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[r12582] by bugman

Merged revisions 9274,9442,9445,9455,9661-9695,9697-9699,9701-9703,9705 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

........
r9274 | bugman | 2009-07-22 15:54:49 +0200 (Wed, 22 Jul 2009) | 5 lines

Created the bmrblib.kinetics.general_relaxation module.

Much work is still to be done.
........
r9442 | bugman | 2009-09-03 14:29:19 +0200 (Thu, 03 Sep 2009) | 17 lines

Updates for Python3k.

The command used was:
2to3 -w \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .

This is from the docs/2to3_checklist document. One print statement change in pystarlib/TagTable.py
had to be manually fixed afterwards, as the end arg to the print statement does not exist in all
python 2.x versions.
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r9445 | bugman | 2009-09-03 14:41:00 +0200 (Thu, 03 Sep 2009) | 3 lines

Updated the specific_fns.__all__ list.
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r9455 | bugman | 2009-09-03 15:24:48 +0200 (Thu, 03 Sep 2009) | 19 lines

More updates for Python3k.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .

This is from the docs/2to3_checklist document.
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r9661 | bugman | 2009-10-08 17:44:25 +0200 (Thu, 08 Oct 2009) | 3 lines

Bug fix for the Relaxation_v3_1.__init__() method - incorrect variable name.
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r9662 | bugman | 2009-10-08 17:46:22 +0200 (Thu, 08 Oct 2009) | 3 lines

More variable name bug fixes.
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r9663 | bugman | 2009-10-08 17:48:49 +0200 (Thu, 08 Oct 2009) | 5 lines

Split the Relaxation_v3_1 class into Relaxation_v3_2.

The general relaxation saveframe category is not in v3.1!
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r9664 | bugman | 2009-10-08 17:49:31 +0200 (Thu, 08 Oct 2009) | 3 lines

Fixed the inheritance of Relaxation_v3_2.
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r9665 | bugman | 2009-10-08 17:51:22 +0200 (Thu, 08 Oct 2009) | 3 lines

Fixes for the Relaxation_v3_1 saveframe class. This should set up all the v3.1 relaxation classes.
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r9666 | bugman | 2009-10-08 18:05:53 +0200 (Thu, 08 Oct 2009) | 5 lines

Added better versioning support to be able to switch to NMR-STAR v3.2 in the future.

This will be easier for completing the general relaxation saveframe without breakage.
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r9667 | bugman | 2009-10-08 18:45:55 +0200 (Thu, 08 Oct 2009) | 5 lines

Wrote add() methods for the Relaxation_v3_1 and Relaxation_v3_2 classes.

This defined a stable API abstracting the saveframe structure from the user of bmrblib.
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r9668 | bugman | 2009-10-08 18:47:22 +0200 (Thu, 08 Oct 2009) | 3 lines

Each Relaxation_v3_* class calls the base class __init__() method.
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r9669 | bugman | 2009-10-08 18:50:04 +0200 (Thu, 08 Oct 2009) | 5 lines

Clean up of the relaxation data bmrb_write() method.

The abstracted bmrblib API is now being called for all relaxation data.
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r9670 | bugman | 2009-10-08 18:51:35 +0200 (Thu, 08 Oct 2009) | 3 lines

Fixes for the calls to the base class __init__() methods.
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r9671 | bugman | 2009-10-08 18:52:36 +0200 (Thu, 08 Oct 2009) | 3 lines

Removed the initialisation of the non-existent v3.0 relaxation saveframes.
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r9672 | bugman | 2009-10-08 18:56:37 +0200 (Thu, 08 Oct 2009) | 3 lines

More fixes for the base class __init__() calling, and removed the placement of datanode into self.
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r9673 | bugman | 2009-10-08 18:58:44 +0200 (Thu, 08 Oct 2009) | 3 lines

Removed the NMR-STAR version arg to the data specific bmrb_write() methods.
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r9674 | bugman | 2009-10-08 18:59:44 +0200 (Thu, 08 Oct 2009) | 3 lines

Fixes for the incorrectly named object 'star' (should have been 'self'!)
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r9675 | bugman | 2009-10-08 19:02:25 +0200 (Thu, 08 Oct 2009) | 5 lines

Changes to generic_fns.relax_data.bmrb_read() for an abstracted bmrblib API.

This part of the API doesn't exist yet.
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r9676 | bugman | 2009-10-08 19:04:05 +0200 (Thu, 08 Oct 2009) | 3 lines

Fix for bmrb_read(). The object is called 'star.relaxation', not 'star.relaxation_data'.
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r9677 | bugman | 2009-10-08 19:05:03 +0200 (Thu, 08 Oct 2009) | 3 lines

Removed a useless, now abstracted loop over the relaxation data types from bmrb_read().
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r9678 | bugman | 2009-10-08 19:13:22 +0200 (Thu, 08 Oct 2009) | 5 lines

Wrote the loop() method for the abstracted relaxation data bmrblib API.

This loops over and returns all relaxation data, regardless of saveframe.
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r9679 | bugman | 2009-10-08 19:14:49 +0200 (Thu, 08 Oct 2009) | 3 lines

Added a version 3.2 specific loop() method for the general relaxation saveframe.
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r9680 | bugman | 2009-10-09 12:01:55 +0200 (Fri, 09 Oct 2009) | 3 lines

Added a docstring to tag_setup().
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r9681 | bugman | 2009-10-09 12:11:09 +0200 (Fri, 09 Oct 2009) | 3 lines

The saveframe objects are no longer private. This was causing major bugs!
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r9682 | bugman | 2009-10-09 12:12:16 +0200 (Fri, 09 Oct 2009) | 3 lines

Removed some debugging code.
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r9683 | bugman | 2009-10-09 12:23:47 +0200 (Fri, 09 Oct 2009) | 3 lines

Modified the BMRB system tests to check versions 3.0, 3.1, and 3.2 of the NMR-STAR definition.
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r9684 | bugman | 2009-10-09 12:44:10 +0200 (Fri, 09 Oct 2009) | 3 lines

Removed some debugging code.
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r9685 | bugman | 2009-10-09 12:44:59 +0200 (Fri, 09 Oct 2009) | 3 lines

Redesigned pack_data() to handle sequence generation.
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r9686 | bugman | 2009-10-09 12:50:52 +0200 (Fri, 09 Oct 2009) | 3 lines

Changed the NMR-STAR version number in the script (for stand alone testing).
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r9687 | bugman | 2009-10-09 13:00:28 +0200 (Fri, 09 Oct 2009) | 3 lines

Significant updates to the BMRB user function module, including the addition of the version arg.
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r9688 | bugman | 2009-10-09 13:02:37 +0200 (Fri, 09 Oct 2009) | 3 lines

Modified the BMRB read/write system test to set the NMR-STAR dictionary version.
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r9689 | bugman | 2009-10-09 13:10:03 +0200 (Fri, 09 Oct 2009) | 3 lines

A number of changes to create the infrastructure for v3.0 and lower of the NMR-STAR dictionary format.
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r9690 | bugman | 2009-10-09 13:11:15 +0200 (Fri, 09 Oct 2009) | 5 lines

Bug fix for the non-version specific NMR-STAR dictionary.

The CSA saveframe was incorrectly setup.
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r9691 | bugman | 2009-10-09 13:15:43 +0200 (Fri, 09 Oct 2009) | 3 lines

Added the missing 'ChiSquaredVal' to the tag_names structure for the base class.
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r9692 | bugman | 2009-10-09 13:24:34 +0200 (Fri, 09 Oct 2009) | 5 lines

Introduced the version arg to the bmrb.read() user function.

This is mainly useful for debugging.
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r9693 | bugman | 2009-10-09 13:25:31 +0200 (Fri, 09 Oct 2009) | 5 lines

Modified the BMRB read/write system test to use the bmrb.read() version arg.

Also reverted the default version number to 3.1.
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r9694 | bugman | 2009-10-09 13:29:58 +0200 (Fri, 09 Oct 2009) | 5 lines

Fix for the NMR_STAR_v3_2 class set up.

This should have been using Relaxation_v3_2.
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r9695 | bugman | 2009-10-09 13:39:58 +0200 (Fri, 09 Oct 2009) | 6 lines

Shifted pystarlib into bmrblib.

The pystarlib software is only used by bmrblib. This also prepares for bmrblib to be spun off as
a stand alone project.
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r9697 | bugman | 2009-10-09 15:48:19 +0200 (Fri, 09 Oct 2009) | 3 lines

Added a docstring to tag_setup().
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r9698 | bugman | 2009-10-09 15:49:42 +0200 (Fri, 09 Oct 2009) | 5 lines

Reworked the entire GeneralRelaxation saveframe code.

Now a rudimentary NMR-STAR v3.2 formatted file is able to be produced and read back in.
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r9699 | bugman | 2009-10-09 16:15:00 +0200 (Fri, 09 Oct 2009) | 3 lines

Updated the GeneralRelaxation saveframe to be more in the NMR-STAR v3.1 style.
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r9701 | bugman | 2009-10-09 18:15:15 +0200 (Fri, 09 Oct 2009) | 3 lines

Modified the translate() method to handle not doing anything.
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r9702 | bugman | 2009-10-09 18:32:18 +0200 (Fri, 09 Oct 2009) | 5 lines

The software saveframe is now being created.

This information does not need to be read from the BMRB file.
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r9703 | bugman | 2009-10-09 18:38:35 +0200 (Fri, 09 Oct 2009) | 3 lines

Added the missing Task tag to the Software saveframe.
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r9705 | bugman | 2009-10-09 18:45:26 +0200 (Fri, 09 Oct 2009) | 3 lines

The SVN repository version number is now sent into the Software saveframe.
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2011-02-19 13:52:26 Tree
[r12581] by bugman

Merged revisions 8834-8860,8864-8878,8880-8881,8883-8892,8904-8908,8912-8915,8921-8922,8924,8930,8934,8937-8955,8959-8962,8964-8970,8973,8975 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

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r8834 | bugman | 2009-02-21 23:50:56 +0100 (Sat, 21 Feb 2009) | 7 lines

Started to create the NMR-STAR dictionary object.

The object is in bmrblib.nmr_star_dict and acts as an abstraction layer between pystarlib and the
specific analysis types. It also will translate the NMR-STAR dictionary subset used by relax for
different versions of the definition. The object is far from complete though.
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r8835 | bugman | 2009-02-21 23:57:38 +0100 (Sat, 21 Feb 2009) | 3 lines

Renamed the pystarlib file object to self.data.
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r8836 | bugman | 2009-02-22 00:05:49 +0100 (Sun, 22 Feb 2009) | 3 lines

Fixed the call to pystarlib.File().
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r8837 | bugman | 2009-02-22 00:16:19 +0100 (Sun, 22 Feb 2009) | 3 lines

Small temporary fix for the file writing.
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r8838 | bugman | 2009-02-22 00:36:22 +0100 (Sun, 22 Feb 2009) | 3 lines

Shifted all the pystarlib code for the relaxation data into the NMR-STAR dictionary object.
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r8839 | bugman | 2009-02-22 10:57:59 +0100 (Sun, 22 Feb 2009) | 3 lines

Shifted many tag names into class variables in preparation for inheritance and multi-version support.
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r8840 | bugman | 2009-02-22 11:04:01 +0100 (Sun, 22 Feb 2009) | 3 lines

Created a package for the support of the supergroup 6 collection of saveframes (kinetic data).
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r8841 | bugman | 2009-02-22 11:14:22 +0100 (Sun, 22 Feb 2009) | 3 lines

Shifted the code for the relaxation data into bmrblib.kinetics.heteronucl_T1_relaxation.
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r8842 | bugman | 2009-02-22 13:15:43 +0100 (Sun, 22 Feb 2009) | 6 lines

Split up the T1 saveframe object.

The main object is now called HeteronuclT1Saveframe. The HeteronuclT1List tag category has been
shifted into its own object, and the other tag categories will be created next.
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r8843 | bugman | 2009-02-22 13:25:13 +0100 (Sun, 22 Feb 2009) | 3 lines

Created the HeteronuclT1Experiment tag category object.
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r8844 | bugman | 2009-02-22 13:29:20 +0100 (Sun, 22 Feb 2009) | 3 lines

Created the unused HeteronuclT1Software tag category class.
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r8845 | bugman | 2009-02-22 13:34:08 +0100 (Sun, 22 Feb 2009) | 3 lines

Code simplification by placement of many objects into the saveframe namespace.
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r8846 | bugman | 2009-02-22 13:40:08 +0100 (Sun, 22 Feb 2009) | 5 lines

Further object simplifications.

The __init__() methods have been shifted into the TagCategory base class in bmrblib.tag_category.
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r8847 | bugman | 2009-02-22 13:49:33 +0100 (Sun, 22 Feb 2009) | 3 lines

Created the T1 tag category.
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r8848 | bugman | 2009-02-22 14:00:14 +0100 (Sun, 22 Feb 2009) | 3 lines

Created the heteronucl_NOEs and heteronucl_T2_relaxation saveframes.
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r8849 | bugman | 2009-02-22 14:43:58 +0100 (Sun, 22 Feb 2009) | 3 lines

Shifted the tag name prefix creation code into bmrblib.tag_category.TagCategory.
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r8850 | bugman | 2009-02-22 14:53:45 +0100 (Sun, 22 Feb 2009) | 7 lines

Code rearrangement.

The BMRB read(), write(), and display() methods called by the user functions has been shifted to
generic_fns. This allows bmrblib to be purely a package providing an API for the NMR-STAR
dictionaries, with reading and writing done by pystarlib.
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r8851 | bugman | 2009-02-22 15:05:06 +0100 (Sun, 22 Feb 2009) | 3 lines

Changed some imports in preparation for support for different NMR-STAR versions.
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r8852 | bugman | 2009-02-22 15:31:48 +0100 (Sun, 22 Feb 2009) | 5 lines

Started to implement different NMR-STAR version support.

There are obvious design issues here, preventing this from working!
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r8853 | bugman | 2009-02-22 15:37:57 +0100 (Sun, 22 Feb 2009) | 3 lines

Some class name changes.
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r8854 | bugman | 2009-02-22 16:23:56 +0100 (Sun, 22 Feb 2009) | 5 lines

Redesign for different NMR-STAR dictionary version support.

All class variables have been converted into dictionaries created upon instantiation.
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r8855 | bugman | 2009-02-22 18:56:52 +0100 (Sun, 22 Feb 2009) | 5 lines

Full implementation of v3.1 NMR-STAR support.

T2's are still missing, causing an import error.
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r8856 | bugman | 2009-02-22 18:58:15 +0100 (Sun, 22 Feb 2009) | 3 lines

Added v3.1 support for the T2.
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r8857 | bugman | 2009-02-22 19:31:56 +0100 (Sun, 22 Feb 2009) | 6 lines

Improvements for the relaxation data storage tag categories.

Different NMR-STAR dictionary definitions are supported and the tag names are now located in the
tag name dictionary.
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r8858 | bugman | 2009-02-22 19:44:35 +0100 (Sun, 22 Feb 2009) | 3 lines

Values of 'None' are now translated to the '?' string.
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r8859 | bugman | 2009-02-22 19:47:09 +0100 (Sun, 22 Feb 2009) | 3 lines

Bug fix for the translate function. The old list was being overwritten.
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r8860 | bugman | 2009-02-22 19:48:45 +0100 (Sun, 22 Feb 2009) | 3 lines

The R2 and NOE data is now translated as well.
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r8864 | bugman | 2009-02-22 23:28:23 +0100 (Sun, 22 Feb 2009) | 3 lines

Updated the __all__ list.
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r8865 | bugman | 2009-02-22 23:33:38 +0100 (Sun, 22 Feb 2009) | 3 lines

Added directories for all the NMR-STAR dictionary supergroups.
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r8866 | bugman | 2009-02-22 23:36:40 +0100 (Sun, 22 Feb 2009) | 3 lines

Converted all directories into empty packages of the NMR-STAR dictionary supergroups.
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r8867 | bugman | 2009-02-22 23:43:13 +0100 (Sun, 22 Feb 2009) | 3 lines

Bug fix for the __all__ list.
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r8868 | bugman | 2009-02-22 23:59:13 +0100 (Sun, 22 Feb 2009) | 3 lines

The BMRB NMR-STAR system test now tries to display some of the relaxation data which should be read.
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r8869 | bugman | 2009-02-23 11:52:25 +0100 (Mon, 23 Feb 2009) | 3 lines

Preparation for the entity saveframe category.
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r8870 | bugman | 2009-02-23 14:01:18 +0100 (Mon, 23 Feb 2009) | 3 lines

Preparation for the v3.1 entity saveframe category.
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r8871 | bugman | 2009-02-23 14:10:02 +0100 (Mon, 23 Feb 2009) | 3 lines

Fixed some miss named variables (this has no effect).
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r8872 | bugman | 2009-02-23 19:59:27 +0100 (Mon, 23 Feb 2009) | 3 lines

Converted the entity saveframe code from the heteronuclear NOE code.
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r8873 | bugman | 2009-02-26 14:45:26 +0100 (Thu, 26 Feb 2009) | 3 lines

Added a check for the number of molecules for the entity saveframe generation.
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r8874 | bugman | 2009-02-26 14:50:09 +0100 (Thu, 26 Feb 2009) | 3 lines

Shifted the non-function entity saveframe creation into the generic_fns.mol_res_spin module.
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r8875 | bugman | 2009-02-26 14:57:28 +0100 (Thu, 26 Feb 2009) | 3 lines

The entity saveframe is now enabled in the NMR_STAR object.
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r8876 | bugman | 2009-02-26 14:58:28 +0100 (Thu, 26 Feb 2009) | 3 lines

Bug fix.
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r8877 | bugman | 2009-02-26 15:14:54 +0100 (Thu, 26 Feb 2009) | 3 lines

Bug fix. The data is in self.sf and not in self!
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r8878 | bugman | 2009-02-26 15:21:28 +0100 (Thu, 26 Feb 2009) | 5 lines

Created the get_molecule_names() function.

This new function returns a list of all the molecule names. bmrb_write_entity() now calls this.
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r8880 | bugman | 2009-02-27 14:33:43 +0100 (Fri, 27 Feb 2009) | 3 lines

The molecules are now looped over in preparation for the molecule assembly.
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r8881 | bugman | 2009-02-27 14:35:07 +0100 (Fri, 27 Feb 2009) | 3 lines

Removed the useless ri_inc variable.
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r8883 | bugman | 2009-02-27 15:11:47 +0100 (Fri, 27 Feb 2009) | 7 lines

Added the missing _Heteronuclear_xx_list.ID tags.

This was pointed out by Eldon Ulrich <elu att bmrb dot wisc dot edu> in the post at
https://mail.gna.org/public/relax-devel/2009-02/msg00025.html (Message-id:
<49A78ABD.2050505@...>).
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r8884 | bugman | 2009-02-27 15:16:54 +0100 (Fri, 27 Feb 2009) | 3 lines

The molecule name is now correctly passed in.
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r8885 | bugman | 2009-02-27 15:56:25 +0100 (Fri, 27 Feb 2009) | 3 lines

Removed some remnant args.
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r8886 | bugman | 2009-02-27 16:04:17 +0100 (Fri, 27 Feb 2009) | 3 lines

The _Entity.ID is now created.
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r8887 | bugman | 2009-02-27 17:18:38 +0100 (Fri, 27 Feb 2009) | 3 lines

Created 2 new functions, get_residue_names() and get_residue_nums().
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r8888 | bugman | 2009-02-27 17:20:49 +0100 (Fri, 27 Feb 2009) | 3 lines

The molecule type is now determined.
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r8889 | bugman | 2009-02-27 17:25:54 +0100 (Fri, 27 Feb 2009) | 3 lines

The residue numbers are being stored in self now.
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r8890 | bugman | 2009-02-27 17:28:52 +0100 (Fri, 27 Feb 2009) | 5 lines

Switched from a RelaxError to 'non-polymer' for anything that isn't a polymer.

A RelaxWarning is thrown so the user can check for FUBAR entries.
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r8891 | bugman | 2009-02-27 18:01:58 +0100 (Fri, 27 Feb 2009) | 3 lines

The translate function now converts all list data elements into strings.
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r8892 | bugman | 2009-02-27 18:02:22 +0100 (Fri, 27 Feb 2009) | 3 lines

The EntityCompIndex saveframe is now being created.
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r8904 | bugman | 2009-03-05 10:00:43 +0100 (Thu, 05 Mar 2009) | 3 lines

Shifted the relaxation data saveframe generation code into generic_fns.relax_data.bmrb_write().
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r8905 | bugman | 2009-03-05 11:34:04 +0100 (Thu, 05 Mar 2009) | 3 lines

The data pipe is no longer needed.
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r8906 | bugman | 2009-03-05 11:48:09 +0100 (Thu, 05 Mar 2009) | 3 lines

Added a catch for spins with no relaxation data in bmrb_write().
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r8907 | bugman | 2009-03-05 15:07:18 +0100 (Thu, 05 Mar 2009) | 3 lines

The Entity saveframes are now being read and the sequence info recreated.
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r8908 | bugman | 2009-03-05 16:23:56 +0100 (Thu, 05 Mar 2009) | 6 lines

Simplified the tag name access.

Now the full tag names (category label + sep + tag name) is being generated by TagCategory.__init__()
so that TagCategory.create_tag_label() doesn't need to be called by the specific saveframes.
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r8912 | bugman | 2009-03-06 11:33:35 +0100 (Fri, 06 Mar 2009) | 5 lines

Added checks for the residue names and numbers, and atom names.

They should not be None.
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r8913 | bugman | 2009-03-06 11:40:20 +0100 (Fri, 06 Mar 2009) | 5 lines

Added some checks for None before hitting the bmrblib code.

This gives more informative error messages.
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r8914 | bugman | 2009-03-06 11:51:53 +0100 (Fri, 06 Mar 2009) | 3 lines

Shifted the BMRB reading and writing test into a script and significantly extended it.
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r8915 | bugman | 2009-03-06 13:43:06 +0100 (Fri, 06 Mar 2009) | 3 lines

Bug fix for the tearDown method. The reset was removing the temp file name!
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r8921 | bugman | 2009-03-06 15:42:34 +0100 (Fri, 06 Mar 2009) | 3 lines

Docstring fix.
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r8922 | bugman | 2009-03-06 15:48:36 +0100 (Fri, 06 Mar 2009) | 3 lines

Extraction of R1 data is now supported by the bmrblib API.
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r8924 | bugman | 2009-03-06 19:17:03 +0100 (Fri, 06 Mar 2009) | 3 lines

Start of the reading of relaxation data from the BMRB NMR-STAR files.
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r8930 | bugman | 2009-03-08 22:43:32 +0100 (Sun, 08 Mar 2009) | 3 lines

Added a call to pack_data() from bmrb_read().
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r8934 | bugman | 2009-03-08 23:38:36 +0100 (Sun, 08 Mar 2009) | 3 lines

Simplified the bmrb_read() function.
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r8937 | bugman | 2009-03-08 23:52:24 +0100 (Sun, 08 Mar 2009) | 3 lines

The gen_seq flag of pack_data() is now set in bmrb_read().
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r8938 | bugman | 2009-03-08 23:56:24 +0100 (Sun, 08 Mar 2009) | 5 lines

Bug fix for the T1.read() method.

The values and errors were being set to the residue number!
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r8939 | bugman | 2009-03-09 11:44:59 +0100 (Mon, 09 Mar 2009) | 3 lines

bmrb_read() now tries to read all relaxation data (from R2, R1, and NOE).
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r8940 | bugman | 2009-03-09 13:45:31 +0100 (Mon, 09 Mar 2009) | 5 lines

Shifted all the Rx data reading code into base classes in relax_base.py.

The R1, R2, and NOE now all use this abstracted code.
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r8941 | bugman | 2009-03-09 13:50:40 +0100 (Mon, 09 Mar 2009) | 3 lines

Added the saveframe category for model-free data.
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r8942 | bugman | 2009-03-09 15:10:26 +0100 (Mon, 09 Mar 2009) | 3 lines

The order_parameters saveframes are now created (although are missing all the contents).
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r8943 | bugman | 2009-03-09 19:44:09 +0100 (Mon, 09 Mar 2009) | 3 lines

Support for all model-free parameters has been added to the BMRB library.
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r8944 | bugman | 2009-03-09 19:59:59 +0100 (Mon, 09 Mar 2009) | 3 lines

The model-free data is now being sent to the BMRB API.
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r8945 | bugman | 2009-03-10 10:48:14 +0100 (Tue, 10 Mar 2009) | 5 lines

Bug fix for the residue numbers.

This is CompIndexID and not SeqID!
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r8946 | bugman | 2009-03-10 11:09:26 +0100 (Tue, 10 Mar 2009) | 6 lines

Large code simplification via abstraction.

Most of the code from the create() method of the non-free TagTables has been abstracted away into
the TagCategory.create_tag_table() method.
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r8947 | bugman | 2009-03-10 11:26:10 +0100 (Tue, 10 Mar 2009) | 5 lines

Added the isotope arg to the relaxation data API parts.

The tag_setup() method has been abstracted back into the kinetics.relax_base.Rx base class.
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r8948 | bugman | 2009-03-10 11:35:50 +0100 (Tue, 10 Mar 2009) | 3 lines

relax now dumps the spin isotope number into the Rx BMRB sections.
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r8949 | bugman | 2009-03-10 11:44:56 +0100 (Tue, 10 Mar 2009) | 3 lines

Added the HeteronuclRxListID tag elements. This just corresponds to the self.rx_inc values.
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r8950 | bugman | 2009-03-10 14:17:38 +0100 (Tue, 10 Mar 2009) | 3 lines

Fixed the relaxation saveframe category values to be version specific.
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r8951 | bugman | 2009-03-10 14:19:36 +0100 (Tue, 10 Mar 2009) | 3 lines

Fixed the reading of relaxation data.
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r8952 | bugman | 2009-03-10 14:27:37 +0100 (Tue, 10 Mar 2009) | 3 lines

Made the model-free saveframe category name version specific.
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r8953 | bugman | 2009-03-10 14:45:09 +0100 (Tue, 10 Mar 2009) | 3 lines

Added the ID TagTable for the heteronuclear data (just a basic data counter).
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r8954 | bugman | 2009-03-10 15:15:00 +0100 (Tue, 10 Mar 2009) | 3 lines

Shifted all the data ID code into the new BaseSaveframe base class.
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r8955 | bugman | 2009-03-10 15:19:03 +0100 (Tue, 10 Mar 2009) | 3 lines

Renamed the bmrblib.tag_category module to bmrblib.base_classes.
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r8959 | bugman | 2009-03-10 17:14:31 +0100 (Tue, 10 Mar 2009) | 5 lines

The CSA and bond length data is now collected, and the CSA part of the BMRB API called.

The API call does not yet exist.
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r8960 | bugman | 2009-03-10 17:28:49 +0100 (Tue, 10 Mar 2009) | 3 lines

Docstring fixes. These are not v3.1 files!
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r8961 | bugman | 2009-03-10 19:28:32 +0100 (Tue, 10 Mar 2009) | 3 lines

Created the CSA parts of the BMRB API.
........
r8962 | bugman | 2009-03-10 19:29:06 +0100 (Tue, 10 Mar 2009) | 3 lines

The isotope number is now passed into the CSA part of the BMRB API.
........
r8964 | bugman | 2009-03-11 14:03:55 +0100 (Wed, 11 Mar 2009) | 3 lines

Docstring addition - CSA must be in ppm.
........
r8965 | bugman | 2009-03-11 15:12:01 +0100 (Wed, 11 Mar 2009) | 3 lines

The CSA is now sent in as ppm values.
........
r8966 | bugman | 2009-03-11 15:16:12 +0100 (Wed, 11 Mar 2009) | 3 lines

Docstring and comment removal of 'NOE'.
........
r8967 | bugman | 2009-03-11 15:22:06 +0100 (Wed, 11 Mar 2009) | 3 lines

Added the ID counter for the Order_param saveframe.
........
r8968 | bugman | 2009-03-11 16:53:49 +0100 (Wed, 11 Mar 2009) | 3 lines

Docstring fixes and the addition of the rex_frq arg to add().
........
r8969 | bugman | 2009-03-11 17:54:22 +0100 (Wed, 11 Mar 2009) | 7 lines

Added the new chi-squared tag.

This new tag is described in the document attached to the post
https://mail.gna.org/public/relax-devel/2009-03/msg00019.html (Message-id:
<49B7463E.7080109@...>).
........
r8970 | bugman | 2009-03-11 18:02:08 +0100 (Wed, 11 Mar 2009) | 7 lines

Updated the order_parameters saveframe to match the new NMR-STAR design.

The new design is described in the document attached to the post
https://mail.gna.org/public/relax-devel/2009-03/msg00019.html (Message-id:
<49B7463E.7080109@...>).
........
r8973 | bugman | 2009-03-12 17:25:11 +0100 (Thu, 12 Mar 2009) | 6 lines

Added a new module for abstracting the relaxation data part of the BMRB API.

This should automatically handle the change from heteronucl_NOEs, heteronucl_T1_relaxation, and
heteronucl_T2_relaxation to the general_relaxation saveframe.
........
r8975 | bugman | 2009-03-12 18:55:46 +0100 (Thu, 12 Mar 2009) | 3 lines

Started to implement support for the General_relaxation saveframe category.
........

2011-02-19 13:47:48 Tree
[r12580] by bugman

Merged revisions 8392-8393,8427,8567-8573 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

........
r8392 | bugman | 2009-01-11 19:05:40 +0100 (Sun, 11 Jan 2009) | 5 lines

Started to dump the relaxation data into the BMRB file.

Much work is still required and the spin specific values are still not there.
........
r8393 | bugman | 2009-01-11 19:22:44 +0100 (Sun, 11 Jan 2009) | 3 lines

The spectrometer frequency in the BMRB is now a float.
........
r8427 | bugman | 2009-01-12 22:20:30 +0100 (Mon, 12 Jan 2009) | 3 lines

All relaxation data is now placed in the BMRB STAR formatted file.
........
r8567 | bugman | 2009-01-21 21:02:14 +0100 (Wed, 21 Jan 2009) | 6 lines

Added a directory for the creation of the 'bmrb' package.

This will include translation tables of the various BMRB NMR-STAR format version, and many BMRB
format related functions.
........
r8568 | bugman | 2009-01-21 21:03:14 +0100 (Wed, 21 Jan 2009) | 3 lines

Converted generic_fns.bmrb into the bmrb package initialisation module.
........
r8569 | bugman | 2009-01-21 21:03:42 +0100 (Wed, 21 Jan 2009) | 3 lines

Copyright update.
........
r8570 | bugman | 2009-01-21 21:04:50 +0100 (Wed, 21 Jan 2009) | 3 lines

Updated the module docstring and added an empty __all__ list.
........
r8571 | bugman | 2009-01-21 21:06:37 +0100 (Wed, 21 Jan 2009) | 3 lines

Import fix and copyright update.
........
r8572 | bugman | 2009-01-21 21:17:17 +0100 (Wed, 21 Jan 2009) | 5 lines

Renamed the bmrb package to bmrblib.

This is to avoid any future (and current) name clashes.
........
r8573 | bugman | 2009-01-21 21:18:35 +0100 (Wed, 21 Jan 2009) | 3 lines

Updates for the renaming to bmrblib.
........

2011-02-19 13:41:53 Tree
[r12579] by bugman

Merged revisions 8153,8369-8388 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

........
r8153 | bugman | 2008-12-05 20:44:46 +0100 (Fri, 05 Dec 2008) | 3 lines

Import fix!
........
r8369 | bugman | 2009-01-11 10:52:13 +0100 (Sun, 11 Jan 2009) | 11 lines

Added a directory for packaging the pystarlib STAR format reader/writer library with relax.

The pystarlib project by Jurgen F. Doreleijers (jurgenfd att gmail dot com) is located at
http://code.google.com/p/pystarlib/.

This packaging with relax is temporary until relax can fully use the library to read and write STAR
files containing relaxation analysis results (model-free for now) for submission to the BMRB. The
pystarlib library also needs to be packaged with distutils for easy installation, prior to
reseparation.
........
r8370 | bugman | 2009-01-11 10:55:33 +0100 (Sun, 11 Jan 2009) | 6 lines

Added all the pystarlib code.

The original SVN repository path for this code is http://pystarlib.googlecode.com/svn/trunk/src/STAR
and the code was copied at r15.
........
r8371 | bugman | 2009-01-11 12:20:07 +0100 (Sun, 11 Jan 2009) | 3 lines

Created a system test for the writing and reading of a BRMB STAR formatted file.
........
r8372 | bugman | 2009-01-11 12:26:41 +0100 (Sun, 11 Jan 2009) | 3 lines

A few fixes for the BMRB system test.
........
r8373 | bugman | 2009-01-11 13:50:12 +0100 (Sun, 11 Jan 2009) | 3 lines

Added a missing import.
........
r8374 | bugman | 2009-01-11 13:54:24 +0100 (Sun, 11 Jan 2009) | 3 lines

Some more missing imports.
........
r8375 | bugman | 2009-01-11 13:57:26 +0100 (Sun, 11 Jan 2009) | 3 lines

A RelaxError is now raised if the specific_fns BMRB methods do not exist.
........
r8376 | bugman | 2009-01-11 14:01:28 +0100 (Sun, 11 Jan 2009) | 3 lines

Added a stub bmrb_write() model-free method.
........
r8377 | bugman | 2009-01-11 14:03:58 +0100 (Sun, 11 Jan 2009) | 3 lines

The bmrb_write() method is now in the model-free specific object.
........
r8378 | bugman | 2009-01-11 14:05:52 +0100 (Sun, 11 Jan 2009) | 3 lines

Activated the specific bmrb_write() methods.
........
r8379 | bugman | 2009-01-11 14:06:26 +0100 (Sun, 11 Jan 2009) | 3 lines

Activated the specific bmrb_read() methods.
........
r8380 | bugman | 2009-01-11 15:46:03 +0100 (Sun, 11 Jan 2009) | 5 lines

Import fixes for pystarlib, as they were all screwed up.

This allows the unit test framework to function and allows importing of the code into relax.
........
r8381 | bugman | 2009-01-11 15:57:41 +0100 (Sun, 11 Jan 2009) | 5 lines

Removed the BMRB STAR file compression abilities from the user functions.

The pystarlib does not support this.
........
r8382 | bugman | 2009-01-11 16:28:13 +0100 (Sun, 11 Jan 2009) | 5 lines

Redesigned the generic BMRB write() function for the pystarlib.File.File class object.

The open_write_file() function should not be used as pystarlib already creates the file.
........
r8383 | bugman | 2009-01-11 16:30:33 +0100 (Sun, 11 Jan 2009) | 3 lines

Added a printout for the write() function.
........
r8384 | bugman | 2009-01-11 16:41:13 +0100 (Sun, 11 Jan 2009) | 5 lines

The pystarlib File object is now initialised and the write() method called.

This produces a relatively empty file.
........
r8385 | bugman | 2009-01-11 17:17:49 +0100 (Sun, 11 Jan 2009) | 5 lines

Fix for the test_rw_bmrb_model_free() system test.

The dir name was being set to the data pipe name!
........
r8386 | bugman | 2009-01-11 17:27:34 +0100 (Sun, 11 Jan 2009) | 3 lines

Fixes for the read() function.
........
r8387 | bugman | 2009-01-11 17:29:45 +0100 (Sun, 11 Jan 2009) | 3 lines

Fix for the write() function. The directory for placing the file into is now created.
........
r8388 | bugman | 2009-01-11 17:33:47 +0100 (Sun, 11 Jan 2009) | 6 lines

Wrote a basic model-free bmrb_read() method.

This simply parses the STAR formatted file, but does not yet put the contents into the relax data
store.
........

2011-02-19 13:39:23 Tree
[r12578] by bugman

Merged revisions 7043-7044,7046 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb

........
r7043 | bugman | 2008-07-31 11:29:45 +0200 (Thu, 31 Jul 2008) | 8 lines

Initial support for the bmrb user functions.

The following BNMRB related user functions now exist (the back end does not yet exist):
bmrb.display()
bmrb.read()
bmrb.write()
........
r7044 | bugman | 2008-07-31 11:36:29 +0200 (Thu, 31 Jul 2008) | 3 lines

Activated the bmrb user functions.
........
r7046 | bugman | 2008-07-31 11:52:39 +0200 (Thu, 31 Jul 2008) | 6 lines

Added some basic BMRB file format displaying/reading/writing functions.

The STAR format parser and model-free specific code needs to be implemented before this code will
work.
........

2011-02-19 13:36:23 Tree
[r12577] by bugman

Initialized merge tracking via "svnmerge" with revisions "1-7041" from
svn+ssh://bugman@.../svn/relax/branches/bmrb

2011-02-18 17:59:57 Tree
[r12576] by bugman

Fix for the PDC system tests - the generic_fns.relax_data.pack_data() args are different in the branch.

2011-02-18 17:29:53 Tree
[r12575] by bugman

Merged revisions 12423-12429,12431-12448,12450,12453,12460,12517-12520,12550-12552,12554-12563,12566 via svnmerge from
svn+ssh://bugman@.../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@.../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@...>,
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.
................
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@.../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@.../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@...>).
........
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.
........
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.
........
r12540 | bugman | 2011-02-17 17:00:44 +0100 (Thu, 17 Feb 2011) | 3 lines

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

Typo fix for the PDC reading system test.
........
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.
........
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.
........
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.
........
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.
........
................
r12552 | bugman | 2011-02-18 11:35:40 +0100 (Fri, 18 Feb 2011) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/bruker_import
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
r12561 | bugman | 2011-02-18 14:49:43 +0100 (Fri, 18 Feb 2011) | 3 lines

Fix for the NOE PDC data conversion script.
................
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.
................
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@.../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).
.....
................

2011-02-18 16:53:37 Tree
[r12574] by bugman

Merged revisions 12423-12429,12431-12448,12450,12453,12460,12517-12520,12550-12552,12554-12563,12566 via svnmerge from
svn+ssh://bugman@.../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@.../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@...>,
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.
................
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@.../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@.../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@...>).
........
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.
........
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.
........
r12540 | bugman | 2011-02-17 17:00:44 +0100 (Thu, 17 Feb 2011) | 3 lines

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

Typo fix for the PDC reading system test.
........
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.
........
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.
........
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.
........
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.
........
................
r12552 | bugman | 2011-02-18 11:35:40 +0100 (Fri, 18 Feb 2011) | 3 lines

Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/bruker_import
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
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.
................
r12561 | bugman | 2011-02-18 14:49:43 +0100 (Fri, 18 Feb 2011) | 3 lines

Fix for the NOE PDC data conversion script.
................
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.
................
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@.../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).
.....
................

2011-02-18 16:51:38 Tree
[r12573] by bugman

Merged revisions 12423-12429,12431-12448,12450,12453,12460,12517-12520,12550-12552,12554-12563,12566 via svnmerge from
svn+ssh://bugman@.../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@.../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@...>,
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.
................
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@.../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@.../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@...>).
........
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.
........
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.
........
r12540 | bugman | 2011-02-17 17:00:44 +0100 (Thu, 17 Feb 2011) | 3 lines

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

Typo fix for the PDC reading system test.
........
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.
........
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.
........
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.
........
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@.../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.
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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@.../svn/relax/tags/1.3.10

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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).
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2011-02-18 16:51:29 Tree
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