Author: bugman
Date: Thu Oct 8 17:42:14 2009
New Revision: 9660
URL: http://svn.gna.org/viewcvs/relax?rev=9660&view=rev
Log:
Merged revisions 9528-9658 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r9528 | bugman | 2009-09-18 14:04:52 +0200 (Fri, 18 Sep 2009) | 3 lines
Created the euler_zyz_to_axis_angle() conversion function.
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r9529 | bugman | 2009-09-18 14:28:37 +0200 (Fri, 18 Sep 2009) | 6 lines
Created axis_angle_to_euler_zyz().
The test_euler_zyz_to_euler_zyz() unit test now checks both
euler_zyz_to_axis_angle() and
axis_angle_to_euler_zyz().
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r9530 | bugman | 2009-09-18 17:38:27 +0200 (Fri, 18 Sep 2009) | 12 lines
Final 1.3 line redesigns of the relax_io module.
The log() and tee() functions have been renamed to io_streams_log() and
io_streams_tee(), and the
old IO.logging_off() class method has been converted to the
io_streams_restore() function. The
io_streams_restore() function is also differently designed, using the true
original IO streams
(sys.__stdin__, sys.__stdout__, and sys.__stderr__).
The IO.delete() method has been converted to a module function.
The IO class has been eliminated.
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r9531 | bugman | 2009-09-18 18:19:26 +0200 (Fri, 18 Sep 2009) | 6 lines
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This
checks the dumping and
reloading of alignment tensors into an XML file.
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r9532 | bugman | 2009-09-18 18:26:40 +0200 (Fri, 18 Sep 2009) | 5 lines
Bug fix for the delete function.
The function was failing if the file was missing!
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r9533 | bugman | 2009-09-18 18:28:05 +0200 (Fri, 18 Sep 2009) | 6 lines
Bug fix for the test suite.
The temporary files were not always deleted if a .bz2 extension was added!
Now relax_io.delete() is
being called to fix this.
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r9534 | bugman | 2009-09-18 18:28:56 +0200 (Fri, 18 Sep 2009) | 3 lines
Reactivated the system tests turned off in r9533.
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r9535 | bugman | 2009-09-18 18:32:41 +0200 (Fri, 18 Sep 2009) | 5 lines
Fix for the data_names() method for when no model has been setup.
This allows the frame order data pipe to be written out prior to the model
setup.
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r9536 | bugman | 2009-09-18 18:43:02 +0200 (Fri, 18 Sep 2009) | 3 lines
Expansion of the test_to_and_from_xml() system test to check more data
structures.
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r9537 | bugman | 2009-09-18 18:47:49 +0200 (Fri, 18 Sep 2009) | 3 lines
The data structures of the AlignTensorList class are now packed into the
XML file.
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r9538 | bugman | 2009-09-18 19:11:30 +0200 (Fri, 18 Sep 2009) | 3 lines
Added the blacklist arg to xml_to_object().
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r9539 | bugman | 2009-09-18 19:15:06 +0200 (Fri, 18 Sep 2009) | 6 lines
Reverted r9538. The wrong file was committed!
The command used was:
svn merge -r9538:9537 .
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r9540 | bugman | 2009-09-18 19:15:40 +0200 (Fri, 18 Sep 2009) | 3 lines
Try again: Added the blacklist arg to xml_to_object().
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r9541 | bugman | 2009-09-18 19:18:14 +0200 (Fri, 18 Sep 2009) | 3 lines
Bug fix, the blacklist args now default to [].
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r9542 | bugman | 2009-09-18 19:19:39 +0200 (Fri, 18 Sep 2009) | 3 lines
Fix for the test_to_and_from_xml() check of the 'reduction' data structure.
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r9543 | bugman | 2009-09-18 19:20:15 +0200 (Fri, 18 Sep 2009) | 3 lines
The 'reduction' data structure is now properly created from the XML file.
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r9544 | bugman | 2009-09-21 13:25:14 +0200 (Mon, 21 Sep 2009) | 6 lines
Modified the frame order grid search.
The angle end points are now avoided (as they are the same as the start
points) and the beta Euler
angle increments are halved, as the search is half of that of alpha and
gamma (0 to pi).
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r9545 | bugman | 2009-09-21 13:53:39 +0200 (Mon, 21 Sep 2009) | 5 lines
Removed the end point of the cone angle from the grid search.
This is unrestricted motion, so is physically not possible.
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r9546 | bugman | 2009-09-21 14:03:55 +0200 (Mon, 21 Sep 2009) | 5 lines
Also halved the number of theta polar angle increments in the frame order
grid search.
This is to match the cone axis azimuthal angle phi.
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r9547 | bugman | 2009-09-21 16:20:58 +0200 (Mon, 21 Sep 2009) | 6 lines
Fix for the missing PDB file error.
The extension '.pdb' was being added to the end so if the missing file
'1F3Y.pdb' was specified,
the RelaxError would say that '1F3Y.pdb.pdb' was missing.
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r9548 | bugman | 2009-09-21 18:44:14 +0200 (Mon, 21 Sep 2009) | 7 lines
Complete redesign of the grid_search() method.
The grid ops structure is no longer created, rather the grid is directly
created to be passed to the
grid search algorithm. The __grid_row() method has been added to create
the row of the grid
corresponding to a certain parameter.
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r9549 | bugman | 2009-09-21 19:37:50 +0200 (Mon, 21 Sep 2009) | 3 lines
Implemented the acos grid search for angular parameters of the frame order
theories.
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r9550 | bugman | 2009-09-21 19:39:41 +0200 (Mon, 21 Sep 2009) | 3 lines
Fixed the call to the grid search.
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r9551 | bugman | 2009-09-21 20:25:52 +0200 (Mon, 21 Sep 2009) | 5 lines
Fix for the __unpack_opt_results() for the new direct calling of the grid
search.
The returned results are different.
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r9552 | bugman | 2009-09-22 11:50:31 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a false, deliberately broken Xplor line to test the parsing of Xplor
NOE files.
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r9553 | bugman | 2009-09-22 12:04:37 +0200 (Tue, 22 Sep 2009) | 3 lines
Bug fix for the reading of Xplor NOE data when a line starts with '#'.
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r9554 | bugman | 2009-09-22 13:15:40 +0200 (Tue, 22 Sep 2009) | 5 lines
Fix for the test_opt_rigid_rand_rot() system test.
The changes to the frame order grid search broke this test.
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r9555 | bugman | 2009-09-22 14:28:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a series of checks to the test_curve_fitting() system test.
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r9556 | bugman | 2009-09-22 14:29:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the relaxation curve fitting grid search for the new design of
the minfx grid search.
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r9557 | bugman | 2009-09-22 14:38:58 +0200 (Tue, 22 Sep 2009) | 3 lines
A bit of a clean up of the relaxation curve fitting minimise() method.
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r9558 | bugman | 2009-09-22 14:52:46 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the N-state model grid search setup around the new minfx
interface.
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r9559 | bugman | 2009-09-22 15:00:03 +0200 (Tue, 22 Sep 2009) | 3 lines
Added a comment line.
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r9560 | bugman | 2009-09-22 15:00:25 +0200 (Tue, 22 Sep 2009) | 3 lines
Another clean out of the grid search setup.
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r9561 | bugman | 2009-09-22 15:16:24 +0200 (Tue, 22 Sep 2009) | 3 lines
Removed some trailing whitespace.
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r9562 | bugman | 2009-09-22 18:18:55 +0200 (Tue, 22 Sep 2009) | 3 lines
Redesigned the model-free grid search setup around the new minfx interface.
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r9563 | bugman | 2009-09-22 19:35:05 +0200 (Tue, 22 Sep 2009) | 3 lines
Modified the grid search calls due to changes in minfx.
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r9564 | bugman | 2009-10-05 10:25:33 +0200 (Mon, 05 Oct 2009) | 10 lines
Bug fix: Added the function __deselect_spins() to remove spins with too
little data.
This fixes bug #14428 (http://gna.org/bugs/?14428) reported by Pierre-Yves
Savard <pierre-yves dott
savard at bcm dot ulaval dot ca>.
The new function is almost identical to that used in the model-free
analysis performed by relax in
that spins with no or too little data, or those which would be over-fit are
removed from the
analysis.
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r9565 | bugman | 2009-10-05 10:26:24 +0200 (Mon, 05 Oct 2009) | 3 lines
Fix for the system test of Art Palmer's Modelfree4 program for the new
__deselect_spins() fn.
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r9566 | bugman | 2009-10-05 11:34:48 +0200 (Mon, 05 Oct 2009) | 3 lines
Added a script for creating Molmol macros to represent the model-free
motions.
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r9567 | bugman | 2009-10-05 12:15:51 +0200 (Mon, 05 Oct 2009) | 3 lines
Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
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r9568 | bugman | 2009-10-06 11:22:21 +0200 (Tue, 06 Oct 2009) | 6 lines
Added the spin_id_col arg to the rdc.read() user function.
This allows 2 different formats for spin identification - spin ID string or
mol name, res name and
num, and spin name and num.
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r9569 | bugman | 2009-10-06 11:25:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed some empty lines.
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r9570 | bugman | 2009-10-06 11:38:20 +0200 (Tue, 06 Oct 2009) | 9 lines
Changes to the pcs.read() and rdc.read() user function interfaces.
Columns are now numbered from 1 - note this will break many things! The
spin_id_col is now accepted
and the spin_id arg is explained.
The docstrings have also been modified all over these user function classes
to replace
'identification string' with 'ID string'.
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r9571 | bugman | 2009-10-06 11:39:22 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the call from the prompt to the generic fns.
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r9572 | bugman | 2009-10-06 12:18:35 +0200 (Tue, 06 Oct 2009) | 6 lines
Created the read_spin_data_file() generator function.
This is designed to replace quite a few inconsistent functions throughout
the generic function code
base. It reads a columnar formatted file with a spin per line.
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r9573 | bugman | 2009-10-06 12:20:20 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generate_spin_id_data_array() so that column numbering starts at 1.
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r9574 | bugman | 2009-10-06 12:28:13 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified generic_fns.rdc.read() to use the new
relax_io.read_spin_data_file().
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r9575 | bugman | 2009-10-06 12:32:17 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for the unit tests of
generic_fns.mol_res_spin.generate_spin_id_data_array().
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r9576 | bugman | 2009-10-06 12:52:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed the calls to rdc.read() and pcs.read() in the system tests.
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r9577 | bugman | 2009-10-06 12:56:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Added a check to see if the file is empty to read_spin_data_file().
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r9578 | bugman | 2009-10-06 13:01:06 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted value.read() to use the new relax_io.read_spin_data_file()
function.
This converts the user function to the 1.3 line design as well.
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r9579 | bugman | 2009-10-06 13:19:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Docstring modification better explaining spin_id.
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r9580 | bugman | 2009-10-06 13:20:57 +0200 (Tue, 06 Oct 2009) | 5 lines
Converted spectrum.read_intensities() to use the new
relax_io.read_spin_data_file() function.
This is only for the generic formatted file.
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r9581 | bugman | 2009-10-06 13:22:23 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of relax_io.read_spin_data_file().
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r9582 | bugman | 2009-10-06 15:26:28 +0200 (Tue, 06 Oct 2009) | 5 lines
Bug fix for the relax_io.read_spin_data_file() function.
The column number check was incorrect due to the column renumbering.
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r9583 | bugman | 2009-10-06 15:46:25 +0200 (Tue, 06 Oct 2009) | 6 lines
The relax_io.read_spin_data_file() function now calls
generic_fns.sequence.validate_sequence().
This is a more advanced check of the sequence information. The
validate_sequence() function has
also been modified to handle single data lines.
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r9584 | bugman | 2009-10-06 16:07:58 +0200 (Tue, 06 Oct 2009) | 3 lines
Wrote spin_id_to_data_list() to convert a single spin ID into a list of
mol, res, and spin names and numbers.
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r9585 | bugman | 2009-10-06 16:13:53 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the sequence.read() user fn to use the new
relax_io.read_spin_data_file() function.
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r9586 | bugman | 2009-10-06 16:14:54 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the spin_id_to_data_list() function.
The spin ID string was incorrectly named.
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r9587 | bugman | 2009-10-06 16:21:16 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line!
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r9588 | bugman | 2009-10-06 16:22:55 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed some calls to sequence.read() in the unit tests.
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r9589 | bugman | 2009-10-06 17:25:41 +0200 (Tue, 06 Oct 2009) | 5 lines
Rewrote the tokenise() function to allow for the '&' boolean operator for
residues and spins.
This allows ':1&:GLY' or '@453&@N' to be parsed.
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r9590 | bugman | 2009-10-06 17:35:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Modified parse_token() to handle multiple tokens simultaneously.
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r9591 | bugman | 2009-10-06 17:38:48 +0200 (Tue, 06 Oct 2009) | 3 lines
Some fixes for the spin_id_to_data_list() function.
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r9592 | bugman | 2009-10-06 17:45:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixes for spin_id_to_data_list(), and now it returns a tuple rather than a
list.
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r9593 | bugman | 2009-10-06 18:06:03 +0200 (Tue, 06 Oct 2009) | 3 lines
Some more fixes for spin_id_to_data_list().
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r9594 | bugman | 2009-10-06 18:11:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Fix for the read() function. The arguments are now properly sent to
generate().
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r9595 | bugman | 2009-10-06 18:19:45 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the test_read() system test.
The residue columns must now be specified.
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r9596 | bugman | 2009-10-06 18:36:04 +0200 (Tue, 06 Oct 2009) | 3 lines
Yet another fix for the new read_spin_data_file() function - hopefully this
will be the last!
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r9597 | bugman | 2009-10-06 18:37:01 +0200 (Tue, 06 Oct 2009) | 3 lines
Added the missing import of read_spin_data_file().
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r9598 | bugman | 2009-10-06 18:40:24 +0200 (Tue, 06 Oct 2009) | 5 lines
Fix for the validate_sequence().
The shifted column numbers were not being taken into account.
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r9599 | bugman | 2009-10-06 18:42:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed the test for error values of zero, as this was killing Dasha!
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r9600 | bugman | 2009-10-06 18:43:38 +0200 (Tue, 06 Oct 2009) | 3 lines
Fixed all the calls to sequence.read() where the default residue columns
were being relied upon.
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r9601 | bugman | 2009-10-06 18:53:57 +0200 (Tue, 06 Oct 2009) | 3 lines
Removed a debugging print statement.
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r9602 | bugman | 2009-10-06 19:07:51 +0200 (Tue, 06 Oct 2009) | 3 lines
Reverted some accidental commenting out of system tests.
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r9603 | bugman | 2009-10-06 19:21:42 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted select.read() and deselect.read() to use the new
relax_io.read_spin_data_file() function.
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r9604 | bugman | 2009-10-06 19:37:39 +0200 (Tue, 06 Oct 2009) | 3 lines
Additions to the select.read() and deselect.read() docstrings.
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r9605 | bugman | 2009-10-06 19:57:12 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9606 | bugman | 2009-10-06 20:07:29 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the relax_data.read() user fn to use the new
relax_io.read_spin_data_file() function.
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r9607 | bugman | 2009-10-06 20:13:44 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header line.
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r9608 | bugman | 2009-10-06 20:22:15 +0200 (Tue, 06 Oct 2009) | 3 lines
Converted the pcs.read() user fn to use the new
relax_io.read_spin_data_file() function.
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r9609 | bugman | 2009-10-06 20:27:10 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9610 | bugman | 2009-10-06 20:28:02 +0200 (Tue, 06 Oct 2009) | 3 lines
Commented out the header lines.
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r9611 | bugman | 2009-10-06 20:29:46 +0200 (Tue, 06 Oct 2009) | 3 lines
Header realignment.
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r9612 | bugman | 2009-10-07 09:43:42 +0200 (Wed, 07 Oct 2009) | 5 lines
Bug fixes for the RDC and PCS read() functions.
The alignment tensor ID had the same variable name as the spin ID!
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r9613 | bugman | 2009-10-07 09:53:40 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed all the alignment ID args and variables 'id' to 'align_id' in the
RDC and PCS user fns.
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r9614 | bugman | 2009-10-07 09:55:26 +0200 (Wed, 07 Oct 2009) | 3 lines
Docstring spelling mistake fix - 'spid_id_col' should be 'spin_id_col'!
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r9615 | bugman | 2009-10-07 10:08:32 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the system tests to use the new 'align_id' args.
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r9616 | bugman | 2009-10-07 10:18:37 +0200 (Wed, 07 Oct 2009) | 6 lines
Removed some unneeded files.
The relaxation delays will be placed into the script itself, and the
generic_intensity2.txt file
will replace generic_intensity.txt.
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r9617 | bugman | 2009-10-07 10:19:57 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed generic_intensity2.txt to generic_intensity.txt.
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r9618 | bugman | 2009-10-07 10:28:59 +0200 (Wed, 07 Oct 2009) | 3 lines
Redesigned the test_read_peak_list_generic() system test.
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r9619 | bugman | 2009-10-07 10:29:47 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the test_read_peak_list_generic2() system test.
This was just duplicating test_read_peak_list_generic().
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r9620 | bugman | 2009-10-07 10:30:21 +0200 (Wed, 07 Oct 2009) | 3 lines
Commented out the header.
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r9621 | bugman | 2009-10-07 11:25:42 +0200 (Wed, 07 Oct 2009) | 3 lines
Added the new error class RelaxArgNotNoneError for when an argument should
be None.
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r9622 | bugman | 2009-10-07 11:28:35 +0200 (Wed, 07 Oct 2009) | 6 lines
Complete redesign of the generic_fns.spectrum module.
This significantly simplifies the code base (much less jumping between
functions) and prepares for
the generically formatted file support.
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r9623 | bugman | 2009-10-07 11:35:45 +0200 (Wed, 07 Oct 2009) | 3 lines
Fixes for the test_read_peak_list_generic() system test.
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r9624 | bugman | 2009-10-07 11:36:44 +0200 (Wed, 07 Oct 2009) | 5 lines
Rewrote the intensity_generic() function.
This is now much simpler (5 lines of code).
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r9625 | bugman | 2009-10-07 11:39:24 +0200 (Wed, 07 Oct 2009) | 3 lines
More fixes for the test_read_peak_list_generic(). It now passes!
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r9626 | bugman | 2009-10-07 12:44:06 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed some unused imports.
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r9627 | bugman | 2009-10-07 14:29:55 +0200 (Wed, 07 Oct 2009) | 6 lines
Wrote the relax_io.write_spin_data_file() function.
This writes spin specific data to a file (can be STDOUT). It will replace
the write_header()
and write_body() functions of generic_fns.sequence.
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r9628 | bugman | 2009-10-07 14:31:29 +0200 (Wed, 07 Oct 2009) | 5 lines
Deleted the write_body(), write_header(), and write_line() functions from
generic_fns.sequence.
This should accelerate the switch to relax_io.write_spin_data_file().
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r9629 | bugman | 2009-10-07 14:34:52 +0200 (Wed, 07 Oct 2009) | 3 lines
Import fixes by shifting to relax_io.write_spin_data_file().
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r9630 | bugman | 2009-10-07 14:41:02 +0200 (Wed, 07 Oct 2009) | 3 lines
Renamed read_spin_data_file() to read_spin_data() and
write_spin_data_file() to write_spin_data().
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r9631 | bugman | 2009-10-07 14:59:07 +0200 (Wed, 07 Oct 2009) | 3 lines
Removed all dependence on write_body() and write_header() from the sequence
module.
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r9632 | bugman | 2009-10-07 15:04:47 +0200 (Wed, 07 Oct 2009) | 3 lines
[... 570 lines stripped ...]
r9660 - in /branches/multi_processor_merge: ./ data/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ samp...