Merged revisions 17179-17181 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
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r17179 | bugman | 2012-07-04 10:51:03 +0200 (Wed, 04 Jul 2012) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-16843" from
svn+ssh://bugman@.../svn/relax/branches/interatomic
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r17180 | bugman | 2012-07-04 11:04:16 +0200 (Wed, 04 Jul 2012) | 1195 lines
Merged revisions 16844-16845,16848-16849,16852-16855,16858-16865,16867-16878,16883,16917,16919-16956,16961-16991,16994-16997,17000-17008,17011-17016,17023-17027,17032-17038,17042-17043,17046-17065,17067-17113,17123-17138,17141,17143-17144,17146-17155,17158-17173,17175-17177 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/interatomic
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r16844 | bugman | 2012-06-11 19:37:17 +0200 (Mon, 11 Jun 2012) | 6 lines
Created the interatomic data list and containers, and added these to the data pipe structures.
This is modelled on the molecule/residue/spin structures. The new containers have is_empty(),
from_xml() and to_xml() methods and should be fully functional with the relax infrastructure.
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r16845 | bugman | 2012-06-11 19:43:02 +0200 (Mon, 11 Jun 2012) | 3 lines
A large number of missing imports for the new data.interatomic module!
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r16848 | bugman | 2012-06-11 19:55:51 +0200 (Mon, 11 Jun 2012) | 3 lines
Fix for the BMRB system tests for the new interatomic data pipe object.
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r16849 | bugman | 2012-06-11 20:08:22 +0200 (Mon, 11 Jun 2012) | 5 lines
Converted the rdc.read user function definition to use the interatomic data objects.
This is currently only for the front ends of the user function.
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r16852 | bugman | 2012-06-11 20:15:20 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted the stereochemistry auto-analysis to use the new rdc.read definition.
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r16853 | bugman | 2012-06-11 20:16:21 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted the rdc.read user function backend to the new interatomic data design.
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r16854 | bugman | 2012-06-11 20:17:55 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted the only sample script which uses the rdc.read user function to the changed definition.
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r16855 | bugman | 2012-06-11 20:20:01 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted some of the test suite RDC data to use the double spin ID format for interatomic data.
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r16858 | bugman | 2012-06-11 20:40:39 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted a few of the N-state model system tests to use the new rdc.read definition.
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r16859 | bugman | 2012-06-11 20:41:25 +0200 (Mon, 11 Jun 2012) | 3 lines
Created the InteratomContainer.id_match() method for checking the spin IDs in both directions for a match.
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r16860 | bugman | 2012-06-11 20:47:41 +0200 (Mon, 11 Jun 2012) | 3 lines
Created the generic_fns.interatomic module and added the return_container() method.
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r16861 | bugman | 2012-06-11 20:55:27 +0200 (Mon, 11 Jun 2012) | 3 lines
Fix for the InteratomList.add_item() method.
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r16862 | bugman | 2012-06-11 20:56:57 +0200 (Mon, 11 Jun 2012) | 3 lines
Added checks to the InteratomList.add_item() method to make sure that the spin IDs already exist.
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r16863 | bugman | 2012-06-11 20:57:56 +0200 (Mon, 11 Jun 2012) | 3 lines
Created the generic_fns.interatomic.create_interatom() function for creating interatomic data containers.
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r16864 | bugman | 2012-06-11 21:01:22 +0200 (Mon, 11 Jun 2012) | 3 lines
The rdc.read user function backend is now adding the RDCs to the interatomic data containers.
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r16865 | bugman | 2012-06-11 21:03:50 +0200 (Mon, 11 Jun 2012) | 5 lines
Shifted some code from InteratomList.add_item() to generic_fns.interatomic.create_interatom().
This is to break a circular import problem.
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r16867 | bugman | 2012-06-11 21:06:51 +0200 (Mon, 11 Jun 2012) | 5 lines
Renamed the interatomic function return_container() to return_interatom().
This is to make the name more unique.
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r16868 | bugman | 2012-06-11 21:07:40 +0200 (Mon, 11 Jun 2012) | 3 lines
Missing imports.
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r16869 | bugman | 2012-06-11 22:25:24 +0200 (Mon, 11 Jun 2012) | 5 lines
The generic_fns.interatomic.create_interatom() function now returns the created container.
This comes from the InteratomicContainer.add_item() method which now also returns the container.
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r16870 | bugman | 2012-06-11 22:26:03 +0200 (Mon, 11 Jun 2012) | 3 lines
Updated another N-state model system test script to the new rdc.read interatomic data design.
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r16871 | bugman | 2012-06-11 22:27:24 +0200 (Mon, 11 Jun 2012) | 3 lines
Shifted the id_match() method to the correct class!
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r16872 | bugman | 2012-06-11 22:31:00 +0200 (Mon, 11 Jun 2012) | 3 lines
Fix for the id_match() method - there are no indices.
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r16873 | bugman | 2012-06-11 22:31:33 +0200 (Mon, 11 Jun 2012) | 3 lines
Lots of updates to the rdc.read user function backend.
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r16874 | bugman | 2012-06-11 22:35:57 +0200 (Mon, 11 Jun 2012) | 3 lines
Created the generic_fns.interatomic.interatomic_loop() generator function.
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r16875 | bugman | 2012-06-11 22:56:07 +0200 (Mon, 11 Jun 2012) | 3 lines
Started to convert the N-state model optimisation code to handle RDCs as interatomic data.
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r16876 | bugman | 2012-06-11 22:57:09 +0200 (Mon, 11 Jun 2012) | 5 lines
The N-state model specific analysis code is now handling RDCs as interatomic data.
This still has a lot of work before it will be functional.
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r16877 | bugman | 2012-06-11 22:59:17 +0200 (Mon, 11 Jun 2012) | 3 lines
Syntax error fix.
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r16878 | bugman | 2012-06-11 23:09:37 +0200 (Mon, 11 Jun 2012) | 3 lines
Converted the structure.vectors user function definition to the new interatomic data design.
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r16883 | bugman | 2012-06-12 17:45:59 +0200 (Tue, 12 Jun 2012) | 3 lines
Expanded the description of the negative gyromagnetic ratio flag for the rdc.read user function.
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r16917 | bugman | 2012-06-17 09:14:35 +0200 (Sun, 17 Jun 2012) | 3 lines
Started to change the structure.vectors backend to handle two spin IDs.
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r16919 | bugman | 2012-06-17 10:25:20 +0200 (Sun, 17 Jun 2012) | 9 lines
Redesigned the model-free dauvergne_protocol.py system test script for the interatomic concept.
The new script will be used to redesign how to set up a model-free analysis using the interatomic
data concept. It adds the new relax_data.dipole_pair user function which will be used to define the
dipolar relaxation interaction (this will inadvertently allow multi-dipole relation). The
heteronuc_type and proton_type parameters have been replaced with the spin_type parameter, as now
both the heternuclear and homonuclear spins need to be loaded into relax.
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r16920 | bugman | 2012-06-17 11:46:11 +0200 (Sun, 17 Jun 2012) | 3 lines
Added the definition for the new relax_data.dipole_pair user function.
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r16921 | bugman | 2012-06-17 13:54:03 +0200 (Sun, 17 Jun 2012) | 5 lines
The bond length setting via value.set has no been merged into relax_data.dipole_pair.
This averaged length is dipole-dipole distance and does not need to be a model-free parameter.
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r16922 | bugman | 2012-06-17 13:54:24 +0200 (Sun, 17 Jun 2012) | 3 lines
Removed the bond length from the model-free parameter list.
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r16923 | bugman | 2012-06-17 22:37:23 +0200 (Sun, 17 Jun 2012) | 3 lines
Created graphics for the magnetic dipole-dipole interaction.
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r16924 | bugman | 2012-06-17 22:37:57 +0200 (Sun, 17 Jun 2012) | 3 lines
Shifted the dipole-dipole graphics to the Wizard directory, as this is a wizard graphic.
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r16925 | bugman | 2012-06-17 23:22:09 +0200 (Sun, 17 Jun 2012) | 3 lines
A few changes to the relax_data.dipole_pair user function definition.
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r16926 | bugman | 2012-06-18 00:12:09 +0200 (Mon, 18 Jun 2012) | 3 lines
Started to add the backend of the relax_data.dipole_pair user function.
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r16927 | bugman | 2012-06-18 09:50:31 +0200 (Mon, 18 Jun 2012) | 5 lines
Created the structural API base are_bonded() method - this is for determining if 2 atoms are bonded.
This is a method stub which raises a RelaxImplementError.
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r16928 | bugman | 2012-06-18 11:06:35 +0200 (Mon, 18 Jun 2012) | 3 lines
Implemented the are_bonded() structural API method for the internal structural object.
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r16929 | bugman | 2012-06-18 11:14:59 +0200 (Mon, 18 Jun 2012) | 6 lines
Added CONECT records to the sphere.pdb file to allow connectivities to be more easily determined.
This is for the internal reader, as the current algorithm for finding attached atoms is distance
based, and as all N atoms of all residues are at [0, 0, 0], this algorithm fails.
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r16930 | bugman | 2012-06-18 11:45:51 +0200 (Mon, 18 Jun 2012) | 3 lines
The relax_data.dipole_pair backend now uses the direct_bond flag.
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r16931 | bugman | 2012-06-18 14:10:00 +0200 (Mon, 18 Jun 2012) | 7 lines
Shifted the relax_data.dipole_pair user function into the new dipole_pair user function class.
This has also been split into two new user functions:
dipole_pair.define used to set up the magnetic dipole-dipole interactions.
dipole_pair.set_dist used to set up the r^-3 averaged interatomic distances.
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r16932 | bugman | 2012-06-18 14:28:36 +0200 (Mon, 18 Jun 2012) | 3 lines
Created a set of icons for the dipole_pair user functions.
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r16933 | bugman | 2012-06-18 14:41:55 +0200 (Mon, 18 Jun 2012) | 3 lines
Refinement of the dipole_pair user function definitions.
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r16934 | bugman | 2012-06-18 14:48:01 +0200 (Mon, 18 Jun 2012) | 3 lines
More refinements of the dipole_pair.define user function definition.
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r16935 | bugman | 2012-06-18 14:48:49 +0200 (Mon, 18 Jun 2012) | 3 lines
Fix for the dipole_pair.define user function - the interatom object can pre-exist, containing other data.
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r16936 | bugman | 2012-06-18 17:27:16 +0200 (Mon, 18 Jun 2012) | 6 lines
Created the dipole_pair.read_dist user function definitions.
This new user function is for simplifying the loading of many different interatomic distances into
relax.
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r16937 | bugman | 2012-06-18 17:35:23 +0200 (Mon, 18 Jun 2012) | 3 lines
Created the backend of the dipole_pair.read_dist user function.
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r16938 | bugman | 2012-06-18 17:59:49 +0200 (Mon, 18 Jun 2012) | 3 lines
Created the dipole_pair.unit_vectors user function definition.
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r16939 | bugman | 2012-06-18 18:19:51 +0200 (Mon, 18 Jun 2012) | 3 lines
Refinement of the dipole_pair user function definitions.
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r16940 | bugman | 2012-06-18 18:21:06 +0200 (Mon, 18 Jun 2012) | 3 lines
Fixed the call to dipole_pair.unit_vectors in the dauvergne_protocol.py system test script.
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r16941 | bugman | 2012-06-18 20:34:12 +0200 (Mon, 18 Jun 2012) | 7 lines
Implemented the dipole_pair.unit_vectors user function backend.
This code originates from the generic_fns.structure.main.vectors() function (the structure.vectors
user function backend). The dipole_pair.unit_vectors user function is designed to replace
structure.vectors.
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r16942 | bugman | 2012-06-19 10:03:29 +0200 (Tue, 19 Jun 2012) | 6 lines
Deletion of the structure.vectors user function as it has been superseded by dipole_pair.unit_vectors.
Only the user function definition has deleted - the backend code will remain so that it can be used
internally.
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r16943 | bugman | 2012-06-19 10:48:23 +0200 (Tue, 19 Jun 2012) | 3 lines
Added a set of icons for nuclear or isotope related usage.
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r16944 | bugman | 2012-06-19 10:49:24 +0200 (Tue, 19 Jun 2012) | 3 lines
Added the nuclear symbol as a wizard graphic.
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r16945 | bugman | 2012-06-19 10:54:07 +0200 (Tue, 19 Jun 2012) | 6 lines
Created the spin.isotope user function.
This is designed to be a permanent replacement for the specific analysis API 'heteronuc_type' and
'proton_type' parameters.
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r16946 | bugman | 2012-06-19 11:01:47 +0200 (Tue, 19 Jun 2012) | 11 lines
Eliminated a number of the specific API parameters relating to dipole-dipole interactions.
These are now provided by the spin.isotope user function and the dipole_pair user functions. The
eliminated parameters are:
'r' - replaced by dipole_pair.set_dist or dipole_pair.read_dist,
'xh_vect' - replaced by dipole_pair.unit_vectors,
'heteronuc_type' - replaced by spin.isotope,
'proton_type' - replaced by spin.isotope,
'attached_proton' - replaced by dipole_pair.define.
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r16947 | bugman | 2012-06-19 11:10:47 +0200 (Tue, 19 Jun 2012) | 5 lines
Changed the dauvergne_protocol.py system test script value.set calls with spin.isotope.
The nuclear isotope is now defined via spin.isotope.
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r16948 | bugman | 2012-06-19 11:22:16 +0200 (Tue, 19 Jun 2012) | 5 lines
Expanded the RelaxNoValueError to handle one or two spin IDs as arguments.
This is to better identify which spins or interatomic data containers are deficient.
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r16949 | bugman | 2012-06-19 11:24:39 +0200 (Tue, 19 Jun 2012) | 7 lines
Modified the check_args() method of the dauvergne_protocol model-free auto-analysis for the new data.
The heteronuc_type and proton_type are now in the spin's isotope variable, and the bond length 'r'
is now the interatomic distance variable 'r'. All spin containers and interatomic data containers
are being checked.
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r16950 | bugman | 2012-06-19 11:38:32 +0200 (Tue, 19 Jun 2012) | 5 lines
Expanded the return_interatom() function to handle a single spin ID.
This function now returns a list of matching interatomic data containers.
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r16951 | bugman | 2012-06-19 11:49:07 +0200 (Tue, 19 Jun 2012) | 3 lines
Started to convert the model-free analysis code to the new interatomic data container design.
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r16952 | bugman | 2012-06-19 12:42:49 +0200 (Tue, 19 Jun 2012) | 3 lines
The interatomic data container now has the dipole_pair flag initialised to False.
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r16953 | bugman | 2012-06-19 12:58:44 +0200 (Tue, 19 Jun 2012) | 3 lines
The model-free analysis is now fully using the new interatomic data container design.
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r16954 | bugman | 2012-06-19 14:10:20 +0200 (Tue, 19 Jun 2012) | 3 lines
Created the RelaxInteratomError and RelaxNoInteratomError classes for interatomic data errors.
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r16955 | bugman | 2012-06-19 14:12:23 +0200 (Tue, 19 Jun 2012) | 8 lines
Expanded the functionality of the generic_fns.interatomic module.
The copy() and exists_data() functions have been added to copy all interatomic data from one data
pipe to another and to check if interatomic data exists within a data pipe respectively. The
create_interatom() function now also accepts a 'pipe' argument so that non-current pipes can be
used.
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r16956 | bugman | 2012-06-19 14:18:15 +0200 (Tue, 19 Jun 2012) | 3 lines
Fixes for the model-free support of the interatomic data container design.
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r16961 | bugman | 2012-06-19 16:21:59 +0200 (Tue, 19 Jun 2012) | 7 lines
Fix for the model-free duplicate_data() method for interatomic data.
This is used by the model_selection user function. The problem was that no proton spins where being
copied as previously there were no proton spins in a model-free analysis. This spins are now needed
to define the dipolar relaxation mechanism.
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r16962 | bugman | 2012-06-19 16:25:34 +0200 (Tue, 19 Jun 2012) | 3 lines
Added a check to the model-free overfit_deselect() to see if a relaxation mechanism is present.
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r16963 | bugman | 2012-06-19 16:38:57 +0200 (Tue, 19 Jun 2012) | 3 lines
The CSA value is now only set for the 15N spins in the dauvergne_protocol.py system test script.
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r16964 | bugman | 2012-06-19 18:30:04 +0200 (Tue, 19 Jun 2012) | 6 lines
The Mf.test_dauvergne_protocol system test now passes with the new interatomic data container design!
This involves lots of changes to the model-free specific code, the dauvergne_protocol auto-analysis,
and modification of the checks in the system test for the additional proton spin containers.
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r16965 | bugman | 2012-06-19 18:40:20 +0200 (Tue, 19 Jun 2012) | 3 lines
Added a verbose flag to the generic_fns.dipole_pair.define() function.
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r16966 | bugman | 2012-06-19 18:54:29 +0200 (Tue, 19 Jun 2012) | 5 lines
Bug fix for the printing out of interatomic data containers.
The __repr__() method wasn't skipping all methods.
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r16967 | bugman | 2012-06-19 19:43:18 +0200 (Tue, 19 Jun 2012) | 3 lines
Basic docstring edit.
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r16968 | bugman | 2012-06-19 19:44:14 +0200 (Tue, 19 Jun 2012) | 3 lines
The import of old relax 1.2 results files is now operational under the interatomic data design.
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r16969 | bugman | 2012-06-19 19:44:36 +0200 (Tue, 19 Jun 2012) | 3 lines
Updated the final_results_trunc_1.3_pre_py2.7.3_v2.bz2 results file for the interatomic data design.
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r16970 | bugman | 2012-06-19 20:13:18 +0200 (Tue, 19 Jun 2012) | 5 lines
Fixes for the dipolar_pair.define user function backend.
The return_interatom() function now returns a list!
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r16971 | bugman | 2012-06-19 20:15:04 +0200 (Tue, 19 Jun 2012) | 6 lines
Added a backwards compatibility hook for converting old XML files to the interatomic data design.
This will convert the variable names, deleting the old, and create proton spins and interatomic data
containers populating them with the old spin parameters.
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r16972 | bugman | 2012-06-19 20:16:26 +0200 (Tue, 19 Jun 2012) | 6 lines
Fix for the XML file loading of the interatomic data container structures.
The backwards compatibility hook of the previous commit creates interatomic data structures,
hence they must be recreated from the XML first.
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r16973 | bugman | 2012-06-19 20:18:06 +0200 (Tue, 19 Jun 2012) | 5 lines
Modified the tylers_peptide.py model-free system test scripts for the unit vector calculation.
The structure.vectors user function has been replaced by dipole_pair.unit_vectors.
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r16974 | bugman | 2012-06-19 20:21:40 +0200 (Tue, 19 Jun 2012) | 3 lines
Fixes for the model-free system test check_read_results_1_3() method for the interatomic data design.
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r16975 | bugman | 2012-06-19 20:24:51 +0200 (Tue, 19 Jun 2012) | 3 lines
The MoleculeContainer XML backwards compatibility hook now deletes the spin 'r_err' and 'r_sim' vars.
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r16976 | bugman | 2012-06-19 20:26:11 +0200 (Tue, 19 Jun 2012) | 3 lines
The relax 1.2 model-free results file reading no longer creates the spin 'attached_proton' variable.
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r16977 | bugman | 2012-06-19 20:26:48 +0200 (Tue, 19 Jun 2012) | 3 lines
Whitespace fix.
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r16978 | bugman | 2012-06-19 20:49:26 +0200 (Tue, 19 Jun 2012) | 5 lines
The Monte Carlo select_all_sims() function is now using the specific skip_function().
This is needed for recreating model-free simulations as deselected proton spin containers now exist.
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r16979 | bugman | 2012-06-19 20:50:23 +0200 (Tue, 19 Jun 2012) | 3 lines
Fix for the backward compatibility hook for MoleculeContainers - the H spin containers are deselected.
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r16980 | bugman | 2012-06-19 20:51:22 +0200 (Tue, 19 Jun 2012) | 6 lines
Fixes for the reading of relax 1.2 results files.
The new 'H' spin containers are now deselected, and the simulation structure creation has been
reverted.
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r16981 | bugman | 2012-06-19 20:54:27 +0200 (Tue, 19 Jun 2012) | 3 lines
Hopefully the last fix for the reading of relax 1.2 results files!
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r16982 | bugman | 2012-06-19 23:18:40 +0200 (Tue, 19 Jun 2012) | 3 lines
Even more fixes for the reading of relax 1.2 results files for the interatomic data design.
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r16983 | bugman | 2012-06-19 23:52:34 +0200 (Tue, 19 Jun 2012) | 3 lines
A fix for the model-free calculate() method for the interatomic data design.
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r16984 | bugman | 2012-06-19 23:55:42 +0200 (Tue, 19 Jun 2012) | 3 lines
Another fix for the model-free calculate() method.
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r16985 | bugman | 2012-06-20 00:11:50 +0200 (Wed, 20 Jun 2012) | 5 lines
The dipole_pair user functions now fail if nothing could be done.
This is for the dipole_pair.define, dipole_pair.read_dist, and dipole_pair.set_dist user functions.
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r16986 | bugman | 2012-06-20 00:32:25 +0200 (Wed, 20 Jun 2012) | 5 lines
Created the sequence.attach_proton user function.
This will be useful for analyses which are missing structural data.
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r16987 | bugman | 2012-06-20 00:40:38 +0200 (Wed, 20 Jun 2012) | 3 lines
Bug fix for the model-free overfit_deselect() method - again for the interatomic design.
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r16988 | bugman | 2012-06-20 00:55:52 +0200 (Wed, 20 Jun 2012) | 3 lines
Rearranged the spin.element user function arguments.
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r16989 | bugman | 2012-06-20 01:00:48 +0200 (Wed, 20 Jun 2012) | 5 lines
The sequence.attach_protons user function now sets the proton element and isotope types.
This reduces the amount of work required from the user.
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r16990 | bugman | 2012-06-20 01:12:31 +0200 (Wed, 20 Jun 2012) | 3 lines
Fix for the dipole_pair.define user function for when no structural data is present.
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r16991 | bugman | 2012-06-20 01:27:01 +0200 (Wed, 20 Jun 2012) | 3 lines
Bug fixes for the model-free back-calculation for the interatomic data design.
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r16994 | bugman | 2012-06-20 01:47:08 +0200 (Wed, 20 Jun 2012) | 3 lines
Bug fix for the dipole_pair.define user function when structural data is missing.
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r16995 | bugman | 2012-06-20 01:51:48 +0200 (Wed, 20 Jun 2012) | 3 lines
Eliminated the RelaxProtonTypeError error and changed the RelaxSpinTypeError message.
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r16996 | bugman | 2012-06-20 02:13:33 +0200 (Wed, 20 Jun 2012) | 3 lines
Conversion of most of the model-free system tests to the interatomic data design.
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r16997 | bugman | 2012-06-20 11:13:14 +0200 (Wed, 20 Jun 2012) | 6 lines
Improvements for the MoleculeContainer backwards compatibility hook for the creation of proton spins.
The proton element and isotope type is now set to 'H' and '1H' respectively. This now means that
the old XML files require less work by the user to convert to the new interatomic data design.
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r17000 | bugman | 2012-06-20 11:26:25 +0200 (Wed, 20 Jun 2012) | 3 lines
Expanded RelaxMultiSpinIDError to be able to print out a list of all the matching spin Ids.
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r17001 | bugman | 2012-06-20 13:35:46 +0200 (Wed, 20 Jun 2012) | 3 lines
Created the list_to_text() RelaxError system function for prettifying the output of RelaxMultiSpinIDError.
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r17002 | bugman | 2012-06-20 14:00:55 +0200 (Wed, 20 Jun 2012) | 6 lines
The return_spin() and return_spin_from_selection() functions can now handle multiple spins.
It the 'multi' flag is supplied, then lists of spins (and associated data) will be returned, rather
than a RelaxMultiSpinIDError error raised.
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r17003 | bugman | 2012-06-20 14:05:04 +0200 (Wed, 20 Jun 2012) | 3 lines
Fix for the return_spin_from_selection() function for a bug introduced in the last commit.
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r17004 | bugman | 2012-06-20 14:16:38 +0200 (Wed, 20 Jun 2012) | 3 lines
The return_spin_from_selection() function now lists all matching spins in RelaxMultiSpinIDError.
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r17005 | bugman | 2012-06-20 15:35:50 +0200 (Wed, 20 Jun 2012) | 6 lines
Bug fix - the spin_id arg for the relax_data.read user function now actually does something.
This argument is passed into the pack_data() function, where it is used to match against the spins
matching each file line. Only if there is a match, is the relaxation data loaded for that spin.
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r17006 | bugman | 2012-06-20 15:40:00 +0200 (Wed, 20 Jun 2012) | 3 lines
Lots of fixes for the model-free system tests.
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r17007 | bugman | 2012-06-20 15:49:26 +0200 (Wed, 20 Jun 2012) | 5 lines
The relax_data.read user function now prints out all of the data read in.
This is to better inform the user that something has happened.
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r17008 | bugman | 2012-06-21 09:59:06 +0200 (Thu, 21 Jun 2012) | 3 lines
More print outs and better data loading checks in the dipole_pair user functions.
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r17011 | bugman | 2012-06-21 10:11:13 +0200 (Thu, 21 Jun 2012) | 5 lines
Bug fix for the return_spin_from_selection() function for the 'multi' flag.
This function needs to handle the case of no spins matching the selection!
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r17012 | bugman | 2012-06-21 10:13:22 +0200 (Thu, 21 Jun 2012) | 5 lines
The structure.get_pos user function now prints out all data and fails if nothing was extracted.
This is to prevent the user from going too far without realising that something is wrong.
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r17013 | bugman | 2012-06-21 10:17:56 +0200 (Thu, 21 Jun 2012) | 5 lines
Improvements and fixes for the generic_fns.relax_data.pack_data() function.
This affects all the relaxation data reading user functions.
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r17014 | bugman | 2012-06-21 10:18:44 +0200 (Thu, 21 Jun 2012) | 3 lines
Improvements for the reading of old 1.2 relax results files for the attached proton spin containers.
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r17015 | bugman | 2012-06-21 10:20:37 +0200 (Thu, 21 Jun 2012) | 6 lines
The model-free data_init() method now sets boolean parameters to the default of False.
This excludes the selection flag which is set to True. The data_init() method no longer uses the
data_names() API method but the self.PARAMS.loop() method for returning the parameter names.
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r17016 | bugman | 2012-06-21 10:22:21 +0200 (Thu, 21 Jun 2012) | 5 lines
Many fixes for the model-free system tests and related data.
Now all model-free tests pass under the new interatomic data design.
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r17023 | bugman | 2012-06-22 14:19:44 +0200 (Fri, 22 Jun 2012) | 3 lines
Updated the generic_fns package __all__ list.
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r17024 | bugman | 2012-06-22 14:20:17 +0200 (Fri, 22 Jun 2012) | 3 lines
Missing import.
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r17025 | bugman | 2012-06-22 14:21:40 +0200 (Fri, 22 Jun 2012) | 3 lines
Removed all of the unit tests of the deleted structure.vectors user function.
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r17026 | bugman | 2012-06-22 14:25:31 +0200 (Fri, 22 Jun 2012) | 5 lines
Eliminated all of the bond length and heteronucleus type value.set units tests.
These are no longer specific analysis parameters.
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r17027 | bugman | 2012-06-22 15:06:24 +0200 (Fri, 22 Jun 2012) | 6 lines
Fix for the relax_data module pack_data() function for the trunk changes of r17021.
For the relax_data.read user function spin_id argument to be respected, the
return_spin_from_selection() function needs to be used to return multiple matching spins.
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r17032 | bugman | 2012-06-22 16:47:44 +0200 (Fri, 22 Jun 2012) | 6 lines
The specific API base skip_function() method now returns False.
This was previously raising a RelaxImplementError, but as Monte Carlo simulations now require this
function, but returning always False, all analyses will be automatically supported.
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r17033 | bugman | 2012-06-22 16:49:36 +0200 (Fri, 22 Jun 2012) | 3 lines
Comment fix.
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r17034 | bugman | 2012-06-22 16:50:09 +0200 (Fri, 22 Jun 2012) | 3 lines
Converted the J(w) mapping specific analysis code to the interatomic data design.
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r17035 | bugman | 2012-06-22 16:50:42 +0200 (Fri, 22 Jun 2012) | 3 lines
Converted all of the J(w) mapping system tests to the interatomic data design.
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r17036 | bugman | 2012-06-22 16:57:03 +0200 (Fri, 22 Jun 2012) | 3 lines
Some clean ups of the jw_mapping module.
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r17037 | bugman | 2012-06-22 17:01:25 +0200 (Fri, 22 Jun 2012) | 3 lines
Converted the consistency testing specific analysis code to the interatomic data design.
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r17038 | bugman | 2012-06-22 17:01:53 +0200 (Fri, 22 Jun 2012) | 3 lines
Converted all of the consistency testing system tests to the interatomic data design.
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r17042 | bugman | 2012-06-22 18:44:13 +0200 (Fri, 22 Jun 2012) | 3 lines
dipole_pair.unit_vectors now raises a RelaxNoInteratomError if not interatomic data is present.
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r17043 | bugman | 2012-06-22 19:04:55 +0200 (Fri, 22 Jun 2012) | 5 lines
Bug fix for the dipole_pair.unit_vectors user function positional checking.
The arg_check.is_float() function needs the raise_error flag turned off.
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r17046 | bugman | 2012-06-25 11:07:47 +0200 (Mon, 25 Jun 2012) | 3 lines
The RelaxNucleusError and RelaxSpinTypeError can now have the spin ID supplied.
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r17047 | bugman | 2012-06-25 12:26:12 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes for some of the N-state model system tests for the interatomic data design.
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r17048 | bugman | 2012-06-25 12:32:32 +0200 (Mon, 25 Jun 2012) | 7 lines
Split the return_interatom() function into two.
The new return_interatom() function is used for returning single interatomic data containers for
perfect matches, whereas the return_interatom_list() function is used to return a list of containers
matching a given spin. This simplifies the behaviour of the module.
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r17049 | bugman | 2012-06-25 12:40:21 +0200 (Mon, 25 Jun 2012) | 3 lines
Fix for the dipole_pair.define user function backend for the return_interatom() changes.
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r17050 | bugman | 2012-06-25 12:43:52 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes for the relax 1.2 model-free results reading code for the return_interatom() changes.
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r17051 | bugman | 2012-06-25 12:50:05 +0200 (Mon, 25 Jun 2012) | 3 lines
Fix for the XML loading backwards compatibility hook for the return_interatom() changes.
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r17052 | bugman | 2012-06-25 12:53:11 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes for the model-free code for the return_interatom() changes.
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r17053 | bugman | 2012-06-25 13:32:12 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes for the J(w) mapping and consistency testing analyses for the return_interatom() changes.
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r17054 | bugman | 2012-06-25 13:39:33 +0200 (Mon, 25 Jun 2012) | 3 lines
Small comment change.
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r17055 | bugman | 2012-06-25 16:24:21 +0200 (Mon, 25 Jun 2012) | 5 lines
Modified InteratomContainer.id_match() to handle a single spin ID and to match to all unique IDs.
This uses the spin container _spin_ids list private metadata structure.
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r17056 | bugman | 2012-06-25 16:47:53 +0200 (Mon, 25 Jun 2012) | 3 lines
A few small changes to the spin IDs used and the print out from the rdc.read user function.
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r17057 | bugman | 2012-06-25 19:48:17 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes to the N-state model minimisation setup and execution code for the interatomic data design.
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r17058 | bugman | 2012-06-25 19:48:48 +0200 (Mon, 25 Jun 2012) | 3 lines
Fixes for the N-state model optimisation target function code for the interatomic data design.
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r17059 | bugman | 2012-06-26 11:09:31 +0200 (Tue, 26 Jun 2012) | 5 lines
Updated all N-state model analysis references to RDCs and NOEs to use the interatomic data containers.
This is mainly for the methods reliant on the base_data_loop() iterator.
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r17060 | bugman | 2012-06-26 14:27:37 +0200 (Tue, 26 Jun 2012) | 3 lines
Converted all of the rdc related functions to the interatomic data container design.
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r17061 | bugman | 2012-06-26 14:28:09 +0200 (Tue, 26 Jun 2012) | 3 lines
A number of fixes for the N-state model target functions for the interatomic data design.
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r17062 | bugman | 2012-06-26 14:29:12 +0200 (Tue, 26 Jun 2012) | 3 lines
Fix for the N-state model _minimise_bc_data() method for the interatomic data design.
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r17063 | bugman | 2012-06-26 17:32:09 +0200 (Tue, 26 Jun 2012) | 3 lines
Modified the interatomic_loop() function so that spin IDs can be used to restrict the looping.
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r17064 | bugman | 2012-06-26 17:45:56 +0200 (Tue, 26 Jun 2012) | 7 lines
Interatomic data containers can now be selected and deselected.
The user functions select.interatom and deselect.interatom have been created mimicking the
equivalent select.spin and deselect.spin functions. Each interatomic data container now has a
select flag.
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r17065 | bugman | 2012-06-26 17:47:56 +0200 (Tue, 26 Jun 2012) | 3 lines
Fix for the interatomic data container is_empty() method for the new variables and methods.
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r17067 | bugman | 2012-06-27 09:59:41 +0200 (Wed, 27 Jun 2012) | 5 lines
Converted the population model RDC test data to the interatomic data design.
The RDC lists now consist of the two spin ID columns and a data column.
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r17068 | bugman | 2012-06-27 10:02:33 +0200 (Wed, 27 Jun 2012) | 5 lines
Fixes for the interatomic_loop() iterator when using selection strings.
The previous approach did not work!
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r17069 | bugman | 2012-06-27 10:04:05 +0200 (Wed, 27 Jun 2012) | 3 lines
Fixes for the interatomic_loop() calls in the interatom selection and deselection user functions.
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r17070 | bugman | 2012-06-27 10:59:41 +0200 (Wed, 27 Jun 2012) | 3 lines
Updated the population N-state model system test script to the new interatomic data design.
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r17071 | bugman | 2012-06-27 16:03:17 +0200 (Wed, 27 Jun 2012) | 5 lines
Converted all RDC data and generations scripts used by the N-state model to the interatom design.
This is the RDC data used in the relax test suite.
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r17072 | bugman | 2012-06-27 17:10:41 +0200 (Wed, 27 Jun 2012) | 3 lines
The rdc.read user function can now handle spin IDs in quotation marks.
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r17073 | bugman | 2012-06-27 17:41:26 +0200 (Wed, 27 Jun 2012) | 3 lines
Fixes for the _minimise_bc_data() model-free method.
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r17074 | bugman | 2012-06-27 17:42:21 +0200 (Wed, 27 Jun 2012) | 5 lines
The select.interatom and deselect.interatom spin ID arguments can now be set to None.
This allows all interatomic data containers to be either selected or deselected.
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r17075 | bugman | 2012-06-27 17:42:39 +0200 (Wed, 27 Jun 2012) | 3 lines
Debugging print out removal.
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r17076 | bugman | 2012-06-27 17:43:06 +0200 (Wed, 27 Jun 2012) | 3 lines
A number of bug fixes for the N-state model target functions.
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r17077 | bugman | 2012-06-27 17:43:37 +0200 (Wed, 27 Jun 2012) | 3 lines
Converted all of the N-state model system and GUI test scripts to the new interatomic data design.
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r17078 | bugman | 2012-06-27 17:50:45 +0200 (Wed, 27 Jun 2012) | 5 lines
The interatomic_loop() now skips deselected containers if the new 'selected' flag is True.
This should speed up the function and simplify its usage.
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r17079 | bugman | 2012-06-27 18:00:59 +0200 (Wed, 27 Jun 2012) | 3 lines
Started to convert the Frame Order test suite RDC data to the new interatomic data design.
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r17080 | bugman | 2012-06-27 18:07:34 +0200 (Wed, 27 Jun 2012) | 6 lines
The InteratomContainer.id_match() method now checks if the spins for the container exist.
This is needed for the InteratomList.add_item() method checks to see if the container already exists
prior to adding it.
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r17081 | bugman | 2012-06-28 10:39:43 +0200 (Thu, 28 Jun 2012) | 5 lines
Shifted the InteratomContainer.id_match() method into the generic_fns.interatomic module.
This is needed to allow the correct data pipes to be matched.
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r17082 | bugman | 2012-06-28 10:56:42 +0200 (Thu, 28 Jun 2012) | 5 lines
Fix for the rdc.write user function backend.
The data is now properly formatted for the relax_io.write_data() function.
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r17083 | bugman | 2012-06-28 11:13:22 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for the N_state_model.test_pcs_to_rdc system test for the interatomic data design.
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r17084 | bugman | 2012-06-28 11:25:49 +0200 (Thu, 28 Jun 2012) | 5 lines
Fix for the lactose N-state model system test script for the interatomic data design.
The interatomic CH2 vectors are now deselected.
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r17085 | bugman | 2012-06-28 11:32:14 +0200 (Thu, 28 Jun 2012) | 3 lines
Interatomic data design fix for the N-state model analysis _minimise_bc_data() method.
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r17086 | bugman | 2012-06-28 11:33:02 +0200 (Thu, 28 Jun 2012) | 3 lines
Fix for the N_state_model.test_metal_pos_opt system test.
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r17087 | bugman | 2012-06-28 11:59:59 +0200 (Thu, 28 Jun 2012) | 3 lines
Fix for the dipole_pair.unit_vectors user function - the vector averaging now occurs after the normalisation.
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r17088 | bugman | 2012-06-28 12:01:03 +0200 (Thu, 28 Jun 2012) | 3 lines
Another interatomic data design fix for the N_state_model.test_pcs_to_rdc system test.
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r17089 | bugman | 2012-06-28 12:15:51 +0200 (Thu, 28 Jun 2012) | 7 lines
Reverted the CaM synthetic randomised data change of r17071, as the data randomisation shouldn't change.
The commands used were:
svn merge -r17071:r17070 synth_rdc_rand
svn merge -r17071:r17070 synth_pcs_rand
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r17090 | bugman | 2012-06-28 14:17:56 +0200 (Thu, 28 Jun 2012) | 3 lines
Created the new Interatomic system test class for testing out the interatomic data containers.
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r17091 | bugman | 2012-06-28 14:22:13 +0200 (Thu, 28 Jun 2012) | 3 lines
The interatomic test suite scripts are now GUI tests as well.
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r17092 | bugman | 2012-06-28 14:24:44 +0200 (Thu, 28 Jun 2012) | 3 lines
Some changes to the Interatomic.test_manipulation system test to better test selection/deselection.
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r17093 | bugman | 2012-06-28 14:27:49 +0200 (Thu, 28 Jun 2012) | 6 lines
Bug fixes for the deselect.interatom and select.interatom user functions.
The interatomic data container loops were skipping deselected containers, but these loops must be
over all containers.
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r17094 | bugman | 2012-06-28 14:43:48 +0200 (Thu, 28 Jun 2012) | 3 lines
Expanded the Interatomic.test_manipulation system test to demonstrate a few current failures.
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r17095 | bugman | 2012-06-28 15:08:23 +0200 (Thu, 28 Jun 2012) | 3 lines
Some fixes for the Interatomic.test_manipulation system test.
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r17096 | bugman | 2012-06-28 15:09:03 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for the dipole_pair.define user function uncovered by the Interatomic.test_manipulation system test.
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r17097 | bugman | 2012-06-28 15:40:35 +0200 (Thu, 28 Jun 2012) | 3 lines
Bug fix for the interatomic_loop() function for when only a single spin ID is used.
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r17098 | bugman | 2012-06-28 15:57:59 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for the N_state_model.test_monte_carlo_sims system test for the interatomic data design.
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r17099 | bugman | 2012-06-28 16:06:40 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for the N_state_model.test_align_fit_rand for the interatomic data design.
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r17100 | bugman | 2012-06-28 16:21:20 +0200 (Thu, 28 Jun 2012) | 5 lines
Fixes for the N_state_model.test_stereochem_analysis system test for the interatomic data design.
Now all N-state model tests pass.
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r17101 | bugman | 2012-06-28 16:46:34 +0200 (Thu, 28 Jun 2012) | 3 lines
Some more fixes for the N_state_model.test_stereochem_analysis system test.
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r17102 | bugman | 2012-06-28 17:23:49 +0200 (Thu, 28 Jun 2012) | 5 lines
Added the are_bonded() and get_molecule() methods for the Scientific Python PDB reader.
This is now needed for defining interatomic vectors in the interatomic data design.
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r17103 | bugman | 2012-06-28 17:27:37 +0200 (Thu, 28 Jun 2012) | 3 lines
Converted all of the Unit_vectors system tests to the interatomic data design.
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r17104 | bugman | 2012-06-28 17:40:26 +0200 (Thu, 28 Jun 2012) | 3 lines
The Scientific Python structural object are_bonded() now uses 2.0 Angstrom as a cutoff radius.
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r17105 | bugman | 2012-06-28 17:40:48 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for 3 of the Structure system tests for the interatomic data design.
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r17106 | bugman | 2012-06-28 18:23:47 +0200 (Thu, 28 Jun 2012) | 3 lines
The relax_io.read_spin_data() function can now handle spin IDs in quotes.
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r17107 | bugman | 2012-06-28 18:34:19 +0200 (Thu, 28 Jun 2012) | 5 lines
Fix for the rdc.read user function - values and errors of None in the file are supported again.
This was broken with the interatomic data redesign.
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r17108 | bugman | 2012-06-28 18:35:01 +0200 (Thu, 28 Jun 2012) | 3 lines
Converted another test suite RDC data file to the interatomic data design.
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r17109 | bugman | 2012-06-28 18:35:37 +0200 (Thu, 28 Jun 2012) | 3 lines
Converted the Rdc.test_rdc_load() system test to the interatomic data design.
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r17110 | bugman | 2012-06-28 19:44:16 +0200 (Thu, 28 Jun 2012) | 5 lines
Fix for the model-free _determine_model_type() method.
This should skip deselected spin rather than spins without relaxation data!
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r17111 | bugman | 2012-06-28 19:56:57 +0200 (Thu, 28 Jun 2012) | 5 lines
Updated the OMP model-free results XML files for the interatomic data container select flag.
The old files were missing the select flag.
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r17112 | bugman | 2012-06-28 20:01:26 +0200 (Thu, 28 Jun 2012) | 3 lines
Fix for the Modelim.test_te_200ns() system test for the interatomic data design.
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r17113 | bugman | 2012-06-28 20:04:03 +0200 (Thu, 28 Jun 2012) | 3 lines
Fixes for all the Relax_data system tests for the interatomic data design.
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r17123 | bugman | 2012-07-02 14:29:44 +0200 (Mon, 02 Jul 2012) | 3 lines
Updated the Modsel.test_aic_mod_sel_diff_tensor() system test of the interatomic data design.
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r17124 | bugman | 2012-07-02 14:30:51 +0200 (Mon, 02 Jul 2012) | 5 lines
Fix for the model-free analysis _assemble_param_vector() method for the new interatomic data design.
The proton spins with no parameters must be skipped.
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r17125 | bugman | 2012-07-02 15:02:34 +0200 (Mon, 02 Jul 2012) | 5 lines
Bug fix for the generic_fns.interatomic.copy() function for when no interatomic data exists.
This now returns without doing anything rather than raising a RelaxError.
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r17126 | bugman | 2012-07-02 15:33:11 +0200 (Mon, 02 Jul 2012) | 3 lines
Updated the Diffusion_tensor system test scripts to the interatomic data design.
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r17127 | bugman | 2012-07-02 15:33:56 +0200 (Mon, 02 Jul 2012) | 5 lines
Fix for the model-free back-calculation of relaxation data for the interatomic data design.
The overfit_deselect() method needs to be called to deselect the proton spin containers.
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r17128 | bugman | 2012-07-02 17:17:51 +0200 (Mon, 02 Jul 2012) | 6 lines
Improvement for the generic_fns.interatomic.return_interatom_list() function.
The spin ID matching is now through the id_match() function, allowing unique but different spin IDs
to be used. This now matches the return_interatom() behaviour.
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r17129 | bugman | 2012-07-02 17:18:45 +0200 (Mon, 02 Jul 2012) | 3 lines
Fixes for the relaxation data bmrb_write() function for the interatomic data design.
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r17130 | bugman | 2012-07-02 17:19:13 +0200 (Mon, 02 Jul 2012) | 3 lines
Fixes for the model-free analysis bmrb_write() method for the interatomic data design.
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r17131 | bugman | 2012-07-02 17:35:38 +0200 (Mon, 02 Jul 2012) | 3 lines
The sequence.attach_protons user function now ignores spins with pre-existing attached protons.
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r17132 | bugman | 2012-07-02 17:52:48 +0200 (Mon, 02 Jul 2012) | 6 lines
The generic_fns.mol_res_spin.index_molecule() function now handles no molecule name given.
If no name is given and only a single molecule is in the current data pipe, then the index of 0 will
be returned.
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r17133 | bugman | 2012-07-02 18:08:29 +0200 (Mon, 02 Jul 2012) | 3 lines
More BMRB function conversions for the interatomic data design.
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r17134 | bugman | 2012-07-02 18:18:26 +0200 (Mon, 02 Jul 2012) | 3 lines
Print out improvements for the relaxation data pack_data() function.
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r17135 | bugman | 2012-07-02 19:59:32 +0200 (Mon, 02 Jul 2012) | 3 lines
More BMRB fixes for the interatomic data design.
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r17136 | bugman | 2012-07-02 20:30:54 +0200 (Mon, 02 Jul 2012) | 3 lines
Fixes for the BMRB system tests for the interatomic data design.
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r17137 | bugman | 2012-07-02 20:53:51 +0200 (Mon, 02 Jul 2012) | 5 lines
A small speed up for the model-free duplicate_data() function.
This is used in model selection.
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r17138 | bugman | 2012-07-02 21:25:03 +0200 (Mon, 02 Jul 2012) | 3 lines
Debugging printout removal.
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r17141 | bugman | 2012-07-02 21:42:29 +0200 (Mon, 02 Jul 2012) | 3 lines
Fix for the model-free duplicate_data() method, again for the interatomic data design.
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r17143 | bugman | 2012-07-02 22:08:15 +0200 (Mon, 02 Jul 2012) | 3 lines
Updated the xh_vector_dist.py system test script to the interatomic data design.
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r17144 | bugman | 2012-07-02 22:09:16 +0200 (Mon, 02 Jul 2012) | 3 lines
Converted generic_fns.structure.geometric.create_vector_dist() to the interatomic data design.
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r17146 | bugman | 2012-07-03 09:28:28 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted generic_fns.angles.spheroid_frame() to the interatomic data design.
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r17147 | bugman | 2012-07-03 09:29:26 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Angles.test_angles() system test and associated script to the interatomic data design.
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r17148 | bugman | 2012-07-03 09:33:47 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the bruker.read user function to the interatomic data design.
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r17149 | bugman | 2012-07-03 10:18:17 +0200 (Tue, 03 Jul 2012) | 8 lines
Better backwards compatibility of old relax results and state XML files for the interatomic design.
The MoleculeContainer._back_compat_hook() method has been shifted into the
Relax_data_store._back_compat_hook() method. This allows the spin containers with attached protons
to be converted (with new spin containers for the attached protons added) after loading of the XML
state.
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r17150 | bugman | 2012-07-03 10:33:35 +0200 (Tue, 03 Jul 2012) | 3 lines
Small fix for the Relax_data_store._back_compat_hook() method.
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r17151 | bugman | 2012-07-03 11:03:15 +0200 (Tue, 03 Jul 2012) | 3 lines
Refinement and fixes for the Relax_data_store._back_compat_hook() method.
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r17152 | bugman | 2012-07-03 11:23:28 +0200 (Tue, 03 Jul 2012) | 3 lines
Fix for the state.load user function for pickled files - _back_compat_hook() is now blacklisted.
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r17153 | bugman | 2012-07-03 12:17:36 +0200 (Tue, 03 Jul 2012) | 3 lines
Fix for the spin.copy user function for GUI use.
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r17154 | bugman | 2012-07-03 12:27:16 +0200 (Tue, 03 Jul 2012) | 3 lines
Fixes for the J(w) mapping and consistency testings scripts so they can run as GUI tests.
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r17155 | bugman | 2012-07-03 12:32:41 +0200 (Tue, 03 Jul 2012) | 3 lines
Fixes for the spin.create user function for GUI usage.
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r17158 | bugman | 2012-07-03 18:19:57 +0200 (Tue, 03 Jul 2012) | 3 lines
Improved a RelaxError message from the dipole_pair.define user function backend.
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r17159 | bugman | 2012-07-03 18:20:36 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the GUI model-free auto-analysis to the interatomic data design.
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r17160 | bugman | 2012-07-03 18:21:12 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Mf.test_mf_auto_analysis() GUI test to the interatomic data design.
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r17161 | bugman | 2012-07-03 20:18:37 +0200 (Tue, 03 Jul 2012) | 3 lines
The State.test_old_state_loading() GUI test now checks the loaded data to a small extent.
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r17162 | bugman | 2012-07-03 20:20:00 +0200 (Tue, 03 Jul 2012) | 5 lines
The dipole_pair.define user function backend now can handle the pipe argument.
This allows it to operate on an alternative data pipe.
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r17163 | bugman | 2012-07-03 20:21:21 +0200 (Tue, 03 Jul 2012) | 6 lines
A number of the generic_fns.mol_res_spin functions now accept the pipe argument.
These include name_spin(), set_spin_element(), and set_spin_isotope() and this allows the functions
to operate on any data pipe.
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r17164 | bugman | 2012-07-03 20:22:55 +0200 (Tue, 03 Jul 2012) | 5 lines
Bug fix for the Relax_data_store._back_compat_hook() function for the interatomic data support.
The calls to functions of the generic_fns package need to operate on a non-current data pipe.
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r17165 | bugman | 2012-07-03 20:29:44 +0200 (Tue, 03 Jul 2012) | 3 lines
Added a wizard graphic (SVG form) for the 13C-1H dipole-dipole pair.
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r17166 | bugman | 2012-07-03 22:06:29 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Modelfree4 interface code to the interatomic data design.
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r17167 | bugman | 2012-07-03 22:07:22 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Palmer.test_palmer_omp() system test to the interatomic data design.
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r17168 | bugman | 2012-07-03 22:14:59 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Palmer.test_palmer() system test to the interatomic data design.
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r17169 | bugman | 2012-07-03 22:33:39 +0200 (Tue, 03 Jul 2012) | 3 lines
Fix for the model-free duplicate_data() method broken by the interatomic data design.
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r17170 | bugman | 2012-07-03 23:20:07 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Dasha interface code to the interatomic data design.
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r17171 | bugman | 2012-07-03 23:20:26 +0200 (Tue, 03 Jul 2012) | 3 lines
Converted the Dasha system test to the interatomic data design.
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r17172 | bugman | 2012-07-04 09:21:11 +0200 (Wed, 04 Jul 2012) | 3 lines
Converted all of the sample scripts to the interatomic data design.
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r17173 | bugman | 2012-07-04 09:21:45 +0200 (Wed, 04 Jul 2012) | 3 lines
A number of clean ups and rearrangements of the system test scripts.
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r17175 | bugman | 2012-07-04 10:40:18 +0200 (Wed, 04 Jul 2012) | 3 lines
Some small edits to clarify the sample scripts.
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r17176 | bugman | 2012-07-04 10:40:56 +0200 (Wed, 04 Jul 2012) | 3 lines
Added a new screenshot of the GUI model-free auto-analysis, as it is now quite different.
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r17177 | bugman | 2012-07-04 10:41:22 +0200 (Wed, 04 Jul 2012) | 3 lines
Converted the relax user manual to the interatomic data design.
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r17181 | bugman | 2012-07-04 11:04:30 +0200 (Wed, 04 Jul 2012) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/interatomic
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