Author: bugman
Date: Fri Feb 18 17:53:37 2011
New Revision: 12575
URL: http://svn.gna.org/viewcvs/relax?rev=12575&view=rev
Log:
Merged revisions
12423-12429,12431-12448,12450,12453,12460,12517-12520,12550-12552,12554-12563,12566
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
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.
................
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).
................
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.
................
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.
................
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.
................
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.
................
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.
................
r12431 | bugman | 2011-01-22 21:55:44 +0100 (Sat, 22 Jan 2011) | 3 lines
The grey icons are now properly named.
................
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.
................
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.
................
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.
................
r12435 | bugman | 2011-01-22 22:20:22 +0100 (Sat, 22 Jan 2011) | 3 lines
Created the dir var for storing the target directory.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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@xxxxxxxxxxx/svn/relax/tags/1.3.9
.....
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).
.....
................
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@Mercurio>,
https://mail.gna.org/public/relax-users/2011-01/msg00029.html.
................
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.
................
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.
................
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!!!
................
r12550 | bugman | 2011-02-18 11:31:46 +0100 (Fri, 18 Feb 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-11635" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import
................
r12551 | bugman | 2011-02-18 11:33:18 +0100 (Fri, 18 Feb 2011) | 79 lines
Merged revisions 11636-11637,12535-12547,12549 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import
........
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.
........
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.
........
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@xxxxxxxxxxxxxxxxx>).
........
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.
........
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.
........
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.
........
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.
........
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.
........
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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r12552 | bugman | 2011-02-18 11:35:40 +0100 (Fri, 18 Feb 2011) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import
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r12554 | bugman | 2011-02-18 12:41:55 +0100 (Fri, 18 Feb 2011) | 3 lines
Added some data files and scripts for checking the consistency of the PDC
data verse relax's data.
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r12555 | bugman | 2011-02-18 12:45:09 +0100 (Fri, 18 Feb 2011) | 3 lines
Some cosmetic changes to the PDC data conversion test script.
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r12556 | bugman | 2011-02-18 14:20:06 +0100 (Fri, 18 Feb 2011) | 3 lines
Added a relax script and R1 data file for relax's optimisation and MC sims
using the PDC file errors.
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r12557 | bugman | 2011-02-18 14:24:01 +0100 (Fri, 18 Feb 2011) | 3 lines
Created the peak height error file errors_R1.txt from testT1.txt.
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r12558 | bugman | 2011-02-18 14:24:52 +0100 (Fri, 18 Feb 2011) | 3 lines
Added residue name and number info to the print out of the convert_data.py
PDC file script.
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r12559 | bugman | 2011-02-18 14:32:10 +0100 (Fri, 18 Feb 2011) | 3 lines
Added a script for converting the PDC NOE data into Python lists.
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r12560 | bugman | 2011-02-18 14:37:50 +0100 (Fri, 18 Feb 2011) | 3 lines
Added a system test for the reading of a PDC NOE file.
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r12561 | bugman | 2011-02-18 14:49:43 +0100 (Fri, 18 Feb 2011) | 3 lines
Fix for the NOE PDC data conversion script.
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r12562 | bugman | 2011-02-18 14:50:37 +0100 (Fri, 18 Feb 2011) | 5 lines
Fix for the test_pdc_read_noe() PDC file reading system test.
The NOE values were actually the errors.
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r12563 | bugman | 2011-02-18 14:51:49 +0100 (Fri, 18 Feb 2011) | 3 lines
Some fixes for the pdc.read() back end so that PDC NOE data files can be
read properly.
................
r12566 | bugman | 2011-02-18 15:19:21 +0100 (Fri, 18 Feb 2011) | 13 lines
Merged the changes to the CHANGES file from the 1.3.10 tag.
The command used was:
svn merge -r12564:12565 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.10
.....
r12565 | bugman | 2011-02-18 15:18:06 +0100 (Fri, 18 Feb 2011) | 3 lines
Changed paths:
M /tags/1.3.10/docs/CHANGES
Updated the CHANGES file for relax version 1.3.10 (see
http://www.nmr-relax.com/download.html).
.....
................
Added:
branches/bmrb/docs/html/icons/
- copied from r12566, 1.3/docs/html/icons/
branches/bmrb/docs/latex/.latex2html-init
- copied unchanged from r12566, 1.3/docs/latex/.latex2html-init
branches/bmrb/generic_fns/pdc.py
- copied unchanged from r12566, 1.3/generic_fns/pdc.py
branches/bmrb/prompt/pdc.py
- copied unchanged from r12566, 1.3/prompt/pdc.py
branches/bmrb/test_suite/shared_data/pdc_files/
- copied from r12566, 1.3/test_suite/shared_data/pdc_files/
branches/bmrb/test_suite/system_tests/pdc.py
- copied unchanged from r12566, 1.3/test_suite/system_tests/pdc.py
Modified:
branches/bmrb/ (props changed)
branches/bmrb/docs/CHANGES
branches/bmrb/docs/html/clean
branches/bmrb/docs/latex/relax.tex
branches/bmrb/generic_fns/__init__.py
branches/bmrb/generic_fns/spectrum.py
branches/bmrb/prompt/__init__.py
branches/bmrb/prompt/interpreter.py
branches/bmrb/scons/manuals.py
branches/bmrb/specific_fns/n_state_model.py
branches/bmrb/test_suite/system_tests/__init__.py
branches/bmrb/test_suite/system_tests/model_free.py
branches/bmrb/test_suite/system_tests/n_state_model.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/CHANGES?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/docs/html/clean
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/html/clean?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/latex/relax.tex?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/__init__.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/spectrum.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/__init__.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/interpreter.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/scons/manuals.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/n_state_model.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/__init__.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/model_free.py?rev=12575&r1=12574&r2=12575&view=diff
Modified: branches/bmrb/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/n_state_model.py?rev=12575&r1=12574&r2=12575&view=diff
r12575 - in /branches/bmrb: ./ docs/ docs/html/ docs/html/icons/ docs/latex/ generic_fns/ prompt/ scons/ specific_fns/ test_...