[r12844]
by
bugman
The Scientific python PDB reading tests are no longer skipped if the module is not installed.
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2011-06-03 15:48:05
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Tree
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[r12843]
by
bugman
Added the PDB reading parts of Scientific python to relax.
This is allowed as the CeCILL licence is GPL compatible. The Scientific python website is
https://sourcesup.cru.fr/projects/scientific-py/, but it hasn't been updated in a long time and
might be a dying project. Therefore the code is now part of relax so it can be used in the future.
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2011-06-03 15:46:57
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Tree
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[r12842]
by
bugman
Some fixes for the subprocess.Popen() calls on MS Windows.
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2011-05-31 16:43:18
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Tree
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[r12841]
by
semor
Updates for the diffusion tensor optimization sample script.
The problem was identified (for sample script "dasha.py")
by Shantanu Bhattacharyya <shantanu01 att cmu dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@...>).
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2011-05-31 14:29:49
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Tree
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[r12840]
by
bugman
Updates for the Dasha sample script.
The problem was identified by Shantanu Bhattacharyya <shantanu01 att cmu dott edu> in the post at
https://mail.gna.org/public/relax-users/2011-05/msg00018.html (Message-id:
<7a068ac7a9e90b8e8d374b334a20d4be.squirrel@...>).
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2011-05-31 12:47:37
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Tree
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[r12839]
by
bugman
Deletion of the multi-processor branch.
This code, which branched early from relax 1.3, is now all in the multi_processor_merge branch.
The newer branch is from a later point in the 1.3 line and is up to date, whereas multi_processor
is stuck with the relax 1.2 designs.
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2011-05-31 11:03:44
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Tree
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[r12838]
by
bugman
Merged revisions 12598-12617,12619-12634,12637-12643,12648,12778-12780,12782-12806,12808-12830 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r12598 | bugman | 2011-02-21 09:54:00 +0100 (Mon, 21 Feb 2011) | 3 lines
Activated the PDC peak intensity type reading, now that the BMRB branch has been merged.
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r12599 | bugman | 2011-02-21 09:59:38 +0100 (Mon, 21 Feb 2011) | 6 lines
Added the Bruker PDC software info to the exp_info module.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00056.html (Message-id:
<4D621CF8.601@...>).
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r12600 | bugman | 2011-02-21 10:22:55 +0100 (Mon, 21 Feb 2011) | 3 lines
Added the Bruker PDC to the exp_info.software_select() backend.
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r12601 | bugman | 2011-02-21 10:28:39 +0100 (Mon, 21 Feb 2011) | 3 lines
The pdc.read() back end is now reading the PDC version information.
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r12602 | bugman | 2011-02-21 10:30:13 +0100 (Mon, 21 Feb 2011) | 5 lines
The setting of the integration method in pdc.read() now works.
This needed to be done after the packing of the relaxation data.
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r12603 | bugman | 2011-02-21 10:32:41 +0100 (Mon, 21 Feb 2011) | 5 lines
The Bruker PDC software is now added to the experimental information.
This will be included in the BMRB deposition file.
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r12604 | bugman | 2011-02-21 16:40:41 +0100 (Mon, 21 Feb 2011) | 6 lines
Updated the Bruker PDC R1 output file.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00060.html (Message-id:
<4D6275CE.6040809@...>).
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r12605 | bugman | 2011-02-21 16:41:01 +0100 (Mon, 21 Feb 2011) | 3 lines
Updated the conversion script for the new R1 PDC file.
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r12606 | bugman | 2011-02-22 14:56:34 +0100 (Tue, 22 Feb 2011) | 8 lines
Updated the R1 Bruker PDC file to a newer version using "variance averaging" for the errors.
See https://mail.gna.org/public/relax-devel/2011-02/msg00066.html (Message-id:
<4D63908C.5060101@...>).
This is instead of the "worst case per peak scenario" option which over estimates the errors.
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r12607 | bugman | 2011-02-22 14:59:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Renamed the convert_data Bruker PDC conversion script to indicate it is for the R1.
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r12608 | bugman | 2011-02-22 15:08:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py to directly read the data out of the Bruker PDC file.
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r12609 | bugman | 2011-02-22 15:12:57 +0100 (Tue, 22 Feb 2011) | 5 lines
Added a catch for the "worst case per peak scenario" option in the PDC.
This will now throw a RelaxError, telling the user to go back to the PDC and use the other option.
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r12610 | bugman | 2011-02-22 15:13:15 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the errors_R1.txt for the new R1 PDC file.
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r12611 | bugman | 2011-02-22 15:13:44 +0100 (Tue, 22 Feb 2011) | 3 lines
Removed a debugging print statement.
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r12612 | bugman | 2011-02-22 15:33:56 +0100 (Tue, 22 Feb 2011) | 3 lines
Convert the pdc.read() back-end to use the \t delimination of the PDC file for parsing.
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r12613 | bugman | 2011-02-22 15:34:26 +0100 (Tue, 22 Feb 2011) | 3 lines
New relax R1 data file for the new testT1.txt PDC data file.
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r12614 | bugman | 2011-02-22 15:37:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py script for the new R1 PDC data.
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r12615 | bugman | 2011-02-22 15:37:31 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the Bruker PDC reading system test for the new R1 data.
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r12616 | bugman | 2011-02-22 15:40:05 +0100 (Tue, 22 Feb 2011) | 3 lines
Fixes for the pdc.read() back-end for the NOE PDC file.
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r12617 | bugman | 2011-02-22 16:51:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updates for the new R1 Bruker PDC file.
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r12619 | bugman | 2011-02-24 12:41:06 +0100 (Thu, 24 Feb 2011) | 6 lines
Updated the Bruker PDC files to the newest versions.
These are taken from the task #7180 (https://gna.org/task/?7180) attached by Peter Neidig as file
#12537, file #12538, and file #12539.
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r12620 | bugman | 2011-02-24 12:48:03 +0100 (Thu, 24 Feb 2011) | 3 lines
The PDC NOE conversion script is now taking the data directly from the PDC file.
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r12621 | bugman | 2011-02-24 12:50:14 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the pdc.read() back-end for reading NOE data out of the new PDC files.
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r12622 | bugman | 2011-02-24 12:50:46 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the PDC reading system tests, the data now matches the new PDC files.
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r12623 | bugman | 2011-02-24 12:53:17 +0100 (Thu, 24 Feb 2011) | 3 lines
The R1 value and error are now being read directly from the PDC file.
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r12624 | bugman | 2011-02-24 12:53:48 +0100 (Thu, 24 Feb 2011) | 3 lines
Decreased the accuracy of the PDC reading system test, as the PDC data is not accurate to 7 places.
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r12625 | bugman | 2011-02-25 14:24:59 +0100 (Fri, 25 Feb 2011) | 9 lines
Removed numpy from the relaxation curve-fitting C module code.
This now expects Python lists as arguments. This should help with incompatibilities between
different Python versions, as this seems to be due to the numpy C interface. See for example
the thread started by Min-Kyu <min-kyu dott cho att vanderbilt dot edu>
https://mail.gna.org/public/relax-users/2011-02/msg00000.html (Message-id:
<001f01cbd24f$350042d0$9f00c870$@cho@...>).
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r12626 | bugman | 2011-02-25 14:26:23 +0100 (Fri, 25 Feb 2011) | 6 lines
Added wrapper methods to the relaxation curve-fitting specific code for the new C modules.
These allow the parameter numpy array from minfx to be converted into a Python list prior to sending
it into the C module.
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r12627 | bugman | 2011-02-25 14:29:07 +0100 (Fri, 25 Feb 2011) | 3 lines
Fix for the back_calc_I C function so that it works under Python 2.5.
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r12628 | bugman | 2011-02-25 14:31:31 +0100 (Fri, 25 Feb 2011) | 3 lines
Added a check for the runpy module.
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r12629 | bugman | 2011-02-25 14:32:27 +0100 (Fri, 25 Feb 2011) | 3 lines
The runpy module is only imported if it exists.
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r12630 | bugman | 2011-02-25 14:33:35 +0100 (Fri, 25 Feb 2011) | 5 lines
Fix for the initialisation of the Bruker_import class.
This allows this module to be loaded in Python 2.4.
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r12631 | bugman | 2011-02-25 14:38:10 +0100 (Fri, 25 Feb 2011) | 3 lines
Scripts can now be run again under Python versions 2.4 or lower.
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r12632 | bugman | 2011-02-25 14:56:04 +0100 (Fri, 25 Feb 2011) | 5 lines
The reference counting appears to not be needed in the C modules.
This allows the modules to be compiled under Python 2.4 or lower.
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r12633 | bugman | 2011-02-25 15:25:42 +0100 (Fri, 25 Feb 2011) | 3 lines
The auto_analyses package modules are now imported by __init__ to force their existence.
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r12634 | bugman | 2011-02-25 18:46:52 +0100 (Fri, 25 Feb 2011) | 8 lines
Loosened all of the model-free tests so that the minimisation statistics are no longer checked.
The same result was being obtained on different platforms, different Python versions, and different
numpy versions, but the minimisation statistics were slightly different. The iter, f_count, g_count
h_count, and warning variables are no longer checked. This will stop users from thinking they have
a problem with their version of relax, after running the test suite.
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r12637 | bugman | 2011-03-01 11:35:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Added graphics for the value user function.
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r12638 | bugman | 2011-03-01 11:36:30 +0100 (Tue, 01 Mar 2011) | 3 lines
Added the value user function graphics to the icon paths.
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r12639 | bugman | 2011-03-01 12:08:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Added a wizard graphic for the value user functions.
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r12640 | bugman | 2011-03-01 12:11:24 +0100 (Tue, 01 Mar 2011) | 3 lines
The value user function wizard graphic is now the correct size.
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r12641 | bugman | 2011-03-01 12:13:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Improvements to the value user function wizard graphic - the tensor background has been deleted.
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r12642 | bugman | 2011-03-01 12:14:53 +0100 (Tue, 01 Mar 2011) | 3 lines
The value wizard graphic is again the wrong size!!!
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r12643 | bugman | 2011-03-01 12:15:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Created an initial value.set() user function GUI element and menu entry.
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r12648 | bugman | 2011-03-01 15:52:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Modified the value.set() user function GUI element so that the parameter element is an input field.
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r12778 | bugman | 2011-03-03 14:14:22 +0100 (Thu, 03 Mar 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12645" from
svn+ssh://bugman@.../svn/relax/branches/relax_data
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r12779 | bugman | 2011-03-03 14:21:42 +0100 (Thu, 03 Mar 2011) | 583 lines
Merged revisions 12647,12649-12767,12769-12777 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/relax_data
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r12647 | bugman | 2011-03-01 15:36:46 +0100 (Tue, 01 Mar 2011) | 3 lines
Redesigned the relax_data.read() user function front end for handling data ID strings.
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r12649 | bugman | 2011-03-01 17:04:07 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been deleted and the pack_data()
function highly modified.
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r12650 | bugman | 2011-03-01 17:05:17 +0100 (Tue, 01 Mar 2011) | 3 lines
The model-free code no longer calls the deleted relax_data.data_init() function.
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r12651 | bugman | 2011-03-01 17:19:26 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplification of the return_value() function.
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r12652 | bugman | 2011-03-01 17:24:07 +0100 (Tue, 01 Mar 2011) | 3 lines
Updates for a number of model-free system tests for the changed relax_data.read() user function.
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r12653 | bugman | 2011-03-01 17:24:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplified the return_data_desc() function.
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r12654 | bugman | 2011-03-01 17:25:20 +0100 (Tue, 01 Mar 2011) | 3 lines
Removal of the test_labels() function, as this was only needed with the old design.
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r12655 | bugman | 2011-03-01 17:25:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12656 | bugman | 2011-03-01 17:32:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Deleted the now useless add_data_to_spin() function.
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r12657 | bugman | 2011-03-01 17:56:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the relax_data.back_calc() function for the new design.
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r12658 | bugman | 2011-03-01 18:05:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.bmrb_read() function to the new ID string design.
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r12659 | bugman | 2011-03-01 18:09:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the back and front ends of the relax_data.copy() user function to the new design.
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r12660 | bugman | 2011-03-01 18:13:01 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted RelaxNoRiError and RelaxRiError to the new ID string design.
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r12661 | bugman | 2011-03-01 18:16:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.delete() user function back and front end to the new design.
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r12662 | bugman | 2011-03-01 18:19:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.display() user function back and front end to the new design.
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r12663 | bugman | 2011-03-01 18:20:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed the useless find_ri_index() function.
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r12664 | bugman | 2011-03-01 18:23:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.peak_intensity_type() user function back and front end to the new design.
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r12665 | bugman | 2011-03-01 18:25:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12666 | bugman | 2011-03-01 18:27:24 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12667 | bugman | 2011-03-01 18:28:18 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the last commit, which should have said relax_data.temp_control().
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r12668 | bugman | 2011-03-01 18:30:27 +0100 (Tue, 01 Mar 2011) | 3 lines
Deletion of the useless update_noe_r1_table() function.
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r12669 | bugman | 2011-03-01 18:33:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.write() user function back and front end to the new design.
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r12670 | bugman | 2011-03-01 18:34:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed a non-existent import.
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r12671 | bugman | 2011-03-01 18:39:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the get_data_names() function for the new ID string design.
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r12672 | bugman | 2011-03-01 18:44:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the relax_data.delete() user function.
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r12673 | bugman | 2011-03-01 18:48:41 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12674 | bugman | 2011-03-01 18:51:54 +0100 (Tue, 01 Mar 2011) | 3 lines
Fixes for the pack_data() function.
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r12675 | bugman | 2011-03-01 19:19:47 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the _minimise_data_setup() method for the new relaxation data ID string design.
The _relax_data_opt_structs() helper method has been created to convert the new data structures into
the old ones used in the optimisation code of maths_fns.mf.
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r12676 | bugman | 2011-03-01 19:22:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free overfit_deselect() method for the new relaxation data structures.
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r12677 | bugman | 2011-03-01 19:28:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free sim_pack_data() method for the new relaxation data structures.
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r12678 | bugman | 2011-03-01 19:30:28 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free create_mc_data() method for the new relaxation data structures.
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r12679 | bugman | 2011-03-01 19:59:45 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed unused code from data_init().
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r12680 | bugman | 2011-03-01 20:12:48 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free model_statistics() method for the new relaxation data structures.
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r12681 | bugman | 2011-03-01 20:31:50 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free calculate() method for the new relaxation data structures.
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r12682 | bugman | 2011-03-01 20:33:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free minimise() method for the new relaxation data structures.
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r12683 | bugman | 2011-03-01 21:04:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Typo fix for _relax_data_opt_structs().
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r12684 | bugman | 2011-03-02 09:57:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed an incorrect arg to the relax_data.write() user function.
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r12685 | bugman | 2011-03-02 10:03:25 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the unit tests relying on the relax_data user functions for the new design.
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r12686 | bugman | 2011-03-02 10:08:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the front end to the relax_data.back_calc() user function for the new design.
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r12687 | bugman | 2011-03-02 10:09:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for one of the relax_data unit tests - one of the obligatory args was missing.
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r12688 | bugman | 2011-03-02 10:13:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the BMRB reading and writing system test script for the new relax data ID string design.
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r12689 | bugman | 2011-03-02 10:18:43 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Rx back calculation system test script for the new relax data ID string design.
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r12690 | bugman | 2011-03-02 10:23:46 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the model-free system test scripts for the new relax data ID string design.
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r12691 | bugman | 2011-03-02 10:34:11 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2 system test to the new relax data ID string design.
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r12692 | bugman | 2011-03-02 10:43:29 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_pse4() system test to the new relax data ID string design.
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r12693 | bugman | 2011-03-02 10:49:28 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_tem1() system test to the new relax data ID string design.
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r12694 | bugman | 2011-03-02 10:54:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the PDC reading system tests to the new relax data ID string design.
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r12695 | bugman | 2011-03-02 10:57:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the pdc.read() user function to the new relax data ID string design.
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r12696 | bugman | 2011-03-02 11:13:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplified the setup_peak_intensity_type() data.exp_info method for the new relax data ID string design.
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r12697 | bugman | 2011-03-02 11:15:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_calibration_setup() for the new relax data ID string design.
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r12698 | bugman | 2011-03-02 11:17:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_control_setup() for the new relax data ID string design.
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r12699 | bugman | 2011-03-02 11:18:19 +0100 (Wed, 02 Mar 2011) | 3 lines
Simple fixes for some of the methods.
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r12700 | bugman | 2011-03-02 11:29:47 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the relaxation data bmrb_write() method for the new relax data ID string design.
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r12701 | bugman | 2011-03-02 11:30:26 +0100 (Wed, 02 Mar 2011) | 3 lines
Deleted the now useless get_peak_intensity_type(), get_temp_calibration(), and get_temp_control().
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r12702 | bugman | 2011-03-02 11:35:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_aic_mod_sel_diff_tensor() system test for the new relax data ID string design.
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r12703 | bugman | 2011-03-02 11:54:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Modelfree4 generic_fns.palmer module for the new relax data ID string design.
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r12704 | bugman | 2011-03-02 11:54:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Syntax fix for the create_mfdata() function.
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r12705 | bugman | 2011-03-02 12:20:44 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the data pipe.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the relax data pipe to be updated to the new structures. The version
information is now being passed from the relax data store from_xml() method.
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r12706 | bugman | 2011-03-02 13:47:13 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the spin container.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the spin container to be updated to the new structures. The version information
is now being passed from the data pipe from_xml() method.
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r12707 | bugman | 2011-03-02 13:49:51 +0100 (Wed, 02 Mar 2011) | 3 lines
All objects starting with '_' are now considered special and skipped, instead of just starting with '__'.
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r12708 | bugman | 2011-03-02 14:05:57 +0100 (Wed, 02 Mar 2011) | 3 lines
Bug fixes for the new _back_compat_hook_ri_data() methods.
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r12709 | bugman | 2011-03-02 14:10:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Some changes to the consistency testing specific code for the new relax data ID string design.
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r12710 | bugman | 2011-03-02 14:21:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the relax_data.copy() back end.
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r12711 | bugman | 2011-03-02 14:23:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the spin container _back_compat_hook_ri_data() method.
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r12712 | bugman | 2011-03-02 14:23:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed a debugging print statement.
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r12713 | bugman | 2011-03-02 14:31:06 +0100 (Wed, 02 Mar 2011) | 3 lines
More fixes for the relax_data.copy() user function back end.
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r12714 | bugman | 2011-03-02 14:31:30 +0100 (Wed, 02 Mar 2011) | 3 lines
Epydoc docstring fixes.
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r12715 | bugman | 2011-03-02 14:39:38 +0100 (Wed, 02 Mar 2011) | 3 lines
Converted all spin.frq[0] to cdp.frq[cdp.ri_ids[0]] as the spin object 'frq' no longer exists.
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r12716 | bugman | 2011-03-02 15:01:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Update of the palmer.py Modelfree4 system test script for the new relax data ID string design.
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r12717 | bugman | 2011-03-02 15:11:06 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the model-free back_calc_ri() method for the new relax data ID string design.
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r12718 | bugman | 2011-03-02 15:11:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the back_calc_ri() method.
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r12719 | bugman | 2011-03-02 15:29:00 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the setting up of model-free optimisation.
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r12720 | bugman | 2011-03-02 15:33:19 +0100 (Wed, 02 Mar 2011) | 3 lines
The relax_data return_value() function can now handle missing data.
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r12721 | bugman | 2011-03-02 15:49:37 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplifications for all of the diffusion tensor system tests.
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r12722 | bugman | 2011-03-02 15:56:10 +0100 (Wed, 02 Mar 2011) | 6 lines
Fixes for the back end of the relax_data.back_calc() user function.
The missing ri_id arg situation was not being handled and spin container ri_data_bc structure was
being constantly overwritten.
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r12723 | bugman | 2011-03-02 16:20:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated many system test scripts for the new relax_data.read() user function interface.
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r12724 | bugman | 2011-03-02 16:29:59 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for SpinContainer._back_compat_hook_ri_data(), the MC sim object is only deleted if it exists.
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r12725 | bugman | 2011-03-02 16:34:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the opt_tm_fns system test module for the local_tm model-free model tests.
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r12726 | bugman | 2011-03-02 16:38:56 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the test_read_relax_data() model-free system test.
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed the relaxation data data structure names from the model-free data_names() method.
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r12728 | bugman | 2011-03-02 17:11:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for a typo in the model-free test_read_results_1_2 system test.
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r12729 | bugman | 2011-03-02 17:13:54 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the test_read_results_1_2 system test - the relaxation data was incorrectly checked.
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r12730 | bugman | 2011-03-02 17:18:12 +0100 (Wed, 02 Mar 2011) | 3 lines
The previous fix from r12729 used the wrong index!!
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r12731 | bugman | 2011-03-02 17:19:37 +0100 (Wed, 02 Mar 2011) | 6 lines
Fix for the model-free _load_relax_data() method.
The method now generates the relaxation data structures itself rather than calling a function which
was deleted from generic_fns.relax_data.
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r12732 | bugman | 2011-03-02 17:31:35 +0100 (Wed, 02 Mar 2011) | 3 lines
Renamed a script so it can be executed as a module.
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r12733 | bugman | 2011-03-02 17:38:00 +0100 (Wed, 02 Mar 2011) | 14 lines
Reverted revision r12727, as this is used in the XML file generation.
The command used was:
svn merge -r12727:12726 .
.....
r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/model_free/main.py
Removed the relaxation data data structure names from the model-free data_names() method.
.....
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r12734 | bugman | 2011-03-02 17:41:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Regenerated the relax 1.3 save file of the OMP model-free results.
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r12735 | bugman | 2011-03-02 17:45:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the frq list of the test_read_results_1_2_pse4 model-free system test.
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r12736 | bugman | 2011-03-02 17:47:20 +0100 (Wed, 02 Mar 2011) | 5 lines
Fix for the relax 1.2 model-free result file _load_relax_data() method.
The relaxation values and errors are only set if they exist.
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r12737 | bugman | 2011-03-02 17:56:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Many fixes for the test_read_results_1_2_tem1 model-free system test.
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r12738 | bugman | 2011-03-02 18:02:21 +0100 (Wed, 02 Mar 2011) | 3 lines
The model-free data_init() method now skips the relaxation data data structures.
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r12739 | bugman | 2011-03-02 18:27:39 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the create_mc_data() model-free method - the ri_type is now being passed into back_calc_ri().
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r12740 | bugman | 2011-03-02 18:32:12 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the _return_data_relax_data() and _return_error_relax_data() common API methods for the new design.
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r12741 | bugman | 2011-03-02 18:37:03 +0100 (Wed, 02 Mar 2011) | 3 lines
User function echoing is now turned on for the interpreter embedded in the SystemTestCase base class.
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r12742 | bugman | 2011-03-02 20:03:10 +0100 (Wed, 02 Mar 2011) | 3 lines
Replaced all instances of cdp.frq[0] with cdp.frq[cdp.ri_ids[0]].
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r12743 | bugman | 2011-03-02 20:21:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Created the new function generic_fns.relax_data.frq_loop() for looping over unique frequencies.
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r12744 | bugman | 2011-03-02 20:29:14 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free calculate() method - spin.relax_error no longer exists.
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r12745 | bugman | 2011-03-02 20:29:52 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free minimise() method when using Levenberg-Marquardt optimisation.
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r12746 | bugman | 2011-03-02 20:37:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the generate_ri.py sample script for the new relax data ID string design.
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r12747 | bugman | 2011-03-02 21:09:36 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the generate_ri.py model-free system test script.
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r12748 | bugman | 2011-03-02 21:10:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the generate_ri.py model-free system test script.
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r12749 | bugman | 2011-03-02 21:13:26 +0100 (Wed, 02 Mar 2011) | 5 lines
Simplifications to the generate_ri.py model-free system test script.
The error calculation function is not required and all functions have been eliminated.
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r12750 | bugman | 2011-03-03 07:57:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Added checks for the relax_data user functions for the ri_type being one of 'R1', 'R2', or 'NOE'.
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r12751 | bugman | 2011-03-03 07:58:21 +0100 (Thu, 03 Mar 2011) | 3 lines
The echoing of user functions on() method no longer shows a print out.
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r12752 | bugman | 2011-03-03 08:28:59 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the call to _relax_data_opt_structs() from _minimise_data_setup().
This was being performed for each relaxation data set, but it should be done only once per spin!
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r12753 | bugman | 2011-03-03 09:37:22 +0100 (Thu, 03 Mar 2011) | 3 lines
The _relax_data_opt_structs() model-free method now handles MC sim data.
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r12754 | bugman | 2011-03-03 09:49:38 +0100 (Thu, 03 Mar 2011) | 3 lines
The model-free sim_pack_data() now converts the sim_data structure into a dictionary with Rx IDs.
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r12755 | bugman | 2011-03-03 10:20:24 +0100 (Thu, 03 Mar 2011) | 3 lines
Alphabetical ordering of functions in the relax_data module.
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r12756 | bugman | 2011-03-03 10:22:52 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a new function called num_frq() for determining the number of frequencies.
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r12757 | bugman | 2011-03-03 10:44:30 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated all of the Dasha module for the new relax data ID string design.
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r12758 | bugman | 2011-03-03 11:07:27 +0100 (Thu, 03 Mar 2011) | 3 lines
The Dasha system test is now thoroughly checking all of the relax data store.
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r12759 | bugman | 2011-03-03 11:16:29 +0100 (Thu, 03 Mar 2011) | 6 lines
Create the specific base class method _sim_pack_relax_data() for packing relaxation data.
This is the method from specific_fns/model_free/main.py, shifted into api_common. The J(w) mapping
and consistency testing code now use this base method as well.
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r12760 | bugman | 2011-03-03 11:19:05 +0100 (Thu, 03 Mar 2011) | 3 lines
Some fixes for the consistency testing calculate() method.
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r12761 | bugman | 2011-03-03 11:24:51 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the test_calc() consistency testing system test for the new design.
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r12762 | bugman | 2011-03-03 11:29:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Fix for the consistency testing calculate() method - the frequency check was incorrect.
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r12763 | bugman | 2011-03-03 11:34:40 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed some references to residues, as these should be spins.
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r12764 | bugman | 2011-03-03 11:39:37 +0100 (Thu, 03 Mar 2011) | 6 lines
Added a check to make sure the relaxation data is of the correct frequency.
The comments have also been updated to be more similar to that of the J(w) mapping module. This is
to allow the J(w) mapping module to be more easily updated to the new design.
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r12765 | bugman | 2011-03-03 11:39:55 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the J(w) mapping module to the new relax data ID string design.
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r12766 | bugman | 2011-03-03 11:42:11 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the copyright notice.
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r12767 | bugman | 2011-03-03 11:42:37 +0100 (Thu, 03 Mar 2011) | 3 lines
Converted the J(w) mapping test_calc() system test to the new relax data ID string design.
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r12769 | bugman | 2011-03-03 12:01:29 +0100 (Thu, 03 Mar 2011) | 5 lines
Shifted the J(w) mapping and consistency testing create_mc_data() to the common methods.
The new method is called _create_mc_relax_data().
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r12770 | bugman | 2011-03-03 12:04:33 +0100 (Thu, 03 Mar 2011) | 3 lines
Deleted the unused relaxation data update_data_structures_spin() function.
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r12771 | bugman | 2011-03-03 12:14:18 +0100 (Thu, 03 Mar 2011) | 3 lines
Some last conversions of the relax_data bmrb_write() function to the new design.
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r12772 | bugman | 2011-03-03 12:16:23 +0100 (Thu, 03 Mar 2011) | 5 lines
Conversion of the diffusion tensor bmrb_write() function to the new relax data ID string design.
Some unused code was simply deleted.
........
r12773 | bugman | 2011-03-03 12:33:50 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the relaxation data bmrb_write() function.
The wrong relaxation data was being sent into the BMRB file.
........
r12774 | bugman | 2011-03-03 12:47:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the relaxation data checks in the BMRB system tests.
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r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed the model-free specific back_calc_ri() method from the specific code API.
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r12776 | bugman | 2011-03-03 13:08:29 +0100 (Thu, 03 Mar 2011) | 16 lines
Reverted r12775, as back_calc_ri should be part of the API.
The command used was:
svn merge -r12775:12774 .
.....
r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/api_base.py
M /branches/relax_data/specific_fns/model_free/main.py
M /branches/relax_data/specific_fns/setup.py
Removed the model-free specific back_calc_ri() method from the specific code API.
.....
........
r12777 | bugman | 2011-03-03 13:09:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the specific API back_calc_ri() method for the new relax data ID string design.
........
................
r12780 | bugman | 2011-03-03 14:23:31 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/relax_data
................
r12782 | bugman | 2011-03-03 14:57:29 +0100 (Thu, 03 Mar 2011) | 3 lines
The relax_data.back_calc() args no longer need to be supplied.
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r12783 | bugman | 2011-03-03 15:08:14 +0100 (Thu, 03 Mar 2011) | 3 lines
Improved the argument checking for the relax_data.back_calc() user function.
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r12784 | bugman | 2011-03-03 15:19:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a very basic system test for the relax_data.back_calc() user function.
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r12785 | bugman | 2011-03-03 15:30:40 +0100 (Thu, 03 Mar 2011) | 5 lines
Fixes for the relax_data.back_calc() back end.
The user function was completely non-functional!
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r12786 | bugman | 2011-03-03 15:33:49 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc data structure is now returned by get_data_name().
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r12787 | bugman | 2011-03-03 15:34:20 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc structure is not initialised by the model-free data_init() method.
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r12788 | bugman | 2011-03-03 15:38:26 +0100 (Thu, 03 Mar 2011) | 3 lines
Added some data checks to the test_back_calc() system test of the relax_data.back_calc() user fn.
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r12789 | bugman | 2011-03-03 15:39:58 +0100 (Thu, 03 Mar 2011) | 3 lines
Added the test_back_calc2() relaxation data system test for back calculation of specific data.
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r12790 | bugman | 2011-03-03 15:42:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Renamed test_back_calc2() to test_back_calc_specific().
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r12791 | bugman | 2011-03-03 15:43:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Created the test_back_calc_new() relaxation data system test for the back calculation of new data.
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r12792 | bugman | 2011-03-04 14:14:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Shifted all of the model-free sample scripts into the new subdirectory sample_scripts/model_free.
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r12793 | bugman | 2011-03-04 14:17:39 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the CV model-free model selection script to the new relax data ID string design.
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r12794 | bugman | 2011-03-04 14:47:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added copyright headers to all of the sample scripts, and updated the introduction text.
This allows users to determine the age of the scripts.
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r12795 | bugman | 2011-03-04 14:57:06 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated all of the sample scripts for the new relaxation data ID string design.
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r12796 | bugman | 2011-03-04 15:02:55 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the OpenDX mapping sample scripts from the relax 1.2 to the 1.3 design.
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r12797 | bugman | 2011-03-04 15:04:16 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for creating plots of experimental verses back calculated relaxation data.
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r12798 | bugman | 2011-03-04 15:31:13 +0100 (Fri, 04 Mar 2011) | 3 lines
Deleted the incomplete and useless N_state_model.py sample script.
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r12799 | bugman | 2011-03-04 15:31:36 +0100 (Fri, 04 Mar 2011) | 3 lines
Created a sample script subdirectory called n_state_model.
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r12800 | bugman | 2011-03-04 15:44:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added two sample scripts for determining the populations of an ensemble of small molecules.
This uses RDCs and PCSs with the N-state model to study the dynamics of small organic molecules.
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r12801 | bugman | 2011-03-04 15:50:56 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for the unsuccessful two domain N-state model optimisation.
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r12802 | bugman | 2011-03-04 16:29:12 +0100 (Fri, 04 Mar 2011) | 3 lines
Fix for the BMRB system test which was broken due to the restructuring of the sample_scripts directory.
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r12803 | bugman | 2011-03-04 16:36:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Fixes for the units tests of relax_data.back_calc() as the args can now be None.
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r12804 | bugman | 2011-03-09 17:05:49 +0100 (Wed, 09 Mar 2011) | 6 lines
Improved the RelaxWarning for the reading of NMRView peaks with missing assignments.
This is in response to bug #17876 (http://gna.org/bugs/?17876) submitted by Elio Cino <herfworm att
gmail dot com>.
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r12805 | bugman | 2011-03-14 18:52:10 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the ancient TODO file, as it is no longer relevant.
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r12806 | bugman | 2011-03-14 18:55:30 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the SRLS analysis type - there is no incentive to develop this part of relax.
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r12808 | bugman | 2011-03-17 12:51:13 +0100 (Thu, 17 Mar 2011) | 5 lines
Split the _bmrb_model_map() method into two as it was not functioning correctly as was too complex.
The two new methods are _from_bmrb_name() and _to_bmrb_name().
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r12809 | bugman | 2011-03-17 12:52:06 +0100 (Thu, 17 Mar 2011) | 3 lines
Removed some remnants of SRLS from the unit tests.
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r12810 | bugman | 2011-03-17 13:30:16 +0100 (Thu, 17 Mar 2011) | 3 lines
The parameter name is now always defined in _sf_model_free_read() when looping over the params.
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r12811 | bugman | 2011-03-17 13:31:08 +0100 (Thu, 17 Mar 2011) | 3 lines
Bug fixes for the _from_bmrb_model() and _to_bmrb_model() methods - the model name is now 'name'.
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r12812 | bugman | 2011-03-17 13:31:59 +0100 (Thu, 17 Mar 2011) | 3 lines
Alphabetical arrangement of the methods.
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r12813 | bugman | 2011-03-17 13:37:11 +0100 (Thu, 17 Mar 2011) | 3 lines
The _from_bmrb_model() method can now handle returning the same name.
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r12814 | bugman | 2011-03-17 13:40:55 +0100 (Thu, 17 Mar 2011) | 5 lines
Removed 'relax_disp' from the VALID_TYPES data pipe type array.
This is supported in the 'relax_disp' branch and not in the main line.
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r12815 | bugman | 2011-03-17 15:20:13 +0100 (Thu, 17 Mar 2011) | 3 lines
The te parameter is now properly converted to ts is the model is one of m5, m6, m7, or m8.
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r12816 | bugman | 2011-03-17 15:22:57 +0100 (Thu, 17 Mar 2011) | 3 lines
Fix for the conversion of te to ts - the model is not always given.
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r12817 | bugman | 2011-03-18 12:19:38 +0100 (Fri, 18 Mar 2011) | 5 lines
Added a new relaxation data function create_frq_label().
This is for generating a frequency label in MHz rounded to the nearest factor of 10.
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r12818 | bugman | 2011-03-18 12:31:36 +0100 (Fri, 18 Mar 2011) | 3 lines
Fix for the new create_frq_label() function.
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r12819 | bugman | 2011-03-24 16:00:41 +0100 (Thu, 24 Mar 2011) | 5 lines
The RDC and PCS Q factor user functions now do nothing when data is missing rather than failing.
A warning is given and the function now simply returns rather than crashing.
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r12820 | bugman | 2011-04-13 10:05:12 +0200 (Wed, 13 Apr 2011) | 3 lines
Expanded the N-state model test_align_fit() system test to check the pcs.back_calc() user function.
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r12821 | bugman | 2011-04-14 16:32:43 +0200 (Thu, 14 Apr 2011) | 7 lines
Bug fix for the N-state model for when only the paramagnetic centre position is optimised.
If the alignment tensor is fixed, as well as the probabilities of the states, then the optimisation
of the paramagnetic centre position was failing as the wrong target function was being used and the
correct one was not set up correctly for this.
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r12822 | bugman | 2011-04-14 17:19:46 +0200 (Thu, 14 Apr 2011) | 3 lines
The grace file created by pcs.corr_plot() now separates each element into its own graph.
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r12823 | bugman | 2011-04-15 10:05:49 +0200 (Fri, 15 Apr 2011) | 6 lines
Fix for bug #18030 (https://gna.org/bugs/?18030).
The problem was that the grid search limits were being scaled iteratively for each successive spin
system. This only affects certain type of custom grid searches.
................
r12824 | semor | 2011-04-17 15:50:38 +0200 (Sun, 17 Apr 2011) | 6 lines
Fixed bug 18037 (https://gna.org/bugs/index.php?18037).
A ":" symbol in the description of a function variable was preventing the
compilation of the user manual using scons.
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r12825 | semor | 2011-04-23 22:42:38 +0200 (Sat, 23 Apr 2011) | 4 lines
Added a missing import.
An import for "sys" was missing in "generic_fns/bmrb.py".
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r12826 | michaelbieri | 2011-05-30 04:17:03 +0200 (Mon, 30 May 2011) | 4 lines
Converted summary into comma separated file (.csv).
Resultstable generated can be opened in Excel or OpenOffice/LibreOffice.
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r12827 | michaelbieri | 2011-05-30 04:22:02 +0200 (Mon, 30 May 2011) | 2 lines
Renamed file parameter.
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r12828 | michaelbieri | 2011-05-30 04:22:51 +0200 (Mon, 30 May 2011) | 2 lines
Opened files are closed properly after writing.
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r12829 | michaelbieri | 2011-05-30 04:28:14 +0200 (Mon, 30 May 2011) | 2 lines
Corrected placement of seperator (comma).
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r12830 | michaelbieri | 2011-05-30 04:38:17 +0200 (Mon, 30 May 2011) | 2 lines
If no diffusion tensor is present, creation of diffusion pdb will be skipped.
................
|
2011-05-31 11:00:10
|
Tree
|
[r12837]
by
bugman
Fixes for the relaxation dispersion system tests.
The install path is now in the status object, and not in __main__.
|
2011-05-31 10:56:16
|
Tree
|
[r12836]
by
bugman
Merged revisions 12598-12617,12619-12634,12637-12643,12648,12778-12780,12782-12806,12808-12830 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r12598 | bugman | 2011-02-21 09:54:00 +0100 (Mon, 21 Feb 2011) | 3 lines
Activated the PDC peak intensity type reading, now that the BMRB branch has been merged.
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r12599 | bugman | 2011-02-21 09:59:38 +0100 (Mon, 21 Feb 2011) | 6 lines
Added the Bruker PDC software info to the exp_info module.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00056.html (Message-id:
<4D621CF8.601@...>).
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r12600 | bugman | 2011-02-21 10:22:55 +0100 (Mon, 21 Feb 2011) | 3 lines
Added the Bruker PDC to the exp_info.software_select() backend.
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r12601 | bugman | 2011-02-21 10:28:39 +0100 (Mon, 21 Feb 2011) | 3 lines
The pdc.read() back end is now reading the PDC version information.
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r12602 | bugman | 2011-02-21 10:30:13 +0100 (Mon, 21 Feb 2011) | 5 lines
The setting of the integration method in pdc.read() now works.
This needed to be done after the packing of the relaxation data.
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r12603 | bugman | 2011-02-21 10:32:41 +0100 (Mon, 21 Feb 2011) | 5 lines
The Bruker PDC software is now added to the experimental information.
This will be included in the BMRB deposition file.
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r12604 | bugman | 2011-02-21 16:40:41 +0100 (Mon, 21 Feb 2011) | 6 lines
Updated the Bruker PDC R1 output file.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00060.html (Message-id:
<4D6275CE.6040809@...>).
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r12605 | bugman | 2011-02-21 16:41:01 +0100 (Mon, 21 Feb 2011) | 3 lines
Updated the conversion script for the new R1 PDC file.
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r12606 | bugman | 2011-02-22 14:56:34 +0100 (Tue, 22 Feb 2011) | 8 lines
Updated the R1 Bruker PDC file to a newer version using "variance averaging" for the errors.
See https://mail.gna.org/public/relax-devel/2011-02/msg00066.html (Message-id:
<4D63908C.5060101@...>).
This is instead of the "worst case per peak scenario" option which over estimates the errors.
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r12607 | bugman | 2011-02-22 14:59:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Renamed the convert_data Bruker PDC conversion script to indicate it is for the R1.
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r12608 | bugman | 2011-02-22 15:08:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py to directly read the data out of the Bruker PDC file.
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r12609 | bugman | 2011-02-22 15:12:57 +0100 (Tue, 22 Feb 2011) | 5 lines
Added a catch for the "worst case per peak scenario" option in the PDC.
This will now throw a RelaxError, telling the user to go back to the PDC and use the other option.
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r12610 | bugman | 2011-02-22 15:13:15 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the errors_R1.txt for the new R1 PDC file.
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r12611 | bugman | 2011-02-22 15:13:44 +0100 (Tue, 22 Feb 2011) | 3 lines
Removed a debugging print statement.
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r12612 | bugman | 2011-02-22 15:33:56 +0100 (Tue, 22 Feb 2011) | 3 lines
Convert the pdc.read() back-end to use the \t delimination of the PDC file for parsing.
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r12613 | bugman | 2011-02-22 15:34:26 +0100 (Tue, 22 Feb 2011) | 3 lines
New relax R1 data file for the new testT1.txt PDC data file.
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r12614 | bugman | 2011-02-22 15:37:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py script for the new R1 PDC data.
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r12615 | bugman | 2011-02-22 15:37:31 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the Bruker PDC reading system test for the new R1 data.
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r12616 | bugman | 2011-02-22 15:40:05 +0100 (Tue, 22 Feb 2011) | 3 lines
Fixes for the pdc.read() back-end for the NOE PDC file.
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r12617 | bugman | 2011-02-22 16:51:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updates for the new R1 Bruker PDC file.
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r12619 | bugman | 2011-02-24 12:41:06 +0100 (Thu, 24 Feb 2011) | 6 lines
Updated the Bruker PDC files to the newest versions.
These are taken from the task #7180 (https://gna.org/task/?7180) attached by Peter Neidig as file
#12537, file #12538, and file #12539.
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r12620 | bugman | 2011-02-24 12:48:03 +0100 (Thu, 24 Feb 2011) | 3 lines
The PDC NOE conversion script is now taking the data directly from the PDC file.
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r12621 | bugman | 2011-02-24 12:50:14 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the pdc.read() back-end for reading NOE data out of the new PDC files.
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r12622 | bugman | 2011-02-24 12:50:46 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the PDC reading system tests, the data now matches the new PDC files.
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r12623 | bugman | 2011-02-24 12:53:17 +0100 (Thu, 24 Feb 2011) | 3 lines
The R1 value and error are now being read directly from the PDC file.
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r12624 | bugman | 2011-02-24 12:53:48 +0100 (Thu, 24 Feb 2011) | 3 lines
Decreased the accuracy of the PDC reading system test, as the PDC data is not accurate to 7 places.
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r12625 | bugman | 2011-02-25 14:24:59 +0100 (Fri, 25 Feb 2011) | 9 lines
Removed numpy from the relaxation curve-fitting C module code.
This now expects Python lists as arguments. This should help with incompatibilities between
different Python versions, as this seems to be due to the numpy C interface. See for example
the thread started by Min-Kyu <min-kyu dott cho att vanderbilt dot edu>
https://mail.gna.org/public/relax-users/2011-02/msg00000.html (Message-id:
<001f01cbd24f$350042d0$9f00c870$@cho@...>).
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r12626 | bugman | 2011-02-25 14:26:23 +0100 (Fri, 25 Feb 2011) | 6 lines
Added wrapper methods to the relaxation curve-fitting specific code for the new C modules.
These allow the parameter numpy array from minfx to be converted into a Python list prior to sending
it into the C module.
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r12627 | bugman | 2011-02-25 14:29:07 +0100 (Fri, 25 Feb 2011) | 3 lines
Fix for the back_calc_I C function so that it works under Python 2.5.
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r12628 | bugman | 2011-02-25 14:31:31 +0100 (Fri, 25 Feb 2011) | 3 lines
Added a check for the runpy module.
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r12629 | bugman | 2011-02-25 14:32:27 +0100 (Fri, 25 Feb 2011) | 3 lines
The runpy module is only imported if it exists.
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r12630 | bugman | 2011-02-25 14:33:35 +0100 (Fri, 25 Feb 2011) | 5 lines
Fix for the initialisation of the Bruker_import class.
This allows this module to be loaded in Python 2.4.
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r12631 | bugman | 2011-02-25 14:38:10 +0100 (Fri, 25 Feb 2011) | 3 lines
Scripts can now be run again under Python versions 2.4 or lower.
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r12632 | bugman | 2011-02-25 14:56:04 +0100 (Fri, 25 Feb 2011) | 5 lines
The reference counting appears to not be needed in the C modules.
This allows the modules to be compiled under Python 2.4 or lower.
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r12633 | bugman | 2011-02-25 15:25:42 +0100 (Fri, 25 Feb 2011) | 3 lines
The auto_analyses package modules are now imported by __init__ to force their existence.
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r12634 | bugman | 2011-02-25 18:46:52 +0100 (Fri, 25 Feb 2011) | 8 lines
Loosened all of the model-free tests so that the minimisation statistics are no longer checked.
The same result was being obtained on different platforms, different Python versions, and different
numpy versions, but the minimisation statistics were slightly different. The iter, f_count, g_count
h_count, and warning variables are no longer checked. This will stop users from thinking they have
a problem with their version of relax, after running the test suite.
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r12637 | bugman | 2011-03-01 11:35:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Added graphics for the value user function.
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r12638 | bugman | 2011-03-01 11:36:30 +0100 (Tue, 01 Mar 2011) | 3 lines
Added the value user function graphics to the icon paths.
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r12639 | bugman | 2011-03-01 12:08:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Added a wizard graphic for the value user functions.
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r12640 | bugman | 2011-03-01 12:11:24 +0100 (Tue, 01 Mar 2011) | 3 lines
The value user function wizard graphic is now the correct size.
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r12641 | bugman | 2011-03-01 12:13:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Improvements to the value user function wizard graphic - the tensor background has been deleted.
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r12642 | bugman | 2011-03-01 12:14:53 +0100 (Tue, 01 Mar 2011) | 3 lines
The value wizard graphic is again the wrong size!!!
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r12643 | bugman | 2011-03-01 12:15:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Created an initial value.set() user function GUI element and menu entry.
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r12648 | bugman | 2011-03-01 15:52:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Modified the value.set() user function GUI element so that the parameter element is an input field.
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r12778 | bugman | 2011-03-03 14:14:22 +0100 (Thu, 03 Mar 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12645" from
svn+ssh://bugman@.../svn/relax/branches/relax_data
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r12779 | bugman | 2011-03-03 14:21:42 +0100 (Thu, 03 Mar 2011) | 583 lines
Merged revisions 12647,12649-12767,12769-12777 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/relax_data
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r12647 | bugman | 2011-03-01 15:36:46 +0100 (Tue, 01 Mar 2011) | 3 lines
Redesigned the relax_data.read() user function front end for handling data ID strings.
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r12649 | bugman | 2011-03-01 17:04:07 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been deleted and the pack_data()
function highly modified.
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r12650 | bugman | 2011-03-01 17:05:17 +0100 (Tue, 01 Mar 2011) | 3 lines
The model-free code no longer calls the deleted relax_data.data_init() function.
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r12651 | bugman | 2011-03-01 17:19:26 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplification of the return_value() function.
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r12652 | bugman | 2011-03-01 17:24:07 +0100 (Tue, 01 Mar 2011) | 3 lines
Updates for a number of model-free system tests for the changed relax_data.read() user function.
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r12653 | bugman | 2011-03-01 17:24:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplified the return_data_desc() function.
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r12654 | bugman | 2011-03-01 17:25:20 +0100 (Tue, 01 Mar 2011) | 3 lines
Removal of the test_labels() function, as this was only needed with the old design.
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r12655 | bugman | 2011-03-01 17:25:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12656 | bugman | 2011-03-01 17:32:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Deleted the now useless add_data_to_spin() function.
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r12657 | bugman | 2011-03-01 17:56:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the relax_data.back_calc() function for the new design.
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r12658 | bugman | 2011-03-01 18:05:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.bmrb_read() function to the new ID string design.
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r12659 | bugman | 2011-03-01 18:09:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the back and front ends of the relax_data.copy() user function to the new design.
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r12660 | bugman | 2011-03-01 18:13:01 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted RelaxNoRiError and RelaxRiError to the new ID string design.
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r12661 | bugman | 2011-03-01 18:16:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.delete() user function back and front end to the new design.
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r12662 | bugman | 2011-03-01 18:19:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.display() user function back and front end to the new design.
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r12663 | bugman | 2011-03-01 18:20:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed the useless find_ri_index() function.
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r12664 | bugman | 2011-03-01 18:23:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.peak_intensity_type() user function back and front end to the new design.
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r12665 | bugman | 2011-03-01 18:25:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12666 | bugman | 2011-03-01 18:27:24 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12667 | bugman | 2011-03-01 18:28:18 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the last commit, which should have said relax_data.temp_control().
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r12668 | bugman | 2011-03-01 18:30:27 +0100 (Tue, 01 Mar 2011) | 3 lines
Deletion of the useless update_noe_r1_table() function.
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r12669 | bugman | 2011-03-01 18:33:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.write() user function back and front end to the new design.
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r12670 | bugman | 2011-03-01 18:34:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed a non-existent import.
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r12671 | bugman | 2011-03-01 18:39:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the get_data_names() function for the new ID string design.
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r12672 | bugman | 2011-03-01 18:44:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the relax_data.delete() user function.
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r12673 | bugman | 2011-03-01 18:48:41 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12674 | bugman | 2011-03-01 18:51:54 +0100 (Tue, 01 Mar 2011) | 3 lines
Fixes for the pack_data() function.
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r12675 | bugman | 2011-03-01 19:19:47 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the _minimise_data_setup() method for the new relaxation data ID string design.
The _relax_data_opt_structs() helper method has been created to convert the new data structures into
the old ones used in the optimisation code of maths_fns.mf.
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r12676 | bugman | 2011-03-01 19:22:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free overfit_deselect() method for the new relaxation data structures.
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r12677 | bugman | 2011-03-01 19:28:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free sim_pack_data() method for the new relaxation data structures.
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r12678 | bugman | 2011-03-01 19:30:28 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free create_mc_data() method for the new relaxation data structures.
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r12679 | bugman | 2011-03-01 19:59:45 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed unused code from data_init().
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r12680 | bugman | 2011-03-01 20:12:48 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free model_statistics() method for the new relaxation data structures.
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r12681 | bugman | 2011-03-01 20:31:50 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free calculate() method for the new relaxation data structures.
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r12682 | bugman | 2011-03-01 20:33:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free minimise() method for the new relaxation data structures.
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r12683 | bugman | 2011-03-01 21:04:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Typo fix for _relax_data_opt_structs().
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r12684 | bugman | 2011-03-02 09:57:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed an incorrect arg to the relax_data.write() user function.
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r12685 | bugman | 2011-03-02 10:03:25 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the unit tests relying on the relax_data user functions for the new design.
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r12686 | bugman | 2011-03-02 10:08:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the front end to the relax_data.back_calc() user function for the new design.
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r12687 | bugman | 2011-03-02 10:09:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for one of the relax_data unit tests - one of the obligatory args was missing.
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r12688 | bugman | 2011-03-02 10:13:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the BMRB reading and writing system test script for the new relax data ID string design.
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r12689 | bugman | 2011-03-02 10:18:43 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Rx back calculation system test script for the new relax data ID string design.
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r12690 | bugman | 2011-03-02 10:23:46 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the model-free system test scripts for the new relax data ID string design.
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r12691 | bugman | 2011-03-02 10:34:11 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2 system test to the new relax data ID string design.
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r12692 | bugman | 2011-03-02 10:43:29 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_pse4() system test to the new relax data ID string design.
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r12693 | bugman | 2011-03-02 10:49:28 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_tem1() system test to the new relax data ID string design.
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r12694 | bugman | 2011-03-02 10:54:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the PDC reading system tests to the new relax data ID string design.
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r12695 | bugman | 2011-03-02 10:57:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the pdc.read() user function to the new relax data ID string design.
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r12696 | bugman | 2011-03-02 11:13:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplified the setup_peak_intensity_type() data.exp_info method for the new relax data ID string design.
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r12697 | bugman | 2011-03-02 11:15:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_calibration_setup() for the new relax data ID string design.
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r12698 | bugman | 2011-03-02 11:17:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_control_setup() for the new relax data ID string design.
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r12699 | bugman | 2011-03-02 11:18:19 +0100 (Wed, 02 Mar 2011) | 3 lines
Simple fixes for some of the methods.
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r12700 | bugman | 2011-03-02 11:29:47 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the relaxation data bmrb_write() method for the new relax data ID string design.
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r12701 | bugman | 2011-03-02 11:30:26 +0100 (Wed, 02 Mar 2011) | 3 lines
Deleted the now useless get_peak_intensity_type(), get_temp_calibration(), and get_temp_control().
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r12702 | bugman | 2011-03-02 11:35:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_aic_mod_sel_diff_tensor() system test for the new relax data ID string design.
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r12703 | bugman | 2011-03-02 11:54:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Modelfree4 generic_fns.palmer module for the new relax data ID string design.
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r12704 | bugman | 2011-03-02 11:54:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Syntax fix for the create_mfdata() function.
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r12705 | bugman | 2011-03-02 12:20:44 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the data pipe.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the relax data pipe to be updated to the new structures. The version
information is now being passed from the relax data store from_xml() method.
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r12706 | bugman | 2011-03-02 13:47:13 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the spin container.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the spin container to be updated to the new structures. The version information
is now being passed from the data pipe from_xml() method.
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r12707 | bugman | 2011-03-02 13:49:51 +0100 (Wed, 02 Mar 2011) | 3 lines
All objects starting with '_' are now considered special and skipped, instead of just starting with '__'.
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r12708 | bugman | 2011-03-02 14:05:57 +0100 (Wed, 02 Mar 2011) | 3 lines
Bug fixes for the new _back_compat_hook_ri_data() methods.
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r12709 | bugman | 2011-03-02 14:10:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Some changes to the consistency testing specific code for the new relax data ID string design.
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r12710 | bugman | 2011-03-02 14:21:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the relax_data.copy() back end.
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r12711 | bugman | 2011-03-02 14:23:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the spin container _back_compat_hook_ri_data() method.
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r12712 | bugman | 2011-03-02 14:23:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed a debugging print statement.
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r12713 | bugman | 2011-03-02 14:31:06 +0100 (Wed, 02 Mar 2011) | 3 lines
More fixes for the relax_data.copy() user function back end.
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r12714 | bugman | 2011-03-02 14:31:30 +0100 (Wed, 02 Mar 2011) | 3 lines
Epydoc docstring fixes.
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r12715 | bugman | 2011-03-02 14:39:38 +0100 (Wed, 02 Mar 2011) | 3 lines
Converted all spin.frq[0] to cdp.frq[cdp.ri_ids[0]] as the spin object 'frq' no longer exists.
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r12716 | bugman | 2011-03-02 15:01:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Update of the palmer.py Modelfree4 system test script for the new relax data ID string design.
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r12717 | bugman | 2011-03-02 15:11:06 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the model-free back_calc_ri() method for the new relax data ID string design.
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r12718 | bugman | 2011-03-02 15:11:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the back_calc_ri() method.
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r12719 | bugman | 2011-03-02 15:29:00 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the setting up of model-free optimisation.
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r12720 | bugman | 2011-03-02 15:33:19 +0100 (Wed, 02 Mar 2011) | 3 lines
The relax_data return_value() function can now handle missing data.
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r12721 | bugman | 2011-03-02 15:49:37 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplifications for all of the diffusion tensor system tests.
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r12722 | bugman | 2011-03-02 15:56:10 +0100 (Wed, 02 Mar 2011) | 6 lines
Fixes for the back end of the relax_data.back_calc() user function.
The missing ri_id arg situation was not being handled and spin container ri_data_bc structure was
being constantly overwritten.
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r12723 | bugman | 2011-03-02 16:20:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated many system test scripts for the new relax_data.read() user function interface.
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r12724 | bugman | 2011-03-02 16:29:59 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for SpinContainer._back_compat_hook_ri_data(), the MC sim object is only deleted if it exists.
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r12725 | bugman | 2011-03-02 16:34:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the opt_tm_fns system test module for the local_tm model-free model tests.
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r12726 | bugman | 2011-03-02 16:38:56 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the test_read_relax_data() model-free system test.
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed the relaxation data data structure names from the model-free data_names() method.
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r12728 | bugman | 2011-03-02 17:11:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for a typo in the model-free test_read_results_1_2 system test.
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r12729 | bugman | 2011-03-02 17:13:54 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the test_read_results_1_2 system test - the relaxation data was incorrectly checked.
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r12730 | bugman | 2011-03-02 17:18:12 +0100 (Wed, 02 Mar 2011) | 3 lines
The previous fix from r12729 used the wrong index!!
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r12731 | bugman | 2011-03-02 17:19:37 +0100 (Wed, 02 Mar 2011) | 6 lines
Fix for the model-free _load_relax_data() method.
The method now generates the relaxation data structures itself rather than calling a function which
was deleted from generic_fns.relax_data.
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r12732 | bugman | 2011-03-02 17:31:35 +0100 (Wed, 02 Mar 2011) | 3 lines
Renamed a script so it can be executed as a module.
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r12733 | bugman | 2011-03-02 17:38:00 +0100 (Wed, 02 Mar 2011) | 14 lines
Reverted revision r12727, as this is used in the XML file generation.
The command used was:
svn merge -r12727:12726 .
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/model_free/main.py
Removed the relaxation data data structure names from the model-free data_names() method.
.....
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r12734 | bugman | 2011-03-02 17:41:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Regenerated the relax 1.3 save file of the OMP model-free results.
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r12735 | bugman | 2011-03-02 17:45:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the frq list of the test_read_results_1_2_pse4 model-free system test.
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r12736 | bugman | 2011-03-02 17:47:20 +0100 (Wed, 02 Mar 2011) | 5 lines
Fix for the relax 1.2 model-free result file _load_relax_data() method.
The relaxation values and errors are only set if they exist.
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r12737 | bugman | 2011-03-02 17:56:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Many fixes for the test_read_results_1_2_tem1 model-free system test.
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r12738 | bugman | 2011-03-02 18:02:21 +0100 (Wed, 02 Mar 2011) | 3 lines
The model-free data_init() method now skips the relaxation data data structures.
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r12739 | bugman | 2011-03-02 18:27:39 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the create_mc_data() model-free method - the ri_type is now being passed into back_calc_ri().
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r12740 | bugman | 2011-03-02 18:32:12 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the _return_data_relax_data() and _return_error_relax_data() common API methods for the new design.
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r12741 | bugman | 2011-03-02 18:37:03 +0100 (Wed, 02 Mar 2011) | 3 lines
User function echoing is now turned on for the interpreter embedded in the SystemTestCase base class.
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r12742 | bugman | 2011-03-02 20:03:10 +0100 (Wed, 02 Mar 2011) | 3 lines
Replaced all instances of cdp.frq[0] with cdp.frq[cdp.ri_ids[0]].
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r12743 | bugman | 2011-03-02 20:21:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Created the new function generic_fns.relax_data.frq_loop() for looping over unique frequencies.
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r12744 | bugman | 2011-03-02 20:29:14 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free calculate() method - spin.relax_error no longer exists.
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r12745 | bugman | 2011-03-02 20:29:52 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free minimise() method when using Levenberg-Marquardt optimisation.
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r12746 | bugman | 2011-03-02 20:37:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the generate_ri.py sample script for the new relax data ID string design.
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r12747 | bugman | 2011-03-02 21:09:36 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the generate_ri.py model-free system test script.
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r12748 | bugman | 2011-03-02 21:10:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the generate_ri.py model-free system test script.
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r12749 | bugman | 2011-03-02 21:13:26 +0100 (Wed, 02 Mar 2011) | 5 lines
Simplifications to the generate_ri.py model-free system test script.
The error calculation function is not required and all functions have been eliminated.
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r12750 | bugman | 2011-03-03 07:57:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Added checks for the relax_data user functions for the ri_type being one of 'R1', 'R2', or 'NOE'.
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r12751 | bugman | 2011-03-03 07:58:21 +0100 (Thu, 03 Mar 2011) | 3 lines
The echoing of user functions on() method no longer shows a print out.
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r12752 | bugman | 2011-03-03 08:28:59 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the call to _relax_data_opt_structs() from _minimise_data_setup().
This was being performed for each relaxation data set, but it should be done only once per spin!
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r12753 | bugman | 2011-03-03 09:37:22 +0100 (Thu, 03 Mar 2011) | 3 lines
The _relax_data_opt_structs() model-free method now handles MC sim data.
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r12754 | bugman | 2011-03-03 09:49:38 +0100 (Thu, 03 Mar 2011) | 3 lines
The model-free sim_pack_data() now converts the sim_data structure into a dictionary with Rx IDs.
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r12755 | bugman | 2011-03-03 10:20:24 +0100 (Thu, 03 Mar 2011) | 3 lines
Alphabetical ordering of functions in the relax_data module.
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r12756 | bugman | 2011-03-03 10:22:52 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a new function called num_frq() for determining the number of frequencies.
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r12757 | bugman | 2011-03-03 10:44:30 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated all of the Dasha module for the new relax data ID string design.
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r12758 | bugman | 2011-03-03 11:07:27 +0100 (Thu, 03 Mar 2011) | 3 lines
The Dasha system test is now thoroughly checking all of the relax data store.
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r12759 | bugman | 2011-03-03 11:16:29 +0100 (Thu, 03 Mar 2011) | 6 lines
Create the specific base class method _sim_pack_relax_data() for packing relaxation data.
This is the method from specific_fns/model_free/main.py, shifted into api_common. The J(w) mapping
and consistency testing code now use this base method as well.
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r12760 | bugman | 2011-03-03 11:19:05 +0100 (Thu, 03 Mar 2011) | 3 lines
Some fixes for the consistency testing calculate() method.
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r12761 | bugman | 2011-03-03 11:24:51 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the test_calc() consistency testing system test for the new design.
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r12762 | bugman | 2011-03-03 11:29:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Fix for the consistency testing calculate() method - the frequency check was incorrect.
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r12763 | bugman | 2011-03-03 11:34:40 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed some references to residues, as these should be spins.
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r12764 | bugman | 2011-03-03 11:39:37 +0100 (Thu, 03 Mar 2011) | 6 lines
Added a check to make sure the relaxation data is of the correct frequency.
The comments have also been updated to be more similar to that of the J(w) mapping module. This is
to allow the J(w) mapping module to be more easily updated to the new design.
........
r12765 | bugman | 2011-03-03 11:39:55 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the J(w) mapping module to the new relax data ID string design.
........
r12766 | bugman | 2011-03-03 11:42:11 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the copyright notice.
........
r12767 | bugman | 2011-03-03 11:42:37 +0100 (Thu, 03 Mar 2011) | 3 lines
Converted the J(w) mapping test_calc() system test to the new relax data ID string design.
........
r12769 | bugman | 2011-03-03 12:01:29 +0100 (Thu, 03 Mar 2011) | 5 lines
Shifted the J(w) mapping and consistency testing create_mc_data() to the common methods.
The new method is called _create_mc_relax_data().
........
r12770 | bugman | 2011-03-03 12:04:33 +0100 (Thu, 03 Mar 2011) | 3 lines
Deleted the unused relaxation data update_data_structures_spin() function.
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r12771 | bugman | 2011-03-03 12:14:18 +0100 (Thu, 03 Mar 2011) | 3 lines
Some last conversions of the relax_data bmrb_write() function to the new design.
........
r12772 | bugman | 2011-03-03 12:16:23 +0100 (Thu, 03 Mar 2011) | 5 lines
Conversion of the diffusion tensor bmrb_write() function to the new relax data ID string design.
Some unused code was simply deleted.
........
r12773 | bugman | 2011-03-03 12:33:50 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the relaxation data bmrb_write() function.
The wrong relaxation data was being sent into the BMRB file.
........
r12774 | bugman | 2011-03-03 12:47:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the relaxation data checks in the BMRB system tests.
........
r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed the model-free specific back_calc_ri() method from the specific code API.
........
r12776 | bugman | 2011-03-03 13:08:29 +0100 (Thu, 03 Mar 2011) | 16 lines
Reverted r12775, as back_calc_ri should be part of the API.
The command used was:
svn merge -r12775:12774 .
.....
r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/api_base.py
M /branches/relax_data/specific_fns/model_free/main.py
M /branches/relax_data/specific_fns/setup.py
Removed the model-free specific back_calc_ri() method from the specific code API.
.....
........
r12777 | bugman | 2011-03-03 13:09:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the specific API back_calc_ri() method for the new relax data ID string design.
........
................
r12780 | bugman | 2011-03-03 14:23:31 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/relax_data
................
r12782 | bugman | 2011-03-03 14:57:29 +0100 (Thu, 03 Mar 2011) | 3 lines
The relax_data.back_calc() args no longer need to be supplied.
................
r12783 | bugman | 2011-03-03 15:08:14 +0100 (Thu, 03 Mar 2011) | 3 lines
Improved the argument checking for the relax_data.back_calc() user function.
................
r12784 | bugman | 2011-03-03 15:19:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a very basic system test for the relax_data.back_calc() user function.
................
r12785 | bugman | 2011-03-03 15:30:40 +0100 (Thu, 03 Mar 2011) | 5 lines
Fixes for the relax_data.back_calc() back end.
The user function was completely non-functional!
................
r12786 | bugman | 2011-03-03 15:33:49 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc data structure is now returned by get_data_name().
................
r12787 | bugman | 2011-03-03 15:34:20 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc structure is not initialised by the model-free data_init() method.
................
r12788 | bugman | 2011-03-03 15:38:26 +0100 (Thu, 03 Mar 2011) | 3 lines
Added some data checks to the test_back_calc() system test of the relax_data.back_calc() user fn.
................
r12789 | bugman | 2011-03-03 15:39:58 +0100 (Thu, 03 Mar 2011) | 3 lines
Added the test_back_calc2() relaxation data system test for back calculation of specific data.
................
r12790 | bugman | 2011-03-03 15:42:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Renamed test_back_calc2() to test_back_calc_specific().
................
r12791 | bugman | 2011-03-03 15:43:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Created the test_back_calc_new() relaxation data system test for the back calculation of new data.
................
r12792 | bugman | 2011-03-04 14:14:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Shifted all of the model-free sample scripts into the new subdirectory sample_scripts/model_free.
................
r12793 | bugman | 2011-03-04 14:17:39 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the CV model-free model selection script to the new relax data ID string design.
................
r12794 | bugman | 2011-03-04 14:47:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added copyright headers to all of the sample scripts, and updated the introduction text.
This allows users to determine the age of the scripts.
................
r12795 | bugman | 2011-03-04 14:57:06 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated all of the sample scripts for the new relaxation data ID string design.
................
r12796 | bugman | 2011-03-04 15:02:55 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the OpenDX mapping sample scripts from the relax 1.2 to the 1.3 design.
................
r12797 | bugman | 2011-03-04 15:04:16 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for creating plots of experimental verses back calculated relaxation data.
................
r12798 | bugman | 2011-03-04 15:31:13 +0100 (Fri, 04 Mar 2011) | 3 lines
Deleted the incomplete and useless N_state_model.py sample script.
................
r12799 | bugman | 2011-03-04 15:31:36 +0100 (Fri, 04 Mar 2011) | 3 lines
Created a sample script subdirectory called n_state_model.
................
r12800 | bugman | 2011-03-04 15:44:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added two sample scripts for determining the populations of an ensemble of small molecules.
This uses RDCs and PCSs with the N-state model to study the dynamics of small organic molecules.
................
r12801 | bugman | 2011-03-04 15:50:56 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for the unsuccessful two domain N-state model optimisation.
................
r12802 | bugman | 2011-03-04 16:29:12 +0100 (Fri, 04 Mar 2011) | 3 lines
Fix for the BMRB system test which was broken due to the restructuring of the sample_scripts directory.
................
r12803 | bugman | 2011-03-04 16:36:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Fixes for the units tests of relax_data.back_calc() as the args can now be None.
................
r12804 | bugman | 2011-03-09 17:05:49 +0100 (Wed, 09 Mar 2011) | 6 lines
Improved the RelaxWarning for the reading of NMRView peaks with missing assignments.
This is in response to bug #17876 (http://gna.org/bugs/?17876) submitted by Elio Cino <herfworm att
gmail dot com>.
................
r12805 | bugman | 2011-03-14 18:52:10 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the ancient TODO file, as it is no longer relevant.
................
r12806 | bugman | 2011-03-14 18:55:30 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the SRLS analysis type - there is no incentive to develop this part of relax.
................
r12808 | bugman | 2011-03-17 12:51:13 +0100 (Thu, 17 Mar 2011) | 5 lines
Split the _bmrb_model_map() method into two as it was not functioning correctly as was too complex.
The two new methods are _from_bmrb_name() and _to_bmrb_name().
................
r12809 | bugman | 2011-03-17 12:52:06 +0100 (Thu, 17 Mar 2011) | 3 lines
Removed some remnants of SRLS from the unit tests.
................
r12810 | bugman | 2011-03-17 13:30:16 +0100 (Thu, 17 Mar 2011) | 3 lines
The parameter name is now always defined in _sf_model_free_read() when looping over the params.
................
r12811 | bugman | 2011-03-17 13:31:08 +0100 (Thu, 17 Mar 2011) | 3 lines
Bug fixes for the _from_bmrb_model() and _to_bmrb_model() methods - the model name is now 'name'.
................
r12812 | bugman | 2011-03-17 13:31:59 +0100 (Thu, 17 Mar 2011) | 3 lines
Alphabetical arrangement of the methods.
................
r12813 | bugman | 2011-03-17 13:37:11 +0100 (Thu, 17 Mar 2011) | 3 lines
The _from_bmrb_model() method can now handle returning the same name.
................
r12814 | bugman | 2011-03-17 13:40:55 +0100 (Thu, 17 Mar 2011) | 5 lines
Removed 'relax_disp' from the VALID_TYPES data pipe type array.
This is supported in the 'relax_disp' branch and not in the main line.
................
r12815 | bugman | 2011-03-17 15:20:13 +0100 (Thu, 17 Mar 2011) | 3 lines
The te parameter is now properly converted to ts is the model is one of m5, m6, m7, or m8.
................
r12816 | bugman | 2011-03-17 15:22:57 +0100 (Thu, 17 Mar 2011) | 3 lines
Fix for the conversion of te to ts - the model is not always given.
................
r12817 | bugman | 2011-03-18 12:19:38 +0100 (Fri, 18 Mar 2011) | 5 lines
Added a new relaxation data function create_frq_label().
This is for generating a frequency label in MHz rounded to the nearest factor of 10.
................
r12818 | bugman | 2011-03-18 12:31:36 +0100 (Fri, 18 Mar 2011) | 3 lines
Fix for the new create_frq_label() function.
................
r12819 | bugman | 2011-03-24 16:00:41 +0100 (Thu, 24 Mar 2011) | 5 lines
The RDC and PCS Q factor user functions now do nothing when data is missing rather than failing.
A warning is given and the function now simply returns rather than crashing.
................
r12820 | bugman | 2011-04-13 10:05:12 +0200 (Wed, 13 Apr 2011) | 3 lines
Expanded the N-state model test_align_fit() system test to check the pcs.back_calc() user function.
................
r12821 | bugman | 2011-04-14 16:32:43 +0200 (Thu, 14 Apr 2011) | 7 lines
Bug fix for the N-state model for when only the paramagnetic centre position is optimised.
If the alignment tensor is fixed, as well as the probabilities of the states, then the optimisation
of the paramagnetic centre position was failing as the wrong target function was being used and the
correct one was not set up correctly for this.
................
r12822 | bugman | 2011-04-14 17:19:46 +0200 (Thu, 14 Apr 2011) | 3 lines
The grace file created by pcs.corr_plot() now separates each element into its own graph.
................
r12823 | bugman | 2011-04-15 10:05:49 +0200 (Fri, 15 Apr 2011) | 6 lines
Fix for bug #18030 (https://gna.org/bugs/?18030).
The problem was that the grid search limits were being scaled iteratively for each successive spin
system. This only affects certain type of custom grid searches.
................
r12824 | semor | 2011-04-17 15:50:38 +0200 (Sun, 17 Apr 2011) | 6 lines
Fixed bug 18037 (https://gna.org/bugs/index.php?18037).
A ":" symbol in the description of a function variable was preventing the
compilation of the user manual using scons.
................
r12825 | semor | 2011-04-23 22:42:38 +0200 (Sat, 23 Apr 2011) | 4 lines
Added a missing import.
An import for "sys" was missing in "generic_fns/bmrb.py".
................
r12826 | michaelbieri | 2011-05-30 04:17:03 +0200 (Mon, 30 May 2011) | 4 lines
Converted summary into comma separated file (.csv).
Resultstable generated can be opened in Excel or OpenOffice/LibreOffice.
................
r12827 | michaelbieri | 2011-05-30 04:22:02 +0200 (Mon, 30 May 2011) | 2 lines
Renamed file parameter.
................
r12828 | michaelbieri | 2011-05-30 04:22:51 +0200 (Mon, 30 May 2011) | 2 lines
Opened files are closed properly after writing.
................
r12829 | michaelbieri | 2011-05-30 04:28:14 +0200 (Mon, 30 May 2011) | 2 lines
Corrected placement of seperator (comma).
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r12830 | michaelbieri | 2011-05-30 04:38:17 +0200 (Mon, 30 May 2011) | 2 lines
If no diffusion tensor is present, creation of diffusion pdb will be skipped.
................
|
2011-05-31 10:24:17
|
Tree
|
[r12835]
by
bugman
Merged revisions 12598-12617,12619-12634,12637-12643,12648,12778-12780,12782-12806,12808-12830 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
................
r12598 | bugman | 2011-02-21 09:54:00 +0100 (Mon, 21 Feb 2011) | 3 lines
Activated the PDC peak intensity type reading, now that the BMRB branch has been merged.
................
r12599 | bugman | 2011-02-21 09:59:38 +0100 (Mon, 21 Feb 2011) | 6 lines
Added the Bruker PDC software info to the exp_info module.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00056.html (Message-id:
<4D621CF8.601@...>).
................
r12600 | bugman | 2011-02-21 10:22:55 +0100 (Mon, 21 Feb 2011) | 3 lines
Added the Bruker PDC to the exp_info.software_select() backend.
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r12601 | bugman | 2011-02-21 10:28:39 +0100 (Mon, 21 Feb 2011) | 3 lines
The pdc.read() back end is now reading the PDC version information.
................
r12602 | bugman | 2011-02-21 10:30:13 +0100 (Mon, 21 Feb 2011) | 5 lines
The setting of the integration method in pdc.read() now works.
This needed to be done after the packing of the relaxation data.
................
r12603 | bugman | 2011-02-21 10:32:41 +0100 (Mon, 21 Feb 2011) | 5 lines
The Bruker PDC software is now added to the experimental information.
This will be included in the BMRB deposition file.
................
r12604 | bugman | 2011-02-21 16:40:41 +0100 (Mon, 21 Feb 2011) | 6 lines
Updated the Bruker PDC R1 output file.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00060.html (Message-id:
<4D6275CE.6040809@...>).
................
r12605 | bugman | 2011-02-21 16:41:01 +0100 (Mon, 21 Feb 2011) | 3 lines
Updated the conversion script for the new R1 PDC file.
................
r12606 | bugman | 2011-02-22 14:56:34 +0100 (Tue, 22 Feb 2011) | 8 lines
Updated the R1 Bruker PDC file to a newer version using "variance averaging" for the errors.
See https://mail.gna.org/public/relax-devel/2011-02/msg00066.html (Message-id:
<4D63908C.5060101@...>).
This is instead of the "worst case per peak scenario" option which over estimates the errors.
................
r12607 | bugman | 2011-02-22 14:59:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Renamed the convert_data Bruker PDC conversion script to indicate it is for the R1.
................
r12608 | bugman | 2011-02-22 15:08:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py to directly read the data out of the Bruker PDC file.
................
r12609 | bugman | 2011-02-22 15:12:57 +0100 (Tue, 22 Feb 2011) | 5 lines
Added a catch for the "worst case per peak scenario" option in the PDC.
This will now throw a RelaxError, telling the user to go back to the PDC and use the other option.
................
r12610 | bugman | 2011-02-22 15:13:15 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the errors_R1.txt for the new R1 PDC file.
................
r12611 | bugman | 2011-02-22 15:13:44 +0100 (Tue, 22 Feb 2011) | 3 lines
Removed a debugging print statement.
................
r12612 | bugman | 2011-02-22 15:33:56 +0100 (Tue, 22 Feb 2011) | 3 lines
Convert the pdc.read() back-end to use the \t delimination of the PDC file for parsing.
................
r12613 | bugman | 2011-02-22 15:34:26 +0100 (Tue, 22 Feb 2011) | 3 lines
New relax R1 data file for the new testT1.txt PDC data file.
................
r12614 | bugman | 2011-02-22 15:37:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py script for the new R1 PDC data.
................
r12615 | bugman | 2011-02-22 15:37:31 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the Bruker PDC reading system test for the new R1 data.
................
r12616 | bugman | 2011-02-22 15:40:05 +0100 (Tue, 22 Feb 2011) | 3 lines
Fixes for the pdc.read() back-end for the NOE PDC file.
................
r12617 | bugman | 2011-02-22 16:51:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updates for the new R1 Bruker PDC file.
................
r12619 | bugman | 2011-02-24 12:41:06 +0100 (Thu, 24 Feb 2011) | 6 lines
Updated the Bruker PDC files to the newest versions.
These are taken from the task #7180 (https://gna.org/task/?7180) attached by Peter Neidig as file
#12537, file #12538, and file #12539.
................
r12620 | bugman | 2011-02-24 12:48:03 +0100 (Thu, 24 Feb 2011) | 3 lines
The PDC NOE conversion script is now taking the data directly from the PDC file.
................
r12621 | bugman | 2011-02-24 12:50:14 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the pdc.read() back-end for reading NOE data out of the new PDC files.
................
r12622 | bugman | 2011-02-24 12:50:46 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the PDC reading system tests, the data now matches the new PDC files.
................
r12623 | bugman | 2011-02-24 12:53:17 +0100 (Thu, 24 Feb 2011) | 3 lines
The R1 value and error are now being read directly from the PDC file.
................
r12624 | bugman | 2011-02-24 12:53:48 +0100 (Thu, 24 Feb 2011) | 3 lines
Decreased the accuracy of the PDC reading system test, as the PDC data is not accurate to 7 places.
................
r12625 | bugman | 2011-02-25 14:24:59 +0100 (Fri, 25 Feb 2011) | 9 lines
Removed numpy from the relaxation curve-fitting C module code.
This now expects Python lists as arguments. This should help with incompatibilities between
different Python versions, as this seems to be due to the numpy C interface. See for example
the thread started by Min-Kyu <min-kyu dott cho att vanderbilt dot edu>
https://mail.gna.org/public/relax-users/2011-02/msg00000.html (Message-id:
<001f01cbd24f$350042d0$9f00c870$@cho@...>).
................
r12626 | bugman | 2011-02-25 14:26:23 +0100 (Fri, 25 Feb 2011) | 6 lines
Added wrapper methods to the relaxation curve-fitting specific code for the new C modules.
These allow the parameter numpy array from minfx to be converted into a Python list prior to sending
it into the C module.
................
r12627 | bugman | 2011-02-25 14:29:07 +0100 (Fri, 25 Feb 2011) | 3 lines
Fix for the back_calc_I C function so that it works under Python 2.5.
................
r12628 | bugman | 2011-02-25 14:31:31 +0100 (Fri, 25 Feb 2011) | 3 lines
Added a check for the runpy module.
................
r12629 | bugman | 2011-02-25 14:32:27 +0100 (Fri, 25 Feb 2011) | 3 lines
The runpy module is only imported if it exists.
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r12630 | bugman | 2011-02-25 14:33:35 +0100 (Fri, 25 Feb 2011) | 5 lines
Fix for the initialisation of the Bruker_import class.
This allows this module to be loaded in Python 2.4.
................
r12631 | bugman | 2011-02-25 14:38:10 +0100 (Fri, 25 Feb 2011) | 3 lines
Scripts can now be run again under Python versions 2.4 or lower.
................
r12632 | bugman | 2011-02-25 14:56:04 +0100 (Fri, 25 Feb 2011) | 5 lines
The reference counting appears to not be needed in the C modules.
This allows the modules to be compiled under Python 2.4 or lower.
................
r12633 | bugman | 2011-02-25 15:25:42 +0100 (Fri, 25 Feb 2011) | 3 lines
The auto_analyses package modules are now imported by __init__ to force their existence.
................
r12634 | bugman | 2011-02-25 18:46:52 +0100 (Fri, 25 Feb 2011) | 8 lines
Loosened all of the model-free tests so that the minimisation statistics are no longer checked.
The same result was being obtained on different platforms, different Python versions, and different
numpy versions, but the minimisation statistics were slightly different. The iter, f_count, g_count
h_count, and warning variables are no longer checked. This will stop users from thinking they have
a problem with their version of relax, after running the test suite.
................
r12637 | bugman | 2011-03-01 11:35:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Added graphics for the value user function.
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r12638 | bugman | 2011-03-01 11:36:30 +0100 (Tue, 01 Mar 2011) | 3 lines
Added the value user function graphics to the icon paths.
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r12639 | bugman | 2011-03-01 12:08:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Added a wizard graphic for the value user functions.
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r12640 | bugman | 2011-03-01 12:11:24 +0100 (Tue, 01 Mar 2011) | 3 lines
The value user function wizard graphic is now the correct size.
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r12641 | bugman | 2011-03-01 12:13:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Improvements to the value user function wizard graphic - the tensor background has been deleted.
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r12642 | bugman | 2011-03-01 12:14:53 +0100 (Tue, 01 Mar 2011) | 3 lines
The value wizard graphic is again the wrong size!!!
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r12643 | bugman | 2011-03-01 12:15:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Created an initial value.set() user function GUI element and menu entry.
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r12648 | bugman | 2011-03-01 15:52:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Modified the value.set() user function GUI element so that the parameter element is an input field.
................
r12778 | bugman | 2011-03-03 14:14:22 +0100 (Thu, 03 Mar 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12645" from
svn+ssh://bugman@.../svn/relax/branches/relax_data
................
r12779 | bugman | 2011-03-03 14:21:42 +0100 (Thu, 03 Mar 2011) | 583 lines
Merged revisions 12647,12649-12767,12769-12777 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/relax_data
........
r12647 | bugman | 2011-03-01 15:36:46 +0100 (Tue, 01 Mar 2011) | 3 lines
Redesigned the relax_data.read() user function front end for handling data ID strings.
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r12649 | bugman | 2011-03-01 17:04:07 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been deleted and the pack_data()
function highly modified.
........
r12650 | bugman | 2011-03-01 17:05:17 +0100 (Tue, 01 Mar 2011) | 3 lines
The model-free code no longer calls the deleted relax_data.data_init() function.
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r12651 | bugman | 2011-03-01 17:19:26 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplification of the return_value() function.
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r12652 | bugman | 2011-03-01 17:24:07 +0100 (Tue, 01 Mar 2011) | 3 lines
Updates for a number of model-free system tests for the changed relax_data.read() user function.
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r12653 | bugman | 2011-03-01 17:24:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplified the return_data_desc() function.
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r12654 | bugman | 2011-03-01 17:25:20 +0100 (Tue, 01 Mar 2011) | 3 lines
Removal of the test_labels() function, as this was only needed with the old design.
........
r12655 | bugman | 2011-03-01 17:25:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12656 | bugman | 2011-03-01 17:32:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Deleted the now useless add_data_to_spin() function.
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r12657 | bugman | 2011-03-01 17:56:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the relax_data.back_calc() function for the new design.
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r12658 | bugman | 2011-03-01 18:05:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.bmrb_read() function to the new ID string design.
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r12659 | bugman | 2011-03-01 18:09:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the back and front ends of the relax_data.copy() user function to the new design.
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r12660 | bugman | 2011-03-01 18:13:01 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted RelaxNoRiError and RelaxRiError to the new ID string design.
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r12661 | bugman | 2011-03-01 18:16:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.delete() user function back and front end to the new design.
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r12662 | bugman | 2011-03-01 18:19:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.display() user function back and front end to the new design.
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r12663 | bugman | 2011-03-01 18:20:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed the useless find_ri_index() function.
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r12664 | bugman | 2011-03-01 18:23:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.peak_intensity_type() user function back and front end to the new design.
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r12665 | bugman | 2011-03-01 18:25:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12666 | bugman | 2011-03-01 18:27:24 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front end to the new design.
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r12667 | bugman | 2011-03-01 18:28:18 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the last commit, which should have said relax_data.temp_control().
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r12668 | bugman | 2011-03-01 18:30:27 +0100 (Tue, 01 Mar 2011) | 3 lines
Deletion of the useless update_noe_r1_table() function.
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r12669 | bugman | 2011-03-01 18:33:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.write() user function back and front end to the new design.
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r12670 | bugman | 2011-03-01 18:34:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed a non-existent import.
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r12671 | bugman | 2011-03-01 18:39:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the get_data_names() function for the new ID string design.
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r12672 | bugman | 2011-03-01 18:44:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the relax_data.delete() user function.
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r12673 | bugman | 2011-03-01 18:48:41 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12674 | bugman | 2011-03-01 18:51:54 +0100 (Tue, 01 Mar 2011) | 3 lines
Fixes for the pack_data() function.
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r12675 | bugman | 2011-03-01 19:19:47 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the _minimise_data_setup() method for the new relaxation data ID string design.
The _relax_data_opt_structs() helper method has been created to convert the new data structures into
the old ones used in the optimisation code of maths_fns.mf.
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r12676 | bugman | 2011-03-01 19:22:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free overfit_deselect() method for the new relaxation data structures.
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r12677 | bugman | 2011-03-01 19:28:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free sim_pack_data() method for the new relaxation data structures.
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r12678 | bugman | 2011-03-01 19:30:28 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free create_mc_data() method for the new relaxation data structures.
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r12679 | bugman | 2011-03-01 19:59:45 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed unused code from data_init().
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r12680 | bugman | 2011-03-01 20:12:48 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free model_statistics() method for the new relaxation data structures.
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r12681 | bugman | 2011-03-01 20:31:50 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free calculate() method for the new relaxation data structures.
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r12682 | bugman | 2011-03-01 20:33:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free minimise() method for the new relaxation data structures.
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r12683 | bugman | 2011-03-01 21:04:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Typo fix for _relax_data_opt_structs().
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r12684 | bugman | 2011-03-02 09:57:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed an incorrect arg to the relax_data.write() user function.
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r12685 | bugman | 2011-03-02 10:03:25 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the unit tests relying on the relax_data user functions for the new design.
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r12686 | bugman | 2011-03-02 10:08:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the front end to the relax_data.back_calc() user function for the new design.
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r12687 | bugman | 2011-03-02 10:09:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for one of the relax_data unit tests - one of the obligatory args was missing.
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r12688 | bugman | 2011-03-02 10:13:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the BMRB reading and writing system test script for the new relax data ID string design.
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r12689 | bugman | 2011-03-02 10:18:43 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Rx back calculation system test script for the new relax data ID string design.
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r12690 | bugman | 2011-03-02 10:23:46 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the model-free system test scripts for the new relax data ID string design.
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r12691 | bugman | 2011-03-02 10:34:11 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2 system test to the new relax data ID string design.
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r12692 | bugman | 2011-03-02 10:43:29 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_pse4() system test to the new relax data ID string design.
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r12693 | bugman | 2011-03-02 10:49:28 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_tem1() system test to the new relax data ID string design.
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r12694 | bugman | 2011-03-02 10:54:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the PDC reading system tests to the new relax data ID string design.
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r12695 | bugman | 2011-03-02 10:57:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the pdc.read() user function to the new relax data ID string design.
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r12696 | bugman | 2011-03-02 11:13:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplified the setup_peak_intensity_type() data.exp_info method for the new relax data ID string design.
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r12697 | bugman | 2011-03-02 11:15:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_calibration_setup() for the new relax data ID string design.
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r12698 | bugman | 2011-03-02 11:17:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_control_setup() for the new relax data ID string design.
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r12699 | bugman | 2011-03-02 11:18:19 +0100 (Wed, 02 Mar 2011) | 3 lines
Simple fixes for some of the methods.
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r12700 | bugman | 2011-03-02 11:29:47 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the relaxation data bmrb_write() method for the new relax data ID string design.
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r12701 | bugman | 2011-03-02 11:30:26 +0100 (Wed, 02 Mar 2011) | 3 lines
Deleted the now useless get_peak_intensity_type(), get_temp_calibration(), and get_temp_control().
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r12702 | bugman | 2011-03-02 11:35:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_aic_mod_sel_diff_tensor() system test for the new relax data ID string design.
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r12703 | bugman | 2011-03-02 11:54:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Modelfree4 generic_fns.palmer module for the new relax data ID string design.
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r12704 | bugman | 2011-03-02 11:54:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Syntax fix for the create_mfdata() function.
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r12705 | bugman | 2011-03-02 12:20:44 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the data pipe.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the relax data pipe to be updated to the new structures. The version
information is now being passed from the relax data store from_xml() method.
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r12706 | bugman | 2011-03-02 13:47:13 +0100 (Wed, 02 Mar 2011) | 7 lines
Added backwards compatibility for the old relaxation data structures in the spin container.
The methods _back_compat_hook() and _back_compat_hook_ri_data() have been added to allow the base
data structures of the spin container to be updated to the new structures. The version information
is now being passed from the data pipe from_xml() method.
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r12707 | bugman | 2011-03-02 13:49:51 +0100 (Wed, 02 Mar 2011) | 3 lines
All objects starting with '_' are now considered special and skipped, instead of just starting with '__'.
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r12708 | bugman | 2011-03-02 14:05:57 +0100 (Wed, 02 Mar 2011) | 3 lines
Bug fixes for the new _back_compat_hook_ri_data() methods.
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r12709 | bugman | 2011-03-02 14:10:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Some changes to the consistency testing specific code for the new relax data ID string design.
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r12710 | bugman | 2011-03-02 14:21:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the relax_data.copy() back end.
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r12711 | bugman | 2011-03-02 14:23:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the spin container _back_compat_hook_ri_data() method.
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r12712 | bugman | 2011-03-02 14:23:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed a debugging print statement.
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r12713 | bugman | 2011-03-02 14:31:06 +0100 (Wed, 02 Mar 2011) | 3 lines
More fixes for the relax_data.copy() user function back end.
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r12714 | bugman | 2011-03-02 14:31:30 +0100 (Wed, 02 Mar 2011) | 3 lines
Epydoc docstring fixes.
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r12715 | bugman | 2011-03-02 14:39:38 +0100 (Wed, 02 Mar 2011) | 3 lines
Converted all spin.frq[0] to cdp.frq[cdp.ri_ids[0]] as the spin object 'frq' no longer exists.
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r12716 | bugman | 2011-03-02 15:01:58 +0100 (Wed, 02 Mar 2011) | 3 lines
Update of the palmer.py Modelfree4 system test script for the new relax data ID string design.
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r12717 | bugman | 2011-03-02 15:11:06 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the model-free back_calc_ri() method for the new relax data ID string design.
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r12718 | bugman | 2011-03-02 15:11:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the back_calc_ri() method.
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r12719 | bugman | 2011-03-02 15:29:00 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the setting up of model-free optimisation.
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r12720 | bugman | 2011-03-02 15:33:19 +0100 (Wed, 02 Mar 2011) | 3 lines
The relax_data return_value() function can now handle missing data.
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r12721 | bugman | 2011-03-02 15:49:37 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplifications for all of the diffusion tensor system tests.
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r12722 | bugman | 2011-03-02 15:56:10 +0100 (Wed, 02 Mar 2011) | 6 lines
Fixes for the back end of the relax_data.back_calc() user function.
The missing ri_id arg situation was not being handled and spin container ri_data_bc structure was
being constantly overwritten.
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r12723 | bugman | 2011-03-02 16:20:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated many system test scripts for the new relax_data.read() user function interface.
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r12724 | bugman | 2011-03-02 16:29:59 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for SpinContainer._back_compat_hook_ri_data(), the MC sim object is only deleted if it exists.
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r12725 | bugman | 2011-03-02 16:34:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the opt_tm_fns system test module for the local_tm model-free model tests.
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r12726 | bugman | 2011-03-02 16:38:56 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the test_read_relax_data() model-free system test.
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed the relaxation data data structure names from the model-free data_names() method.
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r12728 | bugman | 2011-03-02 17:11:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for a typo in the model-free test_read_results_1_2 system test.
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r12729 | bugman | 2011-03-02 17:13:54 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the test_read_results_1_2 system test - the relaxation data was incorrectly checked.
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r12730 | bugman | 2011-03-02 17:18:12 +0100 (Wed, 02 Mar 2011) | 3 lines
The previous fix from r12729 used the wrong index!!
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r12731 | bugman | 2011-03-02 17:19:37 +0100 (Wed, 02 Mar 2011) | 6 lines
Fix for the model-free _load_relax_data() method.
The method now generates the relaxation data structures itself rather than calling a function which
was deleted from generic_fns.relax_data.
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r12732 | bugman | 2011-03-02 17:31:35 +0100 (Wed, 02 Mar 2011) | 3 lines
Renamed a script so it can be executed as a module.
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r12733 | bugman | 2011-03-02 17:38:00 +0100 (Wed, 02 Mar 2011) | 14 lines
Reverted revision r12727, as this is used in the XML file generation.
The command used was:
svn merge -r12727:12726 .
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r12727 | bugman | 2011-03-02 16:51:53 +0100 (Wed, 02 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/model_free/main.py
Removed the relaxation data data structure names from the model-free data_names() method.
.....
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r12734 | bugman | 2011-03-02 17:41:02 +0100 (Wed, 02 Mar 2011) | 3 lines
Regenerated the relax 1.3 save file of the OMP model-free results.
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r12735 | bugman | 2011-03-02 17:45:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the frq list of the test_read_results_1_2_pse4 model-free system test.
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r12736 | bugman | 2011-03-02 17:47:20 +0100 (Wed, 02 Mar 2011) | 5 lines
Fix for the relax 1.2 model-free result file _load_relax_data() method.
The relaxation values and errors are only set if they exist.
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r12737 | bugman | 2011-03-02 17:56:40 +0100 (Wed, 02 Mar 2011) | 3 lines
Many fixes for the test_read_results_1_2_tem1 model-free system test.
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r12738 | bugman | 2011-03-02 18:02:21 +0100 (Wed, 02 Mar 2011) | 3 lines
The model-free data_init() method now skips the relaxation data data structures.
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r12739 | bugman | 2011-03-02 18:27:39 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the create_mc_data() model-free method - the ri_type is now being passed into back_calc_ri().
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r12740 | bugman | 2011-03-02 18:32:12 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the _return_data_relax_data() and _return_error_relax_data() common API methods for the new design.
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r12741 | bugman | 2011-03-02 18:37:03 +0100 (Wed, 02 Mar 2011) | 3 lines
User function echoing is now turned on for the interpreter embedded in the SystemTestCase base class.
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r12742 | bugman | 2011-03-02 20:03:10 +0100 (Wed, 02 Mar 2011) | 3 lines
Replaced all instances of cdp.frq[0] with cdp.frq[cdp.ri_ids[0]].
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r12743 | bugman | 2011-03-02 20:21:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Created the new function generic_fns.relax_data.frq_loop() for looping over unique frequencies.
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r12744 | bugman | 2011-03-02 20:29:14 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free calculate() method - spin.relax_error no longer exists.
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r12745 | bugman | 2011-03-02 20:29:52 +0100 (Wed, 02 Mar 2011) | 3 lines
Fixes for the model-free minimise() method when using Levenberg-Marquardt optimisation.
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r12746 | bugman | 2011-03-02 20:37:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the generate_ri.py sample script for the new relax data ID string design.
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r12747 | bugman | 2011-03-02 21:09:36 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for the generate_ri.py model-free system test script.
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r12748 | bugman | 2011-03-02 21:10:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Another fix for the generate_ri.py model-free system test script.
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r12749 | bugman | 2011-03-02 21:13:26 +0100 (Wed, 02 Mar 2011) | 5 lines
Simplifications to the generate_ri.py model-free system test script.
The error calculation function is not required and all functions have been eliminated.
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r12750 | bugman | 2011-03-03 07:57:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Added checks for the relax_data user functions for the ri_type being one of 'R1', 'R2', or 'NOE'.
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r12751 | bugman | 2011-03-03 07:58:21 +0100 (Thu, 03 Mar 2011) | 3 lines
The echoing of user functions on() method no longer shows a print out.
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r12752 | bugman | 2011-03-03 08:28:59 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the call to _relax_data_opt_structs() from _minimise_data_setup().
This was being performed for each relaxation data set, but it should be done only once per spin!
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r12753 | bugman | 2011-03-03 09:37:22 +0100 (Thu, 03 Mar 2011) | 3 lines
The _relax_data_opt_structs() model-free method now handles MC sim data.
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r12754 | bugman | 2011-03-03 09:49:38 +0100 (Thu, 03 Mar 2011) | 3 lines
The model-free sim_pack_data() now converts the sim_data structure into a dictionary with Rx IDs.
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r12755 | bugman | 2011-03-03 10:20:24 +0100 (Thu, 03 Mar 2011) | 3 lines
Alphabetical ordering of functions in the relax_data module.
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r12756 | bugman | 2011-03-03 10:22:52 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a new function called num_frq() for determining the number of frequencies.
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r12757 | bugman | 2011-03-03 10:44:30 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated all of the Dasha module for the new relax data ID string design.
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r12758 | bugman | 2011-03-03 11:07:27 +0100 (Thu, 03 Mar 2011) | 3 lines
The Dasha system test is now thoroughly checking all of the relax data store.
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r12759 | bugman | 2011-03-03 11:16:29 +0100 (Thu, 03 Mar 2011) | 6 lines
Create the specific base class method _sim_pack_relax_data() for packing relaxation data.
This is the method from specific_fns/model_free/main.py, shifted into api_common. The J(w) mapping
and consistency testing code now use this base method as well.
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r12760 | bugman | 2011-03-03 11:19:05 +0100 (Thu, 03 Mar 2011) | 3 lines
Some fixes for the consistency testing calculate() method.
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r12761 | bugman | 2011-03-03 11:24:51 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the test_calc() consistency testing system test for the new design.
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r12762 | bugman | 2011-03-03 11:29:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Fix for the consistency testing calculate() method - the frequency check was incorrect.
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r12763 | bugman | 2011-03-03 11:34:40 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed some references to residues, as these should be spins.
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r12764 | bugman | 2011-03-03 11:39:37 +0100 (Thu, 03 Mar 2011) | 6 lines
Added a check to make sure the relaxation data is of the correct frequency.
The comments have also been updated to be more similar to that of the J(w) mapping module. This is
to allow the J(w) mapping module to be more easily updated to the new design.
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r12765 | bugman | 2011-03-03 11:39:55 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the J(w) mapping module to the new relax data ID string design.
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r12766 | bugman | 2011-03-03 11:42:11 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the copyright notice.
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r12767 | bugman | 2011-03-03 11:42:37 +0100 (Thu, 03 Mar 2011) | 3 lines
Converted the J(w) mapping test_calc() system test to the new relax data ID string design.
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r12769 | bugman | 2011-03-03 12:01:29 +0100 (Thu, 03 Mar 2011) | 5 lines
Shifted the J(w) mapping and consistency testing create_mc_data() to the common methods.
The new method is called _create_mc_relax_data().
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r12770 | bugman | 2011-03-03 12:04:33 +0100 (Thu, 03 Mar 2011) | 3 lines
Deleted the unused relaxation data update_data_structures_spin() function.
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r12771 | bugman | 2011-03-03 12:14:18 +0100 (Thu, 03 Mar 2011) | 3 lines
Some last conversions of the relax_data bmrb_write() function to the new design.
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r12772 | bugman | 2011-03-03 12:16:23 +0100 (Thu, 03 Mar 2011) | 5 lines
Conversion of the diffusion tensor bmrb_write() function to the new relax data ID string design.
Some unused code was simply deleted.
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r12773 | bugman | 2011-03-03 12:33:50 +0100 (Thu, 03 Mar 2011) | 5 lines
Fix for the relaxation data bmrb_write() function.
The wrong relaxation data was being sent into the BMRB file.
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r12774 | bugman | 2011-03-03 12:47:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Fixes for the relaxation data checks in the BMRB system tests.
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r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed the model-free specific back_calc_ri() method from the specific code API.
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r12776 | bugman | 2011-03-03 13:08:29 +0100 (Thu, 03 Mar 2011) | 16 lines
Reverted r12775, as back_calc_ri should be part of the API.
The command used was:
svn merge -r12775:12774 .
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r12775 | bugman | 2011-03-03 12:59:57 +0100 (Thu, 03 Mar 2011) | 3 lines
Changed paths:
M /branches/relax_data/specific_fns/api_base.py
M /branches/relax_data/specific_fns/model_free/main.py
M /branches/relax_data/specific_fns/setup.py
Removed the model-free specific back_calc_ri() method from the specific code API.
.....
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r12777 | bugman | 2011-03-03 13:09:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Updated the specific API back_calc_ri() method for the new relax data ID string design.
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r12780 | bugman | 2011-03-03 14:23:31 +0100 (Thu, 03 Mar 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/relax_data
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r12782 | bugman | 2011-03-03 14:57:29 +0100 (Thu, 03 Mar 2011) | 3 lines
The relax_data.back_calc() args no longer need to be supplied.
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r12783 | bugman | 2011-03-03 15:08:14 +0100 (Thu, 03 Mar 2011) | 3 lines
Improved the argument checking for the relax_data.back_calc() user function.
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r12784 | bugman | 2011-03-03 15:19:47 +0100 (Thu, 03 Mar 2011) | 3 lines
Created a very basic system test for the relax_data.back_calc() user function.
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r12785 | bugman | 2011-03-03 15:30:40 +0100 (Thu, 03 Mar 2011) | 5 lines
Fixes for the relax_data.back_calc() back end.
The user function was completely non-functional!
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r12786 | bugman | 2011-03-03 15:33:49 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc data structure is now returned by get_data_name().
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r12787 | bugman | 2011-03-03 15:34:20 +0100 (Thu, 03 Mar 2011) | 3 lines
The ri_data_bc structure is not initialised by the model-free data_init() method.
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r12788 | bugman | 2011-03-03 15:38:26 +0100 (Thu, 03 Mar 2011) | 3 lines
Added some data checks to the test_back_calc() system test of the relax_data.back_calc() user fn.
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r12789 | bugman | 2011-03-03 15:39:58 +0100 (Thu, 03 Mar 2011) | 3 lines
Added the test_back_calc2() relaxation data system test for back calculation of specific data.
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r12790 | bugman | 2011-03-03 15:42:46 +0100 (Thu, 03 Mar 2011) | 3 lines
Renamed test_back_calc2() to test_back_calc_specific().
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r12791 | bugman | 2011-03-03 15:43:09 +0100 (Thu, 03 Mar 2011) | 3 lines
Created the test_back_calc_new() relaxation data system test for the back calculation of new data.
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r12792 | bugman | 2011-03-04 14:14:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Shifted all of the model-free sample scripts into the new subdirectory sample_scripts/model_free.
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r12793 | bugman | 2011-03-04 14:17:39 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the CV model-free model selection script to the new relax data ID string design.
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r12794 | bugman | 2011-03-04 14:47:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added copyright headers to all of the sample scripts, and updated the introduction text.
This allows users to determine the age of the scripts.
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r12795 | bugman | 2011-03-04 14:57:06 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated all of the sample scripts for the new relaxation data ID string design.
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r12796 | bugman | 2011-03-04 15:02:55 +0100 (Fri, 04 Mar 2011) | 3 lines
Updated the OpenDX mapping sample scripts from the relax 1.2 to the 1.3 design.
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r12797 | bugman | 2011-03-04 15:04:16 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for creating plots of experimental verses back calculated relaxation data.
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r12798 | bugman | 2011-03-04 15:31:13 +0100 (Fri, 04 Mar 2011) | 3 lines
Deleted the incomplete and useless N_state_model.py sample script.
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r12799 | bugman | 2011-03-04 15:31:36 +0100 (Fri, 04 Mar 2011) | 3 lines
Created a sample script subdirectory called n_state_model.
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r12800 | bugman | 2011-03-04 15:44:26 +0100 (Fri, 04 Mar 2011) | 5 lines
Added two sample scripts for determining the populations of an ensemble of small molecules.
This uses RDCs and PCSs with the N-state model to study the dynamics of small organic molecules.
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r12801 | bugman | 2011-03-04 15:50:56 +0100 (Fri, 04 Mar 2011) | 3 lines
Added a sample script for the unsuccessful two domain N-state model optimisation.
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r12802 | bugman | 2011-03-04 16:29:12 +0100 (Fri, 04 Mar 2011) | 3 lines
Fix for the BMRB system test which was broken due to the restructuring of the sample_scripts directory.
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r12803 | bugman | 2011-03-04 16:36:44 +0100 (Fri, 04 Mar 2011) | 3 lines
Fixes for the units tests of relax_data.back_calc() as the args can now be None.
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r12804 | bugman | 2011-03-09 17:05:49 +0100 (Wed, 09 Mar 2011) | 6 lines
Improved the RelaxWarning for the reading of NMRView peaks with missing assignments.
This is in response to bug #17876 (http://gna.org/bugs/?17876) submitted by Elio Cino <herfworm att
gmail dot com>.
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r12805 | bugman | 2011-03-14 18:52:10 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the ancient TODO file, as it is no longer relevant.
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r12806 | bugman | 2011-03-14 18:55:30 +0100 (Mon, 14 Mar 2011) | 3 lines
Deleted the SRLS analysis type - there is no incentive to develop this part of relax.
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r12808 | bugman | 2011-03-17 12:51:13 +0100 (Thu, 17 Mar 2011) | 5 lines
Split the _bmrb_model_map() method into two as it was not functioning correctly as was too complex.
The two new methods are _from_bmrb_name() and _to_bmrb_name().
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r12809 | bugman | 2011-03-17 12:52:06 +0100 (Thu, 17 Mar 2011) | 3 lines
Removed some remnants of SRLS from the unit tests.
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r12810 | bugman | 2011-03-17 13:30:16 +0100 (Thu, 17 Mar 2011) | 3 lines
The parameter name is now always defined in _sf_model_free_read() when looping over the params.
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r12811 | bugman | 2011-03-17 13:31:08 +0100 (Thu, 17 Mar 2011) | 3 lines
Bug fixes for the _from_bmrb_model() and _to_bmrb_model() methods - the model name is now 'name'.
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r12812 | bugman | 2011-03-17 13:31:59 +0100 (Thu, 17 Mar 2011) | 3 lines
Alphabetical arrangement of the methods.
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r12813 | bugman | 2011-03-17 13:37:11 +0100 (Thu, 17 Mar 2011) | 3 lines
The _from_bmrb_model() method can now handle returning the same name.
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r12814 | bugman | 2011-03-17 13:40:55 +0100 (Thu, 17 Mar 2011) | 5 lines
Removed 'relax_disp' from the VALID_TYPES data pipe type array.
This is supported in the 'relax_disp' branch and not in the main line.
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r12815 | bugman | 2011-03-17 15:20:13 +0100 (Thu, 17 Mar 2011) | 3 lines
The te parameter is now properly converted to ts is the model is one of m5, m6, m7, or m8.
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r12816 | bugman | 2011-03-17 15:22:57 +0100 (Thu, 17 Mar 2011) | 3 lines
Fix for the conversion of te to ts - the model is not always given.
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r12817 | bugman | 2011-03-18 12:19:38 +0100 (Fri, 18 Mar 2011) | 5 lines
Added a new relaxation data function create_frq_label().
This is for generating a frequency label in MHz rounded to the nearest factor of 10.
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r12818 | bugman | 2011-03-18 12:31:36 +0100 (Fri, 18 Mar 2011) | 3 lines
Fix for the new create_frq_label() function.
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r12819 | bugman | 2011-03-24 16:00:41 +0100 (Thu, 24 Mar 2011) | 5 lines
The RDC and PCS Q factor user functions now do nothing when data is missing rather than failing.
A warning is given and the function now simply returns rather than crashing.
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r12820 | bugman | 2011-04-13 10:05:12 +0200 (Wed, 13 Apr 2011) | 3 lines
Expanded the N-state model test_align_fit() system test to check the pcs.back_calc() user function.
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r12821 | bugman | 2011-04-14 16:32:43 +0200 (Thu, 14 Apr 2011) | 7 lines
Bug fix for the N-state model for when only the paramagnetic centre position is optimised.
If the alignment tensor is fixed, as well as the probabilities of the states, then the optimisation
of the paramagnetic centre position was failing as the wrong target function was being used and the
correct one was not set up correctly for this.
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r12822 | bugman | 2011-04-14 17:19:46 +0200 (Thu, 14 Apr 2011) | 3 lines
The grace file created by pcs.corr_plot() now separates each element into its own graph.
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r12823 | bugman | 2011-04-15 10:05:49 +0200 (Fri, 15 Apr 2011) | 6 lines
Fix for bug #18030 (https://gna.org/bugs/?18030).
The problem was that the grid search limits were being scaled iteratively for each successive spin
system. This only affects certain type of custom grid searches.
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r12824 | semor | 2011-04-17 15:50:38 +0200 (Sun, 17 Apr 2011) | 6 lines
Fixed bug 18037 (https://gna.org/bugs/index.php?18037).
A ":" symbol in the description of a function variable was preventing the
compilation of the user manual using scons.
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r12825 | semor | 2011-04-23 22:42:38 +0200 (Sat, 23 Apr 2011) | 4 lines
Added a missing import.
An import for "sys" was missing in "generic_fns/bmrb.py".
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r12826 | michaelbieri | 2011-05-30 04:17:03 +0200 (Mon, 30 May 2011) | 4 lines
Converted summary into comma separated file (.csv).
Resultstable generated can be opened in Excel or OpenOffice/LibreOffice.
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r12827 | michaelbieri | 2011-05-30 04:22:02 +0200 (Mon, 30 May 2011) | 2 lines
Renamed file parameter.
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r12828 | michaelbieri | 2011-05-30 04:22:51 +0200 (Mon, 30 May 2011) | 2 lines
Opened files are closed properly after writing.
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r12829 | michaelbieri | 2011-05-30 04:28:14 +0200 (Mon, 30 May 2011) | 2 lines
Corrected placement of seperator (comma).
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r12830 | michaelbieri | 2011-05-30 04:38:17 +0200 (Mon, 30 May 2011) | 2 lines
If no diffusion tensor is present, creation of diffusion pdb will be skipped.
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2011-05-31 09:44:36
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