[r12583]
by
bugman
Merged revisions 9708,9710-9746,9748-9792 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/bmrb
........
r9708 | bugman | 2009-10-09 18:49:25 +0200 (Fri, 09 Oct 2009) | 3 lines
The SVN repository URL is now sent into the Software saveframe.
........
r9710 | bugman | 2009-10-09 20:22:55 +0200 (Fri, 09 Oct 2009) | 3 lines
The program state is now being saved in the BMRB system test.
........
r9711 | bugman | 2009-10-09 20:24:11 +0200 (Fri, 09 Oct 2009) | 5 lines
Created a data container for storing experimental details.
This will be used extensively for the BMRB file generation.
........
r9712 | bugman | 2009-10-09 20:25:00 +0200 (Fri, 09 Oct 2009) | 5 lines
Created the user function bmrb.software_select().
This currently doesn't do anything.
........
r9713 | bugman | 2009-10-09 20:41:30 +0200 (Fri, 09 Oct 2009) | 5 lines
Created the ContainerList base class object.
This is just a generic list type with XML methods, used to hold basic elements.
........
r9714 | bugman | 2009-10-09 20:46:25 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the system test to force save the program state.
........
r9715 | bugman | 2009-10-09 20:52:52 +0200 (Fri, 09 Oct 2009) | 3 lines
The bmrb.software_select() user function is now more functional.
........
r9716 | bugman | 2009-10-09 21:19:02 +0200 (Fri, 09 Oct 2009) | 3 lines
Expanded the experimental information data container to include all the software info.
........
r9717 | bugman | 2009-10-09 21:20:49 +0200 (Fri, 09 Oct 2009) | 6 lines
Many fixes to the Element and ContainerList to_xml() methods.
The objects within these are now properly converted to XML with the to_xml() method beign called
if it exists.
........
r9718 | bugman | 2009-10-09 21:39:14 +0200 (Fri, 09 Oct 2009) | 3 lines
More info is now being placed into the software containers of the experimental info container.
........
r9719 | bugman | 2009-10-09 21:44:46 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the software task to the software containers.
........
r9720 | bugman | 2009-10-11 15:29:05 +0200 (Sun, 11 Oct 2009) | 3 lines
Updated the __all__ package lists.
........
r9721 | bugman | 2009-10-11 15:41:56 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the bmrb.software() user function for manually specifying the software used.
........
r9722 | bugman | 2009-10-11 15:59:38 +0200 (Sun, 11 Oct 2009) | 3 lines
Shifted the software() and software_select() functions into their own module, 'generic_fns.exp_info'.
........
r9723 | bugman | 2009-10-11 16:04:48 +0200 (Sun, 11 Oct 2009) | 3 lines
Removed the kludgy bmrb_saveframes module and shifted the code into exp_info.
........
r9724 | bugman | 2009-10-11 16:07:31 +0200 (Sun, 11 Oct 2009) | 3 lines
Import fix from the previous module deletion.
........
r9725 | bugman | 2009-10-11 16:35:55 +0200 (Sun, 11 Oct 2009) | 3 lines
All attributes (even those of None) are being stored.
........
r9726 | bugman | 2009-10-11 16:39:43 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the bmrb_write_software() function for dumping the software info into the BMRB file.
........
r9727 | bugman | 2009-10-11 16:59:52 +0200 (Sun, 11 Oct 2009) | 5 lines
TagTable.create_tag_table() now handles single element data.
This allows the single element data to be submitted simultaneously with list data.
........
r9728 | bugman | 2009-10-11 17:05:37 +0200 (Sun, 11 Oct 2009) | 5 lines
Non-list data can now be used by TagTable.create_tag_table().
The method converts to lists on the fly.
........
r9729 | bugman | 2009-10-11 17:06:25 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the software add() method.
........
r9730 | bugman | 2009-10-11 17:14:09 +0200 (Sun, 11 Oct 2009) | 5 lines
Created version.version_full() from the code in generic_fns.exp_info.
The get_revision() and get_url() functions have had the 'get_' part removed.
........
r9731 | bugman | 2009-10-11 17:23:37 +0200 (Sun, 11 Oct 2009) | 3 lines
Shifted the program info into module variables.
........
r9732 | bugman | 2009-10-11 17:26:10 +0200 (Sun, 11 Oct 2009) | 3 lines
Added relax to the BMRB file.
........
r9733 | bugman | 2009-10-11 17:27:43 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the version_full() function due to 'url = url()'!!
........
r9734 | bugman | 2009-10-11 18:45:46 +0200 (Sun, 11 Oct 2009) | 3 lines
Modified bmrb_write_software() to handle if no other software packages are specified.
........
r9735 | bugman | 2009-10-11 18:47:08 +0200 (Sun, 11 Oct 2009) | 3 lines
Changed the default version to 3.2 in the stand alone operation of the BMRB system test.
........
r9736 | bugman | 2009-10-11 18:51:55 +0200 (Sun, 11 Oct 2009) | 3 lines
bmrb_write_software() now throws a RelaxError if no software has been specified.
........
r9737 | bugman | 2009-10-11 19:31:19 +0200 (Sun, 11 Oct 2009) | 3 lines
The element (or atom type) info is being sent into bmrblib.
........
r9738 | bugman | 2009-10-11 19:40:06 +0200 (Sun, 11 Oct 2009) | 3 lines
The element type is now being recorded in the CSA and model-free saveframes.
........
r9739 | bugman | 2009-10-11 19:42:51 +0200 (Sun, 11 Oct 2009) | 3 lines
Fixes for the bmrb_write() method for the new element storage.
........
r9740 | bugman | 2009-10-11 19:58:14 +0200 (Sun, 11 Oct 2009) | 5 lines
Added a call to the non-existent bmrb.citation() user function.
This will be used to design the UI.
........
r9741 | bugman | 2009-10-11 20:06:57 +0200 (Sun, 11 Oct 2009) | 3 lines
Removed the web address part of the DOI number.
........
r9742 | bugman | 2009-10-11 22:50:14 +0200 (Sun, 11 Oct 2009) | 3 lines
Created the add_citation() method for adding citations to the experimental info container.
........
r9743 | bugman | 2009-10-11 22:53:10 +0200 (Sun, 11 Oct 2009) | 3 lines
Simplified the software container setup by absorbing Software and SoftwareList into software_setup().
........
r9744 | bugman | 2009-10-12 00:30:47 +0200 (Mon, 12 Oct 2009) | 3 lines
Created the bmrb.citation() user function.
........
r9745 | bugman | 2009-10-12 00:40:00 +0200 (Mon, 12 Oct 2009) | 3 lines
A number of fixes for the XML storage of the experimental info container.
........
r9746 | bugman | 2009-10-12 11:56:41 +0200 (Mon, 12 Oct 2009) | 3 lines
Fixes for the generic_fns package __all__ list.
........
r9748 | bugman | 2009-10-13 14:11:27 +0200 (Tue, 13 Oct 2009) | 6 lines
Large renamings of the Order_parameters saveframe to Model_free.
The modules still need to be renamed. Everything will be called model_free unless v3.1 or earlier
saveframes are created, then order_parameters will be used.
........
r9749 | bugman | 2009-10-13 14:12:11 +0200 (Tue, 13 Oct 2009) | 3 lines
Renamed the modules from order_parameters* to model_free*.
........
r9750 | bugman | 2009-10-13 14:22:31 +0200 (Tue, 13 Oct 2009) | 3 lines
Set up the NMR-STAR v3.2 model_free saveframe.
........
r9751 | bugman | 2009-10-13 14:32:31 +0200 (Tue, 13 Oct 2009) | 3 lines
The v3.2 model_free saveframe is now correctly created.
........
r9752 | bugman | 2009-10-13 14:35:29 +0200 (Tue, 13 Oct 2009) | 5 lines
Fix for the v3.1 order_parameters saveframe.
SfCategory was set to "model_free", not "order_parameters".
........
r9753 | bugman | 2009-10-13 16:35:05 +0200 (Tue, 13 Oct 2009) | 3 lines
Comment fixes.
........
r9754 | bugman | 2009-10-13 17:21:42 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified translate() so that only strings or lists of strings can ever be returned!
........
r9755 | bugman | 2009-10-13 17:39:17 +0200 (Tue, 13 Oct 2009) | 3 lines
Citations are now being placed into the BMRB submission file.
........
r9756 | bugman | 2009-10-13 18:24:23 +0200 (Tue, 13 Oct 2009) | 3 lines
The relax citations are now placed into the BMRB file.
........
r9757 | bugman | 2009-10-13 18:26:38 +0200 (Tue, 13 Oct 2009) | 3 lines
Removed a debugging print statement.
........
r9758 | bugman | 2009-10-13 19:07:23 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified add_citation() to return the citation ID number.
........
r9759 | bugman | 2009-10-13 19:21:22 +0200 (Tue, 13 Oct 2009) | 3 lines
Modified the BMRB system test to catch the citation ID number and pass it into bmrb.software().
........
r9760 | bugman | 2009-10-13 19:22:24 +0200 (Tue, 13 Oct 2009) | 3 lines
Fix for the BMRB system test. The arg to bmrb.software() should be cite_ids.
........
r9761 | bugman | 2009-10-13 19:32:05 +0200 (Tue, 13 Oct 2009) | 3 lines
Created the is_int_list() function for argument checking.
........
r9762 | bugman | 2009-10-13 19:33:29 +0200 (Tue, 13 Oct 2009) | 3 lines
Created the RelaxNoneListIntError class.
........
r9763 | bugman | 2009-10-13 20:00:34 +0200 (Tue, 13 Oct 2009) | 5 lines
The BMRB SoftwareCitation tag category is now being created.
This points back to the relevant Citation saveframe.
........
r9764 | bugman | 2009-10-13 20:21:14 +0200 (Tue, 13 Oct 2009) | 3 lines
Fixes for the software citations.
........
r9765 | bugman | 2009-10-14 14:46:19 +0200 (Wed, 14 Oct 2009) | 3 lines
Modified the BMRB system test to have citation ID strings, rather than numbers.
........
r9766 | bugman | 2009-10-14 14:52:55 +0200 (Wed, 14 Oct 2009) | 3 lines
Citation ID strings are now handled by the bmrb.citation() user function.
........
r9767 | bugman | 2009-10-14 14:54:03 +0200 (Wed, 14 Oct 2009) | 3 lines
Fix for the bmrb.software() printout (it was saying bmrb.software_select(...))!
........
r9768 | bugman | 2009-10-14 15:27:17 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the get_cite_id_num() method to convert the citation ID string to a citation ID number.
........
r9769 | bugman | 2009-10-14 15:27:54 +0200 (Wed, 14 Oct 2009) | 3 lines
The BMRB file now uses the citation ID numbers properly.
........
r9770 | bugman | 2009-10-14 15:39:29 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the TempCalibrationMethod and TempControlMethod tags to the General Relaxation saveframe.
........
r9771 | bugman | 2009-10-14 15:40:22 +0200 (Wed, 14 Oct 2009) | 3 lines
Changed the label class variable.
........
r9772 | bugman | 2009-10-14 15:51:32 +0200 (Wed, 14 Oct 2009) | 3 lines
Added calls to the relax_data.temp_calibration() and relax_data.temp_control() user functions.
........
r9773 | bugman | 2009-10-14 15:55:39 +0200 (Wed, 14 Oct 2009) | 3 lines
Fix for the call to relax_data.temp_*() in the BMRB system test.
........
r9774 | bugman | 2009-10-14 17:57:26 +0200 (Wed, 14 Oct 2009) | 3 lines
The temperature control and calibration methods are now being placed into the BMRB file.
........
r9775 | bugman | 2009-10-14 18:22:54 +0200 (Wed, 14 Oct 2009) | 3 lines
Added the, as of yet unused, SampleConditionListID tag to the General_relaxation saveframe.
........
r9776 | bugman | 2009-10-14 18:28:40 +0200 (Wed, 14 Oct 2009) | 8 lines
Updated or added the Relaxation_* tags of General_relaxation saveframe.
These include:
Relaxation_coherence_type
Relaxation_type_common_name
Relaxation_val_units
........
r9777 | bugman | 2009-10-14 18:30:36 +0200 (Wed, 14 Oct 2009) | 5 lines
Changed the R1 and R2 common names.
These now match those described at https://mail.gna.org/public/relax-devel/2009-03/msg00037.html.
........
r9778 | bugman | 2009-10-14 18:31:28 +0200 (Wed, 14 Oct 2009) | 3 lines
Changed RelaxationValUnits to match https://mail.gna.org/public/relax-devel/2009-03/msg00037.html.
........
r9779 | bugman | 2009-10-14 19:09:27 +0200 (Wed, 14 Oct 2009) | 3 lines
Expanded the General_relaxation saveframe to accept almost all info into bmrblib.
........
r9780 | bugman | 2009-10-25 22:10:56 +0100 (Sun, 25 Oct 2009) | 3 lines
Expanded the Modelfree saveframe to include much more information.
........
r9781 | bugman | 2009-10-25 22:18:27 +0100 (Sun, 25 Oct 2009) | 3 lines
Expanded the add() method docstring to cover all args.
........
r9782 | bugman | 2009-10-25 22:22:09 +0100 (Sun, 25 Oct 2009) | 3 lines
The software citation IDs are now handled, and all the new model-free info supplied.
........
r9783 | bugman | 2009-10-26 15:26:13 +0100 (Mon, 26 Oct 2009) | 3 lines
The HeteronuclNOE saveframe now only has the temp control and calibration tags for v3.2.
........
r9784 | bugman | 2009-10-26 17:17:15 +0100 (Mon, 26 Oct 2009) | 5 lines
Reintroduced the temp_calibration and temp_control args to Relaxation.add().
These are not used and are provided as dummy args for compatibility between different BMRB formats.
........
r9785 | bugman | 2009-10-26 17:23:24 +0100 (Mon, 26 Oct 2009) | 3 lines
Made the temp calibration v3.2 specific for the heteronuclear NOE saveframe.
........
r9786 | bugman | 2009-10-26 17:28:34 +0100 (Mon, 26 Oct 2009) | 3 lines
Bug fix for the model free saveframe for v3.0 and v3.1 (previously called the OrderParameter saveframe).
........
r9787 | bugman | 2009-10-26 18:18:08 +0100 (Mon, 26 Oct 2009) | 6 lines
Atom info changes in the model-free saveframe.
The 'Atom_ID' tag is now changed to 'Obs_atom_ID' for v3.2. The Obs_atom_type and
Obs_atom_isotope_number tags have been added to the saveframe.
........
r9788 | bugman | 2009-10-26 18:19:18 +0100 (Mon, 26 Oct 2009) | 3 lines
relax now places the isotope number into the BMRB file.
........
r9789 | bugman | 2009-10-26 18:36:35 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a check to see if the element type has been specified.
........
r9790 | bugman | 2009-10-26 18:40:40 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a missing RelaxError import.
........
r9791 | bugman | 2009-10-26 18:46:04 +0100 (Mon, 26 Oct 2009) | 3 lines
Added a call to the non-existent spin.element() user function.
........
r9792 | bugman | 2009-10-26 19:08:38 +0100 (Mon, 26 Oct 2009) | 3 lines
Implemented the spin.element() user function.
........
|
2011-02-19 14:02:05
|
Tree
|
[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.
........
r9445 | bugman | 2009-09-03 14:41:00 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the specific_fns.__all__ list.
........
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.
........
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.
........
r9662 | bugman | 2009-10-08 17:46:22 +0200 (Thu, 08 Oct 2009) | 3 lines
More variable name bug fixes.
........
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!
........
r9664 | bugman | 2009-10-08 17:49:31 +0200 (Thu, 08 Oct 2009) | 3 lines
Fixed the inheritance of Relaxation_v3_2.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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'!)
........
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.
........
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'.
........
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().
........
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.
........
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.
........
r9680 | bugman | 2009-10-09 12:01:55 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
........
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!
........
r9682 | bugman | 2009-10-09 12:12:16 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
........
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.
........
r9684 | bugman | 2009-10-09 12:44:10 +0200 (Fri, 09 Oct 2009) | 3 lines
Removed some debugging code.
........
r9685 | bugman | 2009-10-09 12:44:59 +0200 (Fri, 09 Oct 2009) | 3 lines
Redesigned pack_data() to handle sequence generation.
........
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).
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r9697 | bugman | 2009-10-09 15:48:19 +0200 (Fri, 09 Oct 2009) | 3 lines
Added a docstring to tag_setup().
........
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.
........
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.
........
r9701 | bugman | 2009-10-09 18:15:15 +0200 (Fri, 09 Oct 2009) | 3 lines
Modified the translate() method to handle not doing anything.
........
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.
........
r9703 | bugman | 2009-10-09 18:38:35 +0200 (Fri, 09 Oct 2009) | 3 lines
Added the missing Task tag to the Software saveframe.
........
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.
........
|
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
........
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.
........
r8835 | bugman | 2009-02-21 23:57:38 +0100 (Sat, 21 Feb 2009) | 3 lines
Renamed the pystarlib file object to self.data.
........
r8836 | bugman | 2009-02-22 00:05:49 +0100 (Sun, 22 Feb 2009) | 3 lines
Fixed the call to pystarlib.File().
........
r8837 | bugman | 2009-02-22 00:16:19 +0100 (Sun, 22 Feb 2009) | 3 lines
Small temporary fix for the file writing.
........
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.
........
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.
........
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).
........
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.
........
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.
........
r8843 | bugman | 2009-02-22 13:25:13 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the HeteronuclT1Experiment tag category object.
........
r8844 | bugman | 2009-02-22 13:29:20 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the unused HeteronuclT1Software tag category class.
........
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.
........
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.
........
r8847 | bugman | 2009-02-22 13:49:33 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the T1 tag category.
........
r8848 | bugman | 2009-02-22 14:00:14 +0100 (Sun, 22 Feb 2009) | 3 lines
Created the heteronucl_NOEs and heteronucl_T2_relaxation saveframes.
........
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.
........
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.
........
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.
........
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!
........
r8853 | bugman | 2009-02-22 15:37:57 +0100 (Sun, 22 Feb 2009) | 3 lines
Some class name changes.
........
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.
........
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.
........
r8856 | bugman | 2009-02-22 18:58:15 +0100 (Sun, 22 Feb 2009) | 3 lines
Added v3.1 support for the T2.
........
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.
........
r8858 | bugman | 2009-02-22 19:44:35 +0100 (Sun, 22 Feb 2009) | 3 lines
Values of 'None' are now translated to the '?' string.
........
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.
........
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.
........
r8864 | bugman | 2009-02-22 23:28:23 +0100 (Sun, 22 Feb 2009) | 3 lines
Updated the __all__ list.
........
r8865 | bugman | 2009-02-22 23:33:38 +0100 (Sun, 22 Feb 2009) | 3 lines
Added directories for all the NMR-STAR dictionary supergroups.
........
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.
........
r8867 | bugman | 2009-02-22 23:43:13 +0100 (Sun, 22 Feb 2009) | 3 lines
Bug fix for the __all__ list.
........
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.
........
r8869 | bugman | 2009-02-23 11:52:25 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the entity saveframe category.
........
r8870 | bugman | 2009-02-23 14:01:18 +0100 (Mon, 23 Feb 2009) | 3 lines
Preparation for the v3.1 entity saveframe category.
........
r8871 | bugman | 2009-02-23 14:10:02 +0100 (Mon, 23 Feb 2009) | 3 lines
Fixed some miss named variables (this has no effect).
........
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.
........
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.
........
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.
........
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.
........
r8876 | bugman | 2009-02-26 14:58:28 +0100 (Thu, 26 Feb 2009) | 3 lines
Bug fix.
........
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!
........
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.
........
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.
........
r8881 | bugman | 2009-02-27 14:35:07 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed the useless ri_inc variable.
........
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@...>).
........
r8884 | bugman | 2009-02-27 15:16:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule name is now correctly passed in.
........
r8885 | bugman | 2009-02-27 15:56:25 +0100 (Fri, 27 Feb 2009) | 3 lines
Removed some remnant args.
........
r8886 | bugman | 2009-02-27 16:04:17 +0100 (Fri, 27 Feb 2009) | 3 lines
The _Entity.ID is now created.
........
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().
........
r8888 | bugman | 2009-02-27 17:20:49 +0100 (Fri, 27 Feb 2009) | 3 lines
The molecule type is now determined.
........
r8889 | bugman | 2009-02-27 17:25:54 +0100 (Fri, 27 Feb 2009) | 3 lines
The residue numbers are being stored in self now.
........
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.
........
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.
........
r8892 | bugman | 2009-02-27 18:02:22 +0100 (Fri, 27 Feb 2009) | 3 lines
The EntityCompIndex saveframe is now being created.
........
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().
........
r8905 | bugman | 2009-03-05 11:34:04 +0100 (Thu, 05 Mar 2009) | 3 lines
The data pipe is no longer needed.
........
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().
........
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.
........
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.
........
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.
........
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.
........
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.
........
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!
........
r8921 | bugman | 2009-03-06 15:42:34 +0100 (Fri, 06 Mar 2009) | 3 lines
Docstring fix.
........
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.
........
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.
........
r8930 | bugman | 2009-03-08 22:43:32 +0100 (Sun, 08 Mar 2009) | 3 lines
Added a call to pack_data() from bmrb_read().
........
r8934 | bugman | 2009-03-08 23:38:36 +0100 (Sun, 08 Mar 2009) | 3 lines
Simplified the bmrb_read() function.
........
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().
........
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!
........
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).
........
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.
........
r8941 | bugman | 2009-03-09 13:50:40 +0100 (Mon, 09 Mar 2009) | 3 lines
Added the saveframe category for model-free data.
........
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).
........
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.
........
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.
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
r8951 | bugman | 2009-03-10 14:19:36 +0100 (Tue, 10 Mar 2009) | 3 lines
Fixed the reading of relaxation data.
........
r8952 | bugman | 2009-03-10 14:27:37 +0100 (Tue, 10 Mar 2009) | 3 lines
Made the model-free saveframe category name version specific.
........
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).
........
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.
........
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.
........
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.
........
r8960 | bugman | 2009-03-10 17:28:49 +0100 (Tue, 10 Mar 2009) | 3 lines
Docstring fixes. These are not v3.1 files!
........
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
|
