Author: bugman
Date: Wed Jul 4 11:04:16 2012
New Revision: 17180
URL: http://svn.gna.org/viewcvs/relax?rev=17180&view=rev
Log:
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@xxxxxxxxxxx/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
[... 1428 lines stripped ...]
r17180 - in /trunk: ./ auto_analyses/ data/ docs/latex/ generic_fns/ generic_fns/structure/ graphics/relax_icons/16x16/ grap...