relax SVN archive

Removal of the bruker_import branch for reading the Bruker Protein Dynamics Centre (PDC) file.

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/bruker_import

Merged revisions 11636-11637,12535-12547,12549 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bruker_import

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r11636 | michaelbieri | 2010-10-11 00:25:46 +0200 (Mon, 11 Oct 2010) | 2 lines

Example outputfiles of BRUKER Protein Dynamic Center (PDC) were added.
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r11637 | michaelbieri | 2010-10-11 03:42:10 +0200 (Mon, 11 Oct 2010) | 4 lines

Function to import BRUKER Protein Dynamic Center project is added.

The import will be converted to a relax formatted parameter file, either as a dummy file or saved at a specified location.
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r12535 | bugman | 2011-02-17 16:14:49 +0100 (Thu, 17 Feb 2011) | 7 lines

Updated the PDC R1 data file to version 1.1.5.

This file was sent by Klaus-Peter Neidig <peter dot neidig att bruker-biospin dot de> in the message
https://mail.gna.org/public/relax-devel/2011-01/msg00043.html (Message-id:
<4D3ED3AC.20107@...>).
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r12536 | bugman | 2011-02-17 16:22:15 +0100 (Thu, 17 Feb 2011) | 3 lines

Created the prompt/script interface to the pdc.read() user function.
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r12537 | bugman | 2011-02-17 16:25:56 +0100 (Thu, 17 Feb 2011) | 3 lines

Create a stub of a back-end for the pdc.read() user function.
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r12538 | bugman | 2011-02-17 16:42:14 +0100 (Thu, 17 Feb 2011) | 3 lines

Added a sequence file for the data in these test PDC files.
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r12539 | bugman | 2011-02-17 16:59:31 +0100 (Thu, 17 Feb 2011) | 3 lines

Added a basic system test for the loading of a PDC file.
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r12540 | bugman | 2011-02-17 17:00:44 +0100 (Thu, 17 Feb 2011) | 3 lines

Added some missing imports.
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r12541 | bugman | 2011-02-17 17:01:25 +0100 (Thu, 17 Feb 2011) | 3 lines

Typo fix for the PDC reading system test.
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r12542 | bugman | 2011-02-17 17:30:24 +0100 (Thu, 17 Feb 2011) | 3 lines

Implemented the reading of relaxation data from the PDC file.
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r12543 | bugman | 2011-02-17 17:31:45 +0100 (Thu, 17 Feb 2011) | 3 lines

The PDC system test has been loosened - the precision is not perfect.
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r12544 | bugman | 2011-02-17 17:34:53 +0100 (Thu, 17 Feb 2011) | 3 lines

Added some checks for the current data pipe relaxation data structures to the PDC reading system test.
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r12545 | bugman | 2011-02-18 10:23:00 +0100 (Fri, 18 Feb 2011) | 3 lines

The temperature from the PDC file is now being read, although it isn't used yet.
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r12546 | bugman | 2011-02-18 10:23:37 +0100 (Fri, 18 Feb 2011) | 3 lines

The 'Labelling' line from the PDC file is now used to set the heteronucleus type and spin name.
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r12547 | bugman | 2011-02-18 10:41:25 +0100 (Fri, 18 Feb 2011) | 5 lines

Implemented the code for reading the peak intensity type.

This is not active yet as it can only be used in the BMRB branch.
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r12549 | bugman | 2011-02-18 11:25:45 +0100 (Fri, 18 Feb 2011) | 5 lines

Fix for the integration method block in the pdc.read() back end.

The commented out code requires at least some code in the block.
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Initialized merge tracking via "svnmerge" with revisions "1-11635" from
svn+ssh://bugman@.../svn/relax/branches/bruker_import

Fix for the integration method block in the pdc.read() back end.

The commented out code requires at least some code in the block.

Merged revisions 12423-12429,12431-12448,12450,12453,12460,12517-12520 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r12423 | bugman | 2011-01-21 18:53:04 +0100 (Fri, 21 Jan 2011) | 3 lines

*.old files are now removed by the HTML user manual cleaning script.
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r12424 | bugman | 2011-01-21 18:54:25 +0100 (Fri, 21 Jan 2011) | 6 lines

The relax website http://nmr-relax.com is now referenced in the HTML version of the user manual.

A new button in the navigation bar has been added for this. See
http://www.nmr-relax.com/manual/1.3/relax.html (once the new 1.3.9 version of relax is released).
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r12425 | bugman | 2011-01-21 18:55:09 +0100 (Fri, 21 Jan 2011) | 6 lines

Big improvements to the HTML user manual generation.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html once relax version 1.3.9 is
released.
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r12426 | bugman | 2011-01-22 17:59:44 +0100 (Sat, 22 Jan 2011) | 3 lines

The HTML user manual cleaning script now removes all *.css files.
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r12427 | bugman | 2011-01-22 21:12:14 +0100 (Sat, 22 Jan 2011) | 3 lines

Created an init file for latex2html so that the figures not in this directory are included.
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r12428 | bugman | 2011-01-22 21:47:08 +0100 (Sat, 22 Jan 2011) | 3 lines

Added custom icons for the HTML user manual navigation bar.
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r12429 | bugman | 2011-01-22 21:47:48 +0100 (Sat, 22 Jan 2011) | 3 lines

Added the relax title and custom icon path to the latex2html config file.
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r12431 | bugman | 2011-01-22 21:55:44 +0100 (Sat, 22 Jan 2011) | 3 lines

The grey icons are now properly named.
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r12432 | bugman | 2011-01-22 22:15:37 +0100 (Sat, 22 Jan 2011) | 5 lines

Fixes for the navigation icons sizes in the HTML user manual.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html.
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r12433 | bugman | 2011-01-22 22:17:10 +0100 (Sat, 22 Jan 2011) | 5 lines

Increased the splitting level by one.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12434 | bugman | 2011-01-22 22:19:51 +0100 (Sat, 22 Jan 2011) | 7 lines

The PDF version of the user manual is being partly compiled before the HTML version.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.

The aim is to have the aux and bbl files made so latex2html can use them.
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r12435 | bugman | 2011-01-22 22:20:22 +0100 (Sat, 22 Jan 2011) | 3 lines

Created the dir var for storing the target directory.
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r12436 | bugman | 2011-01-22 22:21:07 +0100 (Sat, 22 Jan 2011) | 5 lines

Removed the -no-math option to hopefully decrease the number of images in the HTML user manual.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12437 | bugman | 2011-01-22 22:40:31 +0100 (Sat, 22 Jan 2011) | 5 lines

Improved the quality of the maths equation images in the HTML user manual.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12438 | bugman | 2011-01-22 22:56:16 +0100 (Sat, 22 Jan 2011) | 5 lines

Added footnote and crossref icons to the HTML user manual.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12439 | bugman | 2011-01-22 23:11:18 +0100 (Sat, 22 Jan 2011) | 5 lines

Set the font size to 12pt in the HTML user manual.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12440 | bugman | 2011-01-22 23:12:08 +0100 (Sat, 22 Jan 2011) | 5 lines

The sections numbers from the PDF manual are now shown.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12441 | bugman | 2011-01-24 16:34:34 +0100 (Mon, 24 Jan 2011) | 7 lines

Removed http://nmr-relax.com from the bottom of all the HTML user manual pages.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.

http://nmr-relax.com is redundant due to all the http://nmr-relax.com links in the navigation bar.
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r12442 | bugman | 2011-01-24 16:37:45 +0100 (Mon, 24 Jan 2011) | 5 lines

Shifted the -local_icons commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12443 | bugman | 2011-01-24 16:39:12 +0100 (Mon, 24 Jan 2011) | 5 lines

Shifted the -html_version commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12444 | bugman | 2011-01-24 16:41:33 +0100 (Mon, 24 Jan 2011) | 5 lines

hifted the -split commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12445 | bugman | 2011-01-24 16:42:55 +0100 (Mon, 24 Jan 2011) | 5 lines

Shifted the -auto_navigation commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12446 | bugman | 2011-01-24 16:44:41 +0100 (Mon, 24 Jan 2011) | 5 lines

Shifted the -external_file commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12447 | bugman | 2011-01-24 16:46:00 +0100 (Mon, 24 Jan 2011) | 5 lines

Shifted the -antialias commmand line arg into the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12448 | bugman | 2011-01-24 16:46:50 +0100 (Mon, 24 Jan 2011) | 5 lines

The antialiasing is now actually in the latex2html init file.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.
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r12450 | bugman | 2011-01-25 09:30:32 +0100 (Tue, 25 Jan 2011) | 7 lines

Forced titles into the navigation bar images in the HTML user manual by tricking latex2html.

This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release.

The titles were added to the image size strings.
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r12453 | bugman | 2011-01-26 21:01:43 +0100 (Wed, 26 Jan 2011) | 14 lines

Merged the changes to the CHANGES file from the 1.3.9 tag.

The command used was:
svn merge -r12451:12452 svn+ssh://bugman@.../svn/relax/tags/1.3.9

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r12452 | bugman | 2011-01-26 20:59:51 +0100 (Wed, 26 Jan 2011) | 3 lines
Changed paths:
M /tags/1.3.9/docs/CHANGES

Updated the CHANGES file for relax version 1.3.9 (see http://www.nmr-relax.com/download.html).
.....
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r12460 | bugman | 2011-01-28 18:47:24 +0100 (Fri, 28 Jan 2011) | 7 lines

Fixes for 2 model-free system tests for a new system which again shows optimisation differences :S

The results are from Tiago Pais <tpais att itqb dott unl dott pt> (Message-id:
<BA08C06336CE4466990EBAFB59D7DFCF@...>,
https://mail.gna.org/public/relax-users/2011-01/msg00029.html.
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r12517 | bugman | 2011-02-07 19:00:09 +0100 (Mon, 07 Feb 2011) | 5 lines

Fix for the N-state model error returning method for when errors are not present.

The spin_id variable was not defined.
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r12518 | bugman | 2011-02-07 19:07:19 +0100 (Mon, 07 Feb 2011) | 3 lines

Fix for the calls to RelaxError in the N-state model return_error() method.
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r12519 | bugman | 2011-02-09 13:20:35 +0100 (Wed, 09 Feb 2011) | 3 lines

Added checks showing that Monte Carlo simulations in the N-state model modify the Q factors.
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r12520 | bugman | 2011-02-09 13:23:19 +0100 (Wed, 09 Feb 2011) | 7 lines

The optimisation of Monte Carlo simulations no longer changes the Q factors and back calculated data.

There was a bug in which the back calculated RDCs and PCSs, as well as the Q factors were being
calculated for each Monte Carlo simulation but stored in the non-MC sim data structures. Therefore
after MC sims, the Q factor and back calculated data would be that of the last simulation!!!
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Implemented the code for reading the peak intensity type.

This is not active yet as it can only be used in the BMRB branch.

The 'Labelling' line from the PDC file is now used to set the heteronucleus type and spin name.

The temperature from the PDC file is now being read, although it isn't used yet.

Added some checks for the current data pipe relaxation data structures to the PDC reading system test.