlo simulation code can now handle dictionary type data.
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r11835 | bugman | 2010-12-15 18:51:02 +0100 (Wed, 15 Dec 2010) | 3 lines
The Grace code can now handle dictionary type data.
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r11847 | bugman | 2010-12-17 10:03:04 +0100 (Fri, 17 Dec 2010) | 3 lines
Fixes for the system tests - the data is now in dictionaries.
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r11850 | bugman | 2010-12-17 10:48:25 +0100 (Fri, 17 Dec 2010) | 3 lines
Redesigned the specific API common method _return_value_general() to
handle dictionaries.
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r11851 | bugman | 2010-12-17 11:12:52 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for the API base method _return_value_general() - not all values have
errors associated with them.
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r11852 | bugman | 2010-12-17 11:43:27 +0100 (Fri, 17 Dec 2010) | 3 lines
The NOE specific analysis now uses the dictionary type structure for the
intensity data structures.
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r11853 | bugman | 2010-12-17 11:44:35 +0100 (Fri, 17 Dec 2010) | 6 lines
The list-type data can also be a numpy array, so the Monte Carlo code can
now handle this.
Previously the data was being converted from an ndarray to a list, but
now this is explicitly
handled.
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r11856 | bugman | 2010-12-17 12:10:25 +0100 (Fri, 17 Dec 2010) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/peak_list_handling
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r11858 | bugman | 2010-12-17 12:46:00 +0100 (Fri, 17 Dec 2010) | 5 lines
Removed all execfile() calls by switching to the script() user function.
This is for security and for handling the execution locking mechanism
properly.
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r11859 | bugman | 2010-12-17 12:57:49 +0100 (Fri, 17 Dec 2010) | 3 lines
Renamed all the frame order scripts so that they have valid module names
and can be imported.
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r11860 | bugman | 2010-12-17 13:00:51 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for running scripts - the '.' character is now disallowed as module
import cannot work.
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r11861 | bugman | 2010-12-17 13:04:44 +0100 (Fri, 17 Dec 2010) | 3 lines
More informative nesting information in the execution lock debugging.
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r11862 | bugman | 2010-12-17 13:23:24 +0100 (Fri, 17 Dec 2010) | 3 lines
Modification of the execution lock debugging print outs.
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r11863 | bugman | 2010-12-17 14:11:23 +0100 (Fri, 17 Dec 2010) | 5 lines
Bug fix - the script path is now being removed from sys.path.
This was causing incorrect scripts to be loaded if exec_script() is run
multiple times.
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r11864 | bugman | 2010-12-17 14:51:20 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for the execution locking when an auto-analysis is launched from a
script.
The lock is not released and a new one acquired. Instead the mechanism is
script, just as it is
for nested scripting.
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r11865 | bugman | 2010-12-17 15:03:00 +0100 (Fri, 17 Dec 2010) | 3 lines
Added a system test for nested scripting.
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r11866 | bugman | 2010-12-17 15:04:02 +0100 (Fri, 17 Dec 2010) | 5 lines
Fix for the Generic.test_nested_scripting() system test.
A data pipe is needed.
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r11867 | bugman | 2010-12-17 15:13:51 +0100 (Fri, 17 Dec 2010) | 5 lines
Nested scripting is now better supported.
The full path of the nested script is not needed if is in the same
directory as the parent script.
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r11873 | bugman | 2010-12-17 16:43:21 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for script execution - the original state is restored if an exception
occurs.
The original working directory is restored and the script path is removed
in all cases by using a
try-finally setup.
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r11879 | bugman | 2010-12-17 17:10:39 +0100 (Fri, 17 Dec 2010) | 3 lines
Added a check that the script ends in '*.py'.
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r11886 | bugman | 2010-12-17 19:59:11 +0100 (Fri, 17 Dec 2010) | 9 lines
Fix for bug #17343 (https://gna.org/bugs/?17343).
This bug was reported by Vitaly Vostri <vvostri att gmail dott com>, also
in the mailing list
message https://mail.gna.org/public/relax-users/2010-12/msg00005.html.
The 'CH2' and 'OT' atoms have been added to the internal PDB reader, for
those incomplete PDB files
in which the element column is missing.
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r11888 | bugman | 2010-12-17 20:19:26 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for script execution - the extension check for '.py' was incorrect!
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r11890 | bugman | 2010-12-17 20:41:01 +0100 (Fri, 17 Dec 2010) | 6 lines
Added test data and a script for testing the reading of CCPN Analysis 2.1
sparky peak lists.
This is data from bug #17341 (https://gna.org/bugs/?17341) submitted by
Madeleine Strickland <M dot
Strickland att bristol dot ac dott uk>.
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r11891 | bugman | 2010-12-17 20:51:17 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for bug #17344 (https://gna.org/bugs/index.php?17344), the broken
grace.view() user function.
This has been broken since January, and is released in relax 1.3.5, but no
one seems to have
noticed :S
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r11892 | bugman | 2010-12-17 20:51:48 +0100 (Fri, 17 Dec 2010) | 3 lines
The grace executable file is now set to '' in the CCPN analysis peak list
system test.
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r11893 | bugman | 2010-12-17 21:11:13 +0100 (Fri, 17 Dec 2010) | 5 lines
Implemented and activated the CCPN Analysis 2.1 peak list reading system
test.
This is to catch bug #17341 (https://gna.org/bugs/index.php?17341).
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r11894 | bugman | 2010-12-17 22:59:29 +0100 (Fri, 17 Dec 2010) | 3 lines
Decreased the number of MC sims to speed up the CCPN Analysis peak list
reading system test.
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r11895 | bugman | 2010-12-17 22:59:53 +0100 (Fri, 17 Dec 2010) | 3 lines
Bug fix for the CCPN Analysis peak list system test.
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r11896 | bugman | 2010-12-17 23:37:16 +0100 (Fri, 17 Dec 2010) | 6 lines
Added support for CCPN Analysis 2.1 peak lists (exported in Sparky format).
This is a fix for bug #17341 (https://gna.org/bugs/index.php?17341)
reported by Madeleine Strickland
<M dott Strickland att bristol dot ac dot uk>.
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r11900 | bugman | 2010-12-19 15:43:54 +0100 (Sun, 19 Dec 2010) | 7 lines
Removed the 2 from CH2 in the atom list in the element determining function.
This is in response to Vitaly Vostrikov's <vvostri att gmail dott com>
message at Message-id:
<AANLkTimYA4H7=WbMwzgpxaTJ6_nArKu=ed9VNdXCSuDB@xxxxxxxxxxxxxx>,
https://mail.gna.org/public/relax-users/2010-12/msg00013.html.
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r11904 | bugman | 2010-12-20 14:05:59 +0100 (Mon, 20 Dec 2010) | 6 lines
Added a system test for reading relax 1.2.x version results files.
This is from Sebastian Morin's PSE-4 data, truncated, and is to catch the
bug of not being able to
handle simulations.
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r11905 | bugman | 2010-12-20 14:18:21 +0100 (Mon, 20 Dec 2010) | 5 lines
Fix for bug #17361 (https://gna.org/bugs/index.php?17361).
The chi2_sim structure should have been initialised to a list, not a
dictionary.
[... 1610 lines stripped ...]
r12326 - in /branches/bruker_import: ./ auto_analyses/ data/ docs/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sa...