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Merged revisions 9528-9658 via svnmerge from

svn+ssh://bugman@.../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

Converted the load_spins() function to use relax_io.write_spin_data().
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r9633 | bugman | 2009-10-07 15:07:56 +0200 (Wed, 07 Oct 2009) | 3 lines

Spacing fixes for write_spin_data().
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r9634 | bugman | 2009-10-07 15:17:25 +0200 (Wed, 07 Oct 2009) | 3 lines

Modified write_spin_data() to dynamically modify the spin ID column widths if the data is too long.
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r9635 | bugman | 2009-10-07 17:49:06 +0200 (Wed, 07 Oct 2009) | 3 lines

Missing import.
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r9636 | bugman | 2009-10-07 17:53:33 +0200 (Wed, 07 Oct 2009) | 3 lines

Converted the file keyword args to read_ and write_spin_data() to normal args.
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r9637 | bugman | 2009-10-07 17:56:40 +0200 (Wed, 07 Oct 2009) | 5 lines

Fixed the write_spin_data() from read().

The file arg must be given, and now as this is set to sys.stdout, STDOUT redirection works again.
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r9638 | bugman | 2009-10-07 18:00:19 +0200 (Wed, 07 Oct 2009) | 5 lines

Fix for the test_write_protein_sequence() unit test.

The output file format is now a little different.
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r9639 | bugman | 2009-10-07 18:16:52 +0200 (Wed, 07 Oct 2009) | 3 lines

Converted value.write() to user relax_io.write_spin_data().
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r9640 | bugman | 2009-10-07 18:18:11 +0200 (Wed, 07 Oct 2009) | 5 lines

Converted the read_spin_data() file arg back to a keyword.

The file_data arg can be used instead!
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r9641 | bugman | 2009-10-07 18:21:07 +0200 (Wed, 07 Oct 2009) | 6 lines

Partial bug fix for bug #14464 (http://gna.org/bugs/?14464).

The problem fix here (only one of a few) was the new design of the user function classes. This was
breaking the docstring fetching script used to generate the relax manual.
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r9642 | bugman | 2009-10-07 18:24:40 +0200 (Wed, 07 Oct 2009) | 3 lines

Modified the output of the user function docstring parsing.
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r9643 | bugman | 2009-10-07 18:48:19 +0200 (Wed, 07 Oct 2009) | 6 lines

Partial bug fix for bug #14464 (https://gna.org/bugs/?14464).

Fix for the PDF manual compilation - os.rename() is being used instead of shutil.move(). No idea
why shutil.move() was no longer working?!?
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r9644 | bugman | 2009-10-07 19:32:19 +0200 (Wed, 07 Oct 2009) | 3 lines

Fixed a call to write_spin_data() which should pass in sys.stdout as the file.
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r9645 | bugman | 2009-10-07 19:33:53 +0200 (Wed, 07 Oct 2009) | 3 lines

Prevented __find_bonded_atoms() from connecting protons in the internal PDB reader.
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r9646 | bugman | 2009-10-07 19:46:04 +0200 (Wed, 07 Oct 2009) | 5 lines

Fix for the retrieval of bond vectors for the N-state model.

The object could also be called 'bond_vect' rather than 'xh_vect'.
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r9647 | bugman | 2009-10-07 19:56:59 +0200 (Wed, 07 Oct 2009) | 3 lines

More fixes for the N-state model for the 'xh_vect' and 'bond_vect' mix up.
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r9648 | bugman | 2009-10-07 19:57:27 +0200 (Wed, 07 Oct 2009) | 3 lines

Removed a debugging print statement.
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r9649 | semor | 2009-10-07 20:30:34 +0200 (Wed, 07 Oct 2009) | 7 lines

Modified the sequence.read() entries in order to reflect the new design.

The sequence.read() function now absolutely needs an argument for res_num_col. Hence, this argument
is now shown in the sample script in order to avoid the users lose time figuring out where their
script went bad...
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r9650 | semor | 2009-10-07 20:37:57 +0200 (Wed, 07 Oct 2009) | 8 lines


Modified the relax_data.read() entries in order to reflect the new design.

The relax_data.read() function now absolutely needs arguments for 'res_num_col', 'data_col' and
'error_col'. Hence, this argument is now shown in the sample script in order to avoid the users
lose time figuring out where their script went bad...
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r9651 | bugman | 2009-10-08 09:24:50 +0200 (Thu, 08 Oct 2009) | 8 lines

Significant improvements to the __find_bonded_atoms() method.

The maximum number of bonds an element can have is now taken into account so that protons are not
thought to be attached to 2 carbons within a 2 Angstrom radius! The atoms closest to the atom of
interest are now connected. Geometry constraints or other advanced techniques are not yet
implemented.
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r9652 | bugman | 2009-10-08 09:45:46 +0200 (Thu, 08 Oct 2009) | 3 lines

Modified the message printed by RelaxInvalidSeqError.
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r9653 | bugman | 2009-10-08 09:46:39 +0200 (Thu, 08 Oct 2009) | 3 lines

read_spin_data() now gives a warning rather than an error if the sequence data in a line is bad.
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r9654 | bugman | 2009-10-08 10:01:18 +0200 (Thu, 08 Oct 2009) | 6 lines

Improvements to the read_spin_data() function.

The data checks now occur during the yield loop. This allows for invalid lines to be skipped while
those with real data are used.
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r9655 | bugman | 2009-10-08 10:24:34 +0200 (Thu, 08 Oct 2009) | 6 lines

Bug fix for __find_bonded_atoms().

The loop over the maximum number of connect atoms was failing if the number of 'connected' atoms was
less.
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r9656 | bugman | 2009-10-08 10:49:12 +0200 (Thu, 08 Oct 2009) | 3 lines

Removed some debugging print statements.
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r9657 | bugman | 2009-10-08 12:30:16 +0200 (Thu, 08 Oct 2009) | 3 lines

Created the structure.delete() user function for deleting all structural information from the cdp.
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r9658 | bugman | 2009-10-08 12:42:22 +0200 (Thu, 08 Oct 2009) | 3 lines

Modified the structure.delete() user function to remove all spin specific structural data.
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bugman 2009-10-08

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changed /branches/multi_processor_merge/docs/latex/fetch_docstrings.py
changed /branches/multi_processor_merge/generic_fns/dasha.py
changed /branches/multi_processor_merge/generic_fns/mol_res_spin.py
changed /branches/multi_processor_merge/generic_fns/palmer.py
changed /branches/multi_processor_merge/generic_fns/pcs.py
changed /branches/multi_processor_merge/generic_fns/rdc.py
changed /branches/multi_processor_merge/generic_fns/relax_data.py
changed /branches/multi_processor_merge/generic_fns/selection.py
changed /branches/multi_processor_merge/generic_fns/sequence.py
changed /branches/multi_processor_merge/generic_fns/spectrum.py
changed /branches/multi_processor_merge/generic_fns/structure/api_base.py
changed /branches/multi_processor_merge/generic_fns/structure/internal.py
changed /branches/multi_processor_merge/generic_fns/structure/main.py
changed /branches/multi_processor_merge/generic_fns/value.py
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changed /branches/multi_processor_merge/maths_fns/rotation_matrix.py
changed /branches/multi_processor_merge/prompt/deselect.py
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changed /branches/multi_processor_merge/prompt/rdc.py
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