svn+ssh://bugman@.../svn/relax/1.3
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r10937 | bugman | 2010-02-25 12:36:30 +0100 (Thu, 25 Feb 2010) | 10 lines
Addition of the relax status singleton object.
See https://mail.gna.org/public/relax-devel/2010-01/msg00094.html and other related posts in the
thread.
The idea is that various parts of relax deposit status information into here that other parts of
relax can then use. For example the Monte Carlo code can place the current simulation number in
there while the relax GUI controller can read these values.
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r10938 | bugman | 2010-02-25 13:52:35 +0100 (Thu, 25 Feb 2010) | 6 lines
The Monte Carlo simulation number is now present in the status singleton.
The value of status.mc_number is set to the simulation number (starting at 0) and at the end is
reset to None.
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r10939 | bugman | 2010-02-25 14:37:11 +0100 (Thu, 25 Feb 2010) | 11 lines
All of the relevant status information about the dAuvergne_protocol auto-analysis is being stored.
This includes:
status.dAuvergne_protocol.diff_model = None # The global diffusion model.
status.dAuvergne_protocol.round = None # The round of optimisation, i.e. the global iteration.
status.dAuvergne_protocol.mf_models = None # The list of model-free models for optimisation, i.e. the global iteration.
status.dAuvergne_protocol.local_mf_models = None # The list of model-free local tm models for optimisation, i.e. the global iteration.
status.dAuvergne_protocol.current_model = None # The current model-free model.
status.dAuvergne_protocol.convergence = False # The convergence of the global model.
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r10940 | bugman | 2010-02-25 14:59:08 +0100 (Thu, 25 Feb 2010) | 7 lines
Bug fix and updates to the generic_fns.angles.wrap_angles() function.
This was not wrapping correctly when the window was not between 0 and 2pi. Epydoc tags have been
added to the docstring, the window size can now be specified and is checked against the bounds as a
sanity check, and comments have been added all over.
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r10941 | bugman | 2010-02-25 15:15:09 +0100 (Thu, 25 Feb 2010) | 5 lines
Fix for a bug introduced in the last revision (r10940).
This affects the spherical angles used to define the spheroidal diffusion tensor major axis.
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r10942 | bugman | 2010-02-25 15:16:53 +0100 (Thu, 25 Feb 2010) | 5 lines
Added a new function fold_spherical_angles() for removing symmetry from spherical angles.
This will be useful for future use of these angles.
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r10943 | bugman | 2010-02-25 15:19:38 +0100 (Thu, 25 Feb 2010) | 5 lines
The fold_spherical_angles() performs a second wrapping in case the angles shift out of the window.
Window size checks have also been added.
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r10944 | bugman | 2010-02-25 15:25:02 +0100 (Thu, 25 Feb 2010) | 5 lines
Added default lower and upper bounds to fold_spherical_angles().
More epydoc tags have been added.
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r10945 | bugman | 2010-02-25 15:31:51 +0100 (Thu, 25 Feb 2010) | 3 lines
The spheroidal diffusion tensor major axis angles are now folded using angles.fold_spherical_angles().
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r10946 | bugman | 2010-02-25 15:55:32 +0100 (Thu, 25 Feb 2010) | 3 lines
Fix for the angles system test for the new folding of the spherical angles.
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r10947 | bugman | 2010-02-25 16:37:43 +0100 (Thu, 25 Feb 2010) | 7 lines
Removed the iteration count check in the test_opt_rigid_rand_rot() system test.
This number is different on a PowerPC chip with Mac OS X, even if the parameter values are
identical. This was identified by Jack Howarth (howarth att bromo dot med dot uc dot edu) in the
post https://mail.gna.org/public/relax-users/2010-02/msg00025.html.
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r10948 | bugman | 2010-02-26 16:36:59 +0100 (Fri, 26 Feb 2010) | 9 lines
Partially removed the need for Fink specific modifications.
This removes the need for the patch given by Jack Howarth <howarth att bromo dot med dot uc dot edu>
in the message https://mail.gna.org/public/relax-users/2010-02/msg00031.html.
A similar python specific path was being used to find Python.h on all architectures, so the include
path was copied and modified to be a bin path.
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r10949 | bugman | 2010-03-09 11:06:06 +0100 (Tue, 09 Mar 2010) | 6 lines
Bug fix for the N-state model cone PDB creation _cone_pdb() method.
The internal structural API had changed. structure.add_struct() is now called
structure.add_molecule().
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r10950 | bugman | 2010-03-09 11:11:05 +0100 (Tue, 09 Mar 2010) | 5 lines
Fix for the N-state model user function n_state_model.cone_pdb().
This was not calling the correct method.
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r10951 | bugman | 2010-03-09 11:15:26 +0100 (Tue, 09 Mar 2010) | 5 lines
Removed the pipe test from the pymol.cone_pdb() user function.
This check is not necessary as a data pipe is not needed for this.
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r10952 | bugman | 2010-03-09 11:44:48 +0100 (Tue, 09 Mar 2010) | 5 lines
Added a new module for holding class objects defining different cone types.
This currently contains the Iso_cone class with the simple method phi_max() to return the cone edge.
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r10953 | bugman | 2010-03-09 11:50:48 +0100 (Tue, 09 Mar 2010) | 5 lines
The cone_edge() method now calls a function to obtain the maximum polar angle.
The cone_edge() arg 'angle' has been changed to 'phi_max_fn'.
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r10954 | bugman | 2010-03-09 11:51:38 +0100 (Tue, 09 Mar 2010) | 3 lines
The frame order and N-state model cone_pdb() methods now use the isotropic cone object.
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r10955 | bugman | 2010-03-09 13:14:32 +0100 (Tue, 09 Mar 2010) | 3 lines
Added a new cone type in the Pseudo_elliptic class.
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r10956 | bugman | 2010-03-09 15:29:59 +0100 (Tue, 09 Mar 2010) | 3 lines
The limit_check() method has been added to the cone objects to determine if a point is inside or not.
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r10957 | bugman | 2010-03-09 19:11:18 +0100 (Tue, 09 Mar 2010) | 7 lines
Converted generate_vector_dist() to use a limit checking function and simplified the code.
The angle arrays are now returned by uniform_vect_dist_spherical_angles() so that
generate_vector_dist() can use any spherical point distribution. The max_angle arg has been changed
to limit_check so that any type of vector distribution can be created.
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r10958 | bugman | 2010-03-09 19:23:46 +0100 (Tue, 09 Mar 2010) | 5 lines
Shifted the calculation of the uniform sphere point positions into angles_uniform().
This removes this replicated code from various functions, allowing for more flexibility.
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r10961 | bugman | 2010-03-10 10:07:35 +0100 (Wed, 10 Mar 2010) | 3 lines
Modified stitch_cone_to_edge() to use the new cone limits function.
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r10962 | bugman | 2010-03-10 16:59:32 +0100 (Wed, 10 Mar 2010) | 9 lines
The diffusion tensor within the PDB frame can now be specified.
This avoids all Euler angle convention problems.
-This line, and those below, will be ignored--
M prompt/diffusion_tensor.py
M generic_fns/diffusion_tensor.py
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r10963 | bugman | 2010-03-10 17:33:53 +0100 (Wed, 10 Mar 2010) | 5 lines
Shifted the model-free _back_calc() method into the analysis specific API as back_calc_ri().
This is now being called by the relax_data.back_calc() user function.
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r10964 | bugman | 2010-03-10 17:38:17 +0100 (Wed, 10 Mar 2010) | 3 lines
The back_calc_ri() analysis specific API method has been activated.
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r10965 | bugman | 2010-03-10 17:39:33 +0100 (Wed, 10 Mar 2010) | 6 lines
Fixes for the back_calc() method.
The find_index() function was already defined (so renamed to find_ri_index()), and the analysis
specific API back_calc_ri() method was incorrectly called.
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r10966 | bugman | 2010-03-10 18:02:28 +0100 (Wed, 10 Mar 2010) | 3 lines
Comment fixes - relax handles spins, not residues now.
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r10967 | bugman | 2010-03-10 18:27:06 +0100 (Wed, 10 Mar 2010) | 5 lines
Fix for the back_calc_ri() API method.
Spins are now skipped if no bond vector information is present (for the spheroids and ellipsoids).
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r10968 | bugman | 2010-03-10 18:28:30 +0100 (Wed, 10 Mar 2010) | 3 lines
Fix for the back_calc() function - if the back-calculation returns no value, the spin is skipped.
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r10969 | bugman | 2010-03-10 18:31:25 +0100 (Wed, 10 Mar 2010) | 5 lines
Updated the generate_ri.py sample script to work with the current relax code base.
This code was old and broken. A copyright notice has been added.
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r10970 | bugman | 2010-03-10 18:45:10 +0100 (Wed, 10 Mar 2010) | 3 lines
The back-calculation of Ri data via model-free and diffusion tensors has been added to the system tests.
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r10971 | bugman | 2010-03-10 20:18:42 +0100 (Wed, 10 Mar 2010) | 3 lines
Added the cones module to the __all__ package list.
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r10972 | bugman | 2010-03-10 20:23:23 +0100 (Wed, 10 Mar 2010) | 5 lines
Added theta_max() methods to all the isotropic cone classes.
This is for determining theta from the phi polar angle.
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r10973 | bugman | 2010-03-10 20:26:26 +0100 (Wed, 10 Mar 2010) | 3 lines
Modified the cone_edge() function to add atoms for the latitude lines as well.
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r10974 | bugman | 2010-03-11 11:31:06 +0100 (Thu, 11 Mar 2010) | 3 lines
Rewrote the stitch_cone_to_edge() function to handle the arbitrarily shaped cones.
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r10975 | bugman | 2010-03-11 11:46:06 +0100 (Thu, 11 Mar 2010) | 3 lines
cone_pdb() now takes the new EDG residue for the cone edge into account.
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r10976 | bugman | 2010-03-11 13:36:22 +0100 (Thu, 11 Mar 2010) | 3 lines
Created the new fn create_cone_pdb() which can be used to create PDB file representations of cones.
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r10977 | bugman | 2010-03-11 13:40:24 +0100 (Thu, 11 Mar 2010) | 3 lines
Fix for create_cone_pdb() for when a rotation matrix is supplied.
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r10978 | bugman | 2010-03-11 13:42:36 +0100 (Thu, 11 Mar 2010) | 5 lines
Bug fix for cone_edge() for when a rotation matrix is supplied.
The latitude points were not being rotated.
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r10979 | bugman | 2010-03-11 13:44:26 +0100 (Thu, 11 Mar 2010) | 5 lines
Bug fix for create_cone_pdb() for when a rotation matrix is supplied.
The cone central axis was not being rotated!
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r10980 | bugman | 2010-03-11 13:45:57 +0100 (Thu, 11 Mar 2010) | 3 lines
Renamed the pivot point to the apex in create_cone_pdb().
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r10981 | bugman | 2010-03-11 15:54:13 +0100 (Thu, 11 Mar 2010) | 5 lines
Various point distributions can now be used for the cone PDB representations.
This includes the original 'uniform' distribution and now the 'regular' distribution.
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r10982 | bugman | 2010-03-12 10:27:05 +0100 (Fri, 12 Mar 2010) | 3 lines
Fix for the cone_edge() function for a non-zero apex position.
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r10983 | bugman | 2010-03-12 11:43:27 +0100 (Fri, 12 Mar 2010) | 6 lines
Bug fix for back_calc_ri()!
The bug was introduced at r10967. The check for missing data was not performing correctly, causing
the Monte Carlo simulations to be stuck in an infinite loop!
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r10984 | bugman | 2010-03-12 11:55:46 +0100 (Fri, 12 Mar 2010) | 5 lines
Bug fix for the generate_vector_dist() function.
The limits function was being called even if not supplied! This change fixes that.
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r10985 | bugman | 2010-03-12 15:02:29 +0100 (Fri, 12 Mar 2010) | 5 lines
Removed the pipe check from the pymol.command() user function.
This is not necessary.
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r10986 | bugman | 2010-03-12 19:20:40 +0100 (Fri, 12 Mar 2010) | 3 lines
Added the import of pymol modules to the dependency checks.
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r10987 | bugman | 2010-03-12 19:45:37 +0100 (Fri, 12 Mar 2010) | 7 lines
Started to redesign the generic_fns.pymol module to use the pymol python package.
This involves much renaming of the PyMOL pipe object which is not the PyMOL executable object. This
attempts to use the pymol python package, and if not available PyMOL will be run from the command
line as a pipe.
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r10988 | bugman | 2010-03-12 19:49:27 +0100 (Fri, 12 Mar 2010) | 3 lines
Renamed the prompt and generic_fns pymol modules to pymol_control to avoid the clash with real PyMOL.
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r10989 | bugman | 2010-03-12 19:56:55 +0100 (Fri, 12 Mar 2010) | 5 lines
Renamed the initialised PyMOL executable object from 'pymol' to 'pymol_ob'.
This is to avoid the name clash with the pymol python package.
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r10990 | bugman | 2010-03-14 12:13:15 +0100 (Sun, 14 Mar 2010) | 3 lines
Added a series of new cone types to generic_fns.structure.cones.
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r10999 | bugman | 2010-03-15 14:39:01 +0100 (Mon, 15 Mar 2010) | 6 lines
Redesigned the ImportErrorTestCase class so that the test failure clearly explains what went wrong.
The traceback is now stored and later printed, the exception is not passed in, rather strings with
the module name and traceback, and comments and docstrings have been added.
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r11000 | bugman | 2010-03-15 14:48:49 +0100 (Mon, 15 Mar 2010) | 7 lines
Copied the relax installation path into __main__.install_path.
The import of the PyMOL clobbered sys.path!!! Therefore relax does not touch this array any more.
Instead __main__.install_path is used to store where relax is installed. This should avoid all
problems with sys.path.
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r11001 | bugman | 2010-03-15 15:01:04 +0100 (Mon, 15 Mar 2010) | 3 lines
Fixes for the renaming of the pymol modules to pymol_control.
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r11002 | bugman | 2010-03-15 15:01:28 +0100 (Mon, 15 Mar 2010) | 3 lines
More fixes for the install path change to __main__.install_path.
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r11004 | bugman | 2010-03-16 00:27:51 +0100 (Tue, 16 Mar 2010) | 3 lines
Renamed the pymol modules to pymol_control in the __all__ lists and unit tests.
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r11005 | bugman | 2010-03-16 00:32:39 +0100 (Tue, 16 Mar 2010) | 5 lines
Improvements to the handling of the PyMOL Python packages.
The methods have been alphabetically ordered as well.
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r11006 | bugman | 2010-03-16 01:34:20 +0100 (Tue, 16 Mar 2010) | 6 lines
Fix for the docstring fetching script.
The relax prompt interface is no longer run as the user functions are directly located in the
_locals private dictionary.
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r11007 | bugman | 2010-03-16 01:43:32 +0100 (Tue, 16 Mar 2010) | 5 lines
Converted the user function exec_info object to be private.
This was bad in 2 ways, it was visible to the user and it was killing the fetch_docstring.py script.
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r11008 | bugman | 2010-03-16 01:52:03 +0100 (Tue, 16 Mar 2010) | 5 lines
Fixes for some error messages in fetch_docstrings.py.
This should have been writing to stderr, not sys!
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r11009 | bugman | 2010-03-16 01:55:36 +0100 (Tue, 16 Mar 2010) | 5 lines
Removed the epydoc tags from the on() and off() methods.
These are user functions, and the tags were killing fetch_docstrings.py.
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r11010 | bugman | 2010-03-16 02:13:12 +0100 (Tue, 16 Mar 2010) | 8 lines
Temporary set up the svnmerge properties to merge the bieri_gui branch back into the 1.3 line.
The command used was:
svnmerge.py init svn+ssh://bugman@.../svn/relax/branches/bieri_gui
This will be used solely to test if this branch can be merged.
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r11011 | bugman | 2010-03-16 14:20:25 +0100 (Tue, 16 Mar 2010) | 6 lines
Reverted r11004 as this, for some unknown reason, undid the changes of r11001.
The command used was:
svn merge -r11004:11003 .
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r11012 | bugman | 2010-03-16 14:26:19 +0100 (Tue, 16 Mar 2010) | 6 lines
Bug fix for the minimisation user functions.
This was introduced accidentally in r11007. The reference self._exec_info was accidentally set to
self.__exec_info.
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r11013 | bugman | 2010-03-16 15:07:25 +0100 (Tue, 16 Mar 2010) | 6 lines
Reverted the temporary r11010 for testing the merging of the bieri_gui branch.
The command used was:
svn merge -r11010:r11009 .
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r11014 | bugman | 2010-03-16 18:05:47 +0100 (Tue, 16 Mar 2010) | 30 lines
Reverted r9348 as this breaks on Mac OS X newline characters!!!! Retarded python 3.0!
The command used was:
[edau@... relax-1.3]$ svn merge -r9348:9347 .
--- Reverse-merging r9348 into '.':
U prompt/interpreter.py
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r9348 | bugman | 2009-08-21 10:50:08 +0200 (Fri, 21 Aug 2009) | 18 lines
Changed paths:
M /1.3/prompt/interpreter.py
The execfile statement has been replaced with a call to the exec(compile()) function.
This was done with the python 2.x to 3.x script with the commands:
2to3 -w -f exec relax .
The change is in preparation for Python 3.0, and relax still works with Python versions 2.4, 2.5,
and 2.6. The syntax has changed from:
execfile(script_file, local)
to:
exec(compile(open(script_file).read(), script_file, 'exec'), local)
Hmmm, not much of a language simplification!
.....
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r11015 | bugman | 2010-03-16 18:18:35 +0100 (Tue, 16 Mar 2010) | 5 lines
Fix for the ellipsoid() function for the new param_types == 3 (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) data.
The ordering Dx <= Dy <= Dz was not being used so the rhombicity was incorrectly calculated.
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r11016 | bugman | 2010-03-16 18:42:07 +0100 (Tue, 16 Mar 2010) | 5 lines
Another bug fix for the ellipsoid() function for the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter set.
The Euler angles which were in radians were being converted from deg to rad!!!
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r11017 | bugman | 2010-03-17 01:31:41 +0100 (Wed, 17 Mar 2010) | 10 lines
Creation of the NOE auto-analysis module.
This is a modified copy of the sample script created by Michael Bieri.
The key references are:
Start: https://mail.gna.org/public/relax-devel/2010-03/msg00051.html,
The file: https://mail.gna.org/public/relax-devel/2010-03/msg00052.html,
Details: https://mail.gna.org/public/relax-devel/2010-03/msg00054.html.
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r11018 | bugman | 2010-03-17 15:01:49 +0100 (Wed, 17 Mar 2010) | 7 lines
Bug fix for the local_tm_models status value.
This was identified by Daniel Pérez <daniel dott perez att mol dott biol dott ethz dott ch> in the
post at https://mail.gna.org/public/relax-users/2010-03/msg00004.html (Message-id:
<3C30C4A9-75D1-4986-9CE5-0ECA364B723B@...>).
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r11019 | bugman | 2010-03-17 18:41:46 +0100 (Wed, 17 Mar 2010) | 3 lines
Added 4 system tests for the setting ellipsoidal diffusion tensor (the 4 different param sets).
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r11020 | bugman | 2010-03-18 10:40:24 +0100 (Thu, 18 Mar 2010) | 3 lines
Added the noe module to the auto_analyses.__all__ list.
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r11021 | bugman | 2010-03-18 15:09:00 +0100 (Thu, 18 Mar 2010) | 10 lines
Final bug fix for the ellipsoid() function for the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter set.
The 2304 unique Euler angle values for a rank-2 tensor with no skew (12 axis orders, 2 frames of
ref., 2 directions (forwards + reverse), 4 rotational symmetries (pi rotations about each
eigenvector), 2 handednesses (left + right), and 6 eigenvalue orders) are now all properly handled.
The resultant Euler angle values are a single set of the 2304, matching that already used in relax
(zyz, rotated axis system, reverse direction, rotational symmetry collapse to 0 <= alpha, beta,
gamma <= pi, right handedness, and Dx <= Dy <= Dz).
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r11022 | bugman | 2010-03-18 19:24:45 +0100 (Thu, 18 Mar 2010) | 7 lines
Added relaxation data for a diffusion tensor with no internal motion.
A script has been added to generate a uniform distribution of vectors (output to PDB) and the
corresponding relaxation data for a simple ellipsoidal diffusion tensor. All vectors are rigidly
attached to the molecule.
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r11023 | bugman | 2010-03-18 19:30:01 +0100 (Thu, 18 Mar 2010) | 5 lines
The relaxation data from diffusion tensor script now calculates the data at multiple field strengths.
The new data has also been added to the repository.
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r11024 | bugman | 2010-03-18 19:47:02 +0100 (Thu, 18 Mar 2010) | 3 lines
Added the infrastructure to start to check the diffusion tensor optimisation.
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r11025 | bugman | 2010-03-18 19:48:32 +0100 (Thu, 18 Mar 2010) | 3 lines
Added errors to the diffusion tensor relaxation data.
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r11026 | bugman | 2010-03-18 19:52:27 +0100 (Thu, 18 Mar 2010) | 3 lines
The diffusion tensor optimisation script now optimises.
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r11027 | bugman | 2010-03-19 10:56:36 +0100 (Fri, 19 Mar 2010) | 3 lines
Small fix for generate_vector_dist() for when no atoms currently exist in the molecule container.
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r11028 | bugman | 2010-03-19 10:58:07 +0100 (Fri, 19 Mar 2010) | 6 lines
Fix for the internal structural object PDB writing.
The PDB format was not being followed correctly! The TER record comes after ATOM records but before
HETATM records. It is not needed if there are no ATOM records.
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r11029 | bugman | 2010-03-19 11:04:28 +0100 (Fri, 19 Mar 2010) | 3 lines
Removed the grid search and started optimisation of the ellipsoid diff tensor at the solution.
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r11030 | bugman | 2010-03-19 11:35:10 +0100 (Fri, 19 Mar 2010) | 5 lines
A few small fixes for the generate_data.py script.
The bond length is now 1.02 Angstrom.
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r11031 | bugman | 2010-03-19 14:08:27 +0100 (Fri, 19 Mar 2010) | 3 lines
The diffusion tensor system test scripts are now located in the scripts/diff_tensor directory.
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r11032 | bugman | 2010-03-19 14:17:01 +0100 (Fri, 19 Mar 2010) | 3 lines
Shifted the diffusion tensor optimisation system test to be specific to the ellipsoid.
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r11033 | bugman | 2010-03-19 14:18:05 +0100 (Fri, 19 Mar 2010) | 3 lines
Fix for the path used in the ellipsoid diff tensor optimisation script.
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r11034 | bugman | 2010-03-19 14:30:50 +0100 (Fri, 19 Mar 2010) | 3 lines
Shifted the data generation script to the base directory to be used by all tensor types.
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r11035 | bugman | 2010-03-19 14:31:58 +0100 (Fri, 19 Mar 2010) | 3 lines
Copied the script to be modified for using the module in the parent directory.
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r11036 | bugman | 2010-03-19 14:37:05 +0100 (Fri, 19 Mar 2010) | 3 lines
test_suite.shared_data.diffusion_tensor.generate_data is now a module and used by the ellipsoid.
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r11037 | bugman | 2010-03-19 14:40:42 +0100 (Fri, 19 Mar 2010) | 3 lines
Relaxation data for the sphere and spheroid is now being generated.
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r11038 | bugman | 2010-03-19 14:48:22 +0100 (Fri, 19 Mar 2010) | 3 lines
Created the sphere and spheroid diffusion tensor optimisation system tests.
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r11039 | bugman | 2010-03-19 14:51:52 +0100 (Fri, 19 Mar 2010) | 3 lines
Modified the diffusion tensor optimisation system test script for stand-alone operation.
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r11040 | bugman | 2010-03-19 15:01:44 +0100 (Fri, 19 Mar 2010) | 3 lines
The optimised spherical diffusion tensor data is now being checked.
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r11041 | bugman | 2010-03-19 15:04:17 +0100 (Fri, 19 Mar 2010) | 3 lines
Copied the tensor_opt.py script to start testing the relaxation data back calculation by relax.
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r11042 | bugman | 2010-03-19 15:22:09 +0100 (Fri, 19 Mar 2010) | 3 lines
Modified the ri_back_calc.py to back calculate the relaxation data for the given tensor.
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r11043 | bugman | 2010-03-19 15:34:21 +0100 (Fri, 19 Mar 2010) | 6 lines
Fix for the generate_data.pdb() function.
The returned vectors are now rotated to the diffusion tensor frame and are rearranged to match the
PDB file residue ordering.
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r11044 | bugman | 2010-03-19 15:46:53 +0100 (Fri, 19 Mar 2010) | 3 lines
Added system tests checking the back-calculated relaxation data for all diffusion tensor types.
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r11045 | bugman | 2010-03-19 16:49:14 +0100 (Fri, 19 Mar 2010) | 3 lines
The values from the ellipsoid optimisation is now carefully checked.
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r11046 | bugman | 2010-03-19 17:13:25 +0100 (Fri, 19 Mar 2010) | 5 lines
Fix for the tensor_setup() function.
The Dx, Dy, and Dz values were not being used (they were hardcoded).
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r11047 | bugman | 2010-03-19 17:23:31 +0100 (Fri, 19 Mar 2010) | 3 lines
The unit bond vector is now normalised - just in case - in the ri_data() function.
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r11048 | bugman | 2010-03-19 18:39:55 +0100 (Fri, 19 Mar 2010) | 5 lines
The PDB vectors are no longer rotated.
However the vectors are now rotated into the diffusion frame for the calculation of the relaxation data.
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r11049 | bugman | 2010-03-19 18:41:54 +0100 (Fri, 19 Mar 2010) | 5 lines
Bug fixes for the ri back-calculation and diff tensor optimisation system test scripts.
The angles units of radians needs to be specified!
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r11050 | bugman | 2010-03-21 22:45:31 +0100 (Sun, 21 Mar 2010) | 6 lines
Improvement for the relaxation data back-calculated for the diffusion tensors.
The back-calculated relaxation data now taked the truncation of the atom positions in the PDB into
account.
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r11053 | bugman | 2010-03-29 11:50:39 +0200 (Mon, 29 Mar 2010) | 5 lines
Modified the spheroid diffusion tensor data generation so that Z is the symmetry axis.
This will allow direct mapping of Euler angles to spherical angles!
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r11054 | bugman | 2010-03-29 14:46:43 +0200 (Mon, 29 Mar 2010) | 3 lines
Fixes for the tests of the spheroid diffusion tensor.
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r11055 | bugman | 2010-03-29 17:24:46 +0200 (Mon, 29 Mar 2010) | 3 lines
The unit bond vectors are now normalised using the numpy.linalg.norm() function.
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r11056 | bugman | 2010-03-29 17:27:15 +0200 (Mon, 29 Mar 2010) | 5 lines
The simulation of PDB coordinate truncation now occurs after vector scaling by r.
This should now be a more accurate representation and allow relax to find these values exactly.
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r11057 | bugman | 2010-03-29 17:40:08 +0200 (Mon, 29 Mar 2010) | 3 lines
The spheroid diffusion tensor optimisation test now checks the values.
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r11058 | bugman | 2010-03-29 17:41:46 +0200 (Mon, 29 Mar 2010) | 3 lines
The ellipsoidal diff tensor relaxation data was not fully regenerated in r11056.
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r11059 | bugman | 2010-03-29 17:44:32 +0200 (Mon, 29 Mar 2010) | 6 lines
The ellipsoidal diff tensor check in check_ellipsoid() now functions better.
The diffusion elements are scaled down to the order of 1 so that the assertAlmostEqual() calls do
not fail with tiny machine precision differences.
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r11070 | bugman | 2010-04-12 15:25:06 +0200 (Mon, 12 Apr 2010) | 5 lines
Bug fix - 'local_mf_model' should have been called 'local_tm_model'.
This problem was identified by Michael (http://gna.org/task/?6847#comment44).
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r11071 | bugman | 2010-04-12 16:54:23 +0200 (Mon, 12 Apr 2010) | 8 lines
Correct repetitions spectra (again...)
This corresponds to the patch patch_load__correct_repetitions_spectra from Michael (in
http://gna.org/support/download.php?file_id=8921).
Repeated spectra are set correctly and unresolved file is read correctly.
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r11085 | bugman | 2010-04-14 09:22:27 +0200 (Wed, 14 Apr 2010) | 6 lines
Fix for bug #15874 (http://gna.org/bugs/?15874).
A truth condition was being asked of a numpy array. This is not allowed. It is now checked against
None!
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r11087 | bugman | 2010-04-20 11:44:35 +0200 (Tue, 20 Apr 2010) | 5 lines
Added some calls to value.display() and value.write().
This demonstrates the failure of these user functions!
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r11088 | bugman | 2010-04-20 11:46:14 +0200 (Tue, 20 Apr 2010) | 5 lines
Fix for 3 of the 'value' user functions.
These were calling the non-existent self.__relax__.
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r11089 | bugman | 2010-04-20 11:47:52 +0200 (Tue, 20 Apr 2010) | 5 lines
Fix for the molmol.clear_history() user function.
This was calling the non-existent self.__relax__ structure.
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r11090 | bugman | 2010-04-20 13:49:47 +0200 (Tue, 20 Apr 2010) | 3 lines
Wrote the back end for the rdc.display() and rdc.write() user functions.
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r11091 | bugman | 2010-04-20 14:42:53 +0200 (Tue, 20 Apr 2010) | 3 lines
Wrote the back end for the pcs.display() and pcs.write() user functions.
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r11092 | bugman | 2010-04-21 11:00:41 +0200 (Wed, 21 Apr 2010) | 3 lines
Added 2 system tests for alignment tensor optimisation using DNA PCS data.
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r11093 | bugman | 2010-04-21 12:22:09 +0200 (Wed, 21 Apr 2010) | 5 lines
Clean up of the RDC and PCS modules.
All the residual code from the relax_data module has been eliminated.
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r11094 | bugman | 2010-04-21 14:22:15 +0200 (Wed, 21 Apr 2010) | 5 lines
Added a call to pcs.display() in the DNA PCS system test.
This is to test out the operation of this user function.
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r11095 | bugman | 2010-04-21 15:37:04 +0200 (Wed, 21 Apr 2010) | 3 lines
Fix for the RDC and PCS display() and write() user functions for when no errors exist.
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r11096 | bugman | 2010-04-21 15:38:59 +0200 (Wed, 21 Apr 2010) | 5 lines
Docstring fix for the read() function.
This is the PCS, not RDC.
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r11097 | bugman | 2010-04-21 15:39:50 +0200 (Wed, 21 Apr 2010) | 3 lines
Removal of a few unused imports.
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r11098 | bugman | 2010-04-21 17:52:06 +0200 (Wed, 21 Apr 2010) | 5 lines
Added calls to rdc.display() and pcs.display() to the lactose N-state model system test.
This adds more checks for these user functions.
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r11099 | bugman | 2010-04-21 19:14:32 +0200 (Wed, 21 Apr 2010) | 5 lines
Converted the spin RDC and PCS data structures to dictionaries using align_id as a key.
This is a big structural update which solves many problems with incomplete data.
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r11144 | bugman | 2010-04-27 16:04:51 +0200 (Tue, 27 Apr 2010) | 6 lines
Created some test RDC and PCS data to test the handling of missing data.
This includes entire data sets missing, spins missing from one type of data, and individual spins
missing.
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r11145 | bugman | 2010-04-27 16:08:02 +0200 (Tue, 27 Apr 2010) | 5 lines
Wrote a script for testing the missing RDC and PCS data.
This uses the N-state model with N=1, so direct testing of the single state to 4 tensors.
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r11146 | bugman | 2010-04-27 16:17:54 +0200 (Tue, 27 Apr 2010) | 5 lines
Created the test_missing_data N-state model system test.
This should pull out a few hard to find bugs.
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r11147 | bugman | 2010-04-27 16:20:11 +0200 (Tue, 27 Apr 2010) | 5 lines
Loosened a value check in the test_pcs_fit_zero_pos N-state model system test.
This was sometimes failing, but the value was correct enough.
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r11148 | bugman | 2010-04-27 16:22:01 +0200 (Tue, 27 Apr 2010) | 5 lines
Created a truncated version of the LE.pdb file for the RDC and PCS system tests.
This contains just the atoms for PCS and RDCs, and will significantly speed up the tests.
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r11149 | bugman | 2010-04-27 17:05:09 +0200 (Tue, 27 Apr 2010) | 5 lines
Modified the dna_pcs_fit.py N-state model system test script to use the truncated PDB file.
This speeds the system test up by orders of magnitude.
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r11150 | bugman | 2010-04-27 17:30:47 +0200 (Tue, 27 Apr 2010) | 3 lines
Fixes for the structure.load_spins() user function docstring for RNA/DNA work.
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r11151 | bugman | 2010-04-27 17:35:45 +0200 (Tue, 27 Apr 2010) | 3 lines
Removed a debugging print statement.
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r11152 | bugman | 2010-04-27 17:45:01 +0200 (Tue, 27 Apr 2010) | 6 lines
Bug fix for the __det_pdb_element() method.
RNA PDB files with missing element information is now handled properly. The stripping of the "'"
was being ignored.
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r11153 | bugman | 2010-04-27 17:55:04 +0200 (Tue, 27 Apr 2010) | 7 lines
Big bug fixes for the _minimise_setup_pcs() and _minimise_setup_rdcs() methods.
This allows the missing data PCS and RDC optimisation system test to pass. Many problems were
solved to allow all types of data with anything missing (one spin in one alignment, one spin in all
RDC or all PCS lists, or entire RDC or PCS lists for one alignment).
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r11154 | bugman | 2010-04-27 17:58:00 +0200 (Tue, 27 Apr 2010) | 7 lines
The n_state_model.select_model() user function can now change the model.
Previously a RelaxError was thrown, but now a warning is given that the model is changing. This
allows the 'population' N-state model to be optimised by first optimising the 'fixed' model and then
switching to 'population'.
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r11155 | bugman | 2010-04-27 17:59:14 +0200 (Tue, 27 Apr 2010) | 3 lines
Fixed the Q-factor calculating functions to handle missing RDC or PCS lists.
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r11156 | bugman | 2010-04-27 18:03:40 +0200 (Tue, 27 Apr 2010) | 5 lines
Forked the test_lactose_n_state() system test for both the 'population' and 'fixed' models.
The 2 new system tests are test_lactose_n_state_fixed() and test_lactose_n_state_population().
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r11157 | bugman | 2010-04-27 18:15:55 +0200 (Tue, 27 Apr 2010) | 6 lines
Implemented dfunc_tensor_opt() and d2func_tensor_opt() allowing all optimisation algorithms to be used.
The 'fixed' N-state model can now be optimised using Newton optimisation. On my machine, the
performance vs. Nelder-Mead simplex for ~20 states is a drop from ~1 hour to less than one minute!
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r11158 | bugman | 2010-04-27 18:39:26 +0200 (Tue, 27 Apr 2010) | 6 lines
Created a system test for the 'population' N-state model with missing data.
This should thoroughly test out this model! First the 'fixed' model is optimised, and then the
'population' model optimised from that starting point. This is to keep the test fast.
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r11159 | bugman | 2010-04-27 18:51:21 +0200 (Tue, 27 Apr 2010) | 3 lines
Modified the RDC and PCS read() function to not add align_id to the cdp structures if no data is present.
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r11160 | bugman | 2010-04-27 18:57:55 +0200 (Tue, 27 Apr 2010) | 5 lines
Removed the calls to rdc.display() and pcs.display().
These were rightfully failing for the empty data lists, so should not be tested.
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r11161 | bugman | 2010-04-27 20:11:41 +0200 (Tue, 27 Apr 2010) | 3 lines
Added the pymol_macro method to the specific object API.
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r11162 | bugman | 2010-04-28 11:26:03 +0200 (Wed, 28 Apr 2010) | 5 lines
The weights of each state are now set to equal probability prior to the 'population' opt.
This is in the 'population' N-state model system test script.
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r11163 | bugman | 2010-04-28 16:35:26 +0200 (Wed, 28 Apr 2010) | 6 lines
Huge bug fix for the 'population' N-state model.
The probabilities of each state was being set to that of the last state. This is fatal for this
model. Earlier code did not have this problem, but it is unknown when this bug was introduced.
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r11164 | bugman | 2010-04-28 17:04:06 +0200 (Wed, 28 Apr 2010) | 5 lines
Fix for the _update_model() method for handling missing RDC and PCS data.
The alignment tensor initialisation order was being mixed up!
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r11165 | bugman | 2010-04-28 17:50:40 +0200 (Wed, 28 Apr 2010) | 6 lines
Another fix for _update_model().
This was introduced in the last change. The alignment tensors are only updated if alignment data
is loaded.
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r11166 | bugman | 2010-04-28 18:53:08 +0200 (Wed, 28 Apr 2010) | 5 lines
Another fix for the huge bug identified in r11163.
This is for the PCS part - this was also using equal weights for all states set to pN!
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r11167 | bugman | 2010-04-28 19:48:53 +0200 (Wed, 28 Apr 2010) | 5 lines
Bug fix for the 'population' N-state model optimisation.
Constraints must be used at all times for this to work!!!
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r11168 | bugman | 2010-04-29 14:52:20 +0200 (Thu, 29 Apr 2010) | 7 lines
Bug fix for the N-state model 'fixed' and 'population' models.
If too many tensors are initialised in comparison to PCS and RDC alignments, then the parameter
vector or parameter number was not being correctly assembled. The cdp.align_ids is now being used
to validate all setups.
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r11169 | bugman | 2010-04-29 15:38:02 +0200 (Thu, 29 Apr 2010) | 3 lines
Updated and corrected all the Hessian method docstrings.
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r11170 | bugman | 2010-04-29 19:00:51 +0200 (Thu, 29 Apr 2010) | 5 lines
Created the d2func_population() Hessian target function for the N-state model.
This may either be buggy or too sparse to run Newton optimisation well!
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r11171 | bugman | 2010-04-29 19:06:52 +0200 (Thu, 29 Apr 2010) | 3 lines
Updates to the 'population' N-state model system test script.
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r11172 | bugman | 2010-05-03 00:52:26 +0200 (Mon, 03 May 2010) | 7 lines
Bug fix for when structural models are loaded out of order.
Now the API generator method model_loop() is being used by the scientific python and internal
structural objects. The bond vectors and atomic positions are now loaded into the spin containers
in correct numerical model order.
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r11173 | bugman | 2010-05-03 00:54:06 +0200 (Mon, 03 May 2010) | 5 lines
Added 3 system tests for the correct loading of XH bond vectors into the spin containers.
This catches the previously fixed model looping bug.
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r11174 | bugman | 2010-05-03 00:57:22 +0200 (Mon, 03 May 2010) | 7 lines
Bug fix for a very long standing bug!
This is the 'population' N-state model bug whereby the last probability, which is not a parameter,
has a negative value. The constraint was not being scaled! So the constraint was actually a
probability 0 <= pN <= 100!!!
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r11175 | bugman | 2010-05-03 01:05:30 +0200 (Mon, 03 May 2010) | 3 lines
Shorted the 'population' N-state model system test and randomise the model loading order.
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r11185 | bugman | 2010-05-11 16:48:07 +0200 (Tue, 11 May 2010) | 3 lines
Added some checks to properly inform the user as to what data is missing.
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r11186 | bugman | 2010-05-14 15:53:21 +0200 (Fri, 14 May 2010) | 3 lines
Docstring fix for the vect_dist_spherical_angles() function.
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r11187 | bugman | 2010-05-18 14:15:13 +0200 (Tue, 18 May 2010) | 5 lines
Added a check for the RDC RMS based Q-factor.
This is to check that relax matches both of Pales' Q-factors - which it does.
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r11188 | bugman | 2010-05-18 17:54:30 +0200 (Tue, 18 May 2010) | 3 lines
Broke some nasty circular import caused by importing the generic_fns.grace module.
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r11189 | bugman | 2010-05-18 18:32:14 +0200 (Tue, 18 May 2010) | 3 lines
Set names are now only written if they are not None.
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r11206 | bugman | 2010-05-19 10:49:53 +0200 (Wed, 19 May 2010) | 8 lines
Created the rdc.corr_plot() and pcs_corr_plot() user functions.
These are for creating correlation plots of measured vs. back-calculated RDCs and PCSs.
A couple of N-state model methods (return_grace_string() and return_units()) were added to allow the
user functions to work.
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r11207 | bugman | 2010-05-19 11:31:30 +0200 (Wed, 19 May 2010) | 6 lines
Added a maximum global iteration arg and check into the dauvergne_protocol.py module.
This was requested by Michael in the commit for r11194 at
https://mail.gna.org/public/relax-commits/2010-05/msg00022.html.
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r11208 | bugman | 2010-05-20 09:24:42 +0200 (Thu, 20 May 2010) | 16 lines
Bug fix for catching the looping around the universal solution in the dauvergne_protocol module.
This was first identified by Seb in the post at
https://mail.gna.org/public/relax-users/2007-09/msg00010.html (Message-id:
<46EEA6B2.90606@...>).
The problem was the automatic looping over optimisation cycles in the full_analysis.py script. This
code is now in the dauvergne_protocol auto_analyses module. The issue was a never-ending looping
around the universal solution (the optimisation minimum combined with Occam's razor or the model
selection minimum). This should now be caught and the protocol terminated at the end of the first
completed loop. The fix was to compare the chi2, selected models, diffusion tensor, and model-free
parameters to every iteration, starting from the first. This will not be optimal if the protocol is
interrupted in the middle of one such loop, but will just mean that a few extra iterations will be
required to complete the loop.
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r11209 | bugman | 2010-05-21 16:17:46 +0200 (Fri, 21 May 2010) | 3 lines
Modified the relax checklist to include minfx bundling.
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r11210 | bugman | 2010-05-21 16:59:46 +0200 (Fri, 21 May 2010) | 3 lines
More updates to the release checklist.
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r11223 | bugman | 2010-06-08 14:40:49 +0200 (Tue, 08 Jun 2010) | 3 lines
The RDC and PCS correlation plots now do not show deselected spins.
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r11224 | bugman | 2010-06-09 09:54:56 +0200 (Wed, 09 Jun 2010) | 5 lines
Small fix for the grace.write_xy_header() function.
The symbol numbers now range only between the legal values of 1 to 10.
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r11230 | bugman | 2010-06-11 13:46:02 +0200 (Fri, 11 Jun 2010) | 3 lines
Bug fix for the control of PyMOL (as a module).
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r11231 | bugman | 2010-06-11 14:02:28 +0200 (Fri, 11 Jun 2010) | 6 lines
Added a method for translating pymol.cmd.do() commands into specific pymol.cmd functions.
This prevents problems with commands being executed asynchronously. For example images were being
saved before ray-tracing was complete.
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r11232 | bugman | 2010-06-11 14:56:04 +0200 (Fri, 11 Jun 2010) | 6 lines
Reverted r11231 as this is not the best way to control pymol.
The command used was:
svn merge -r11231:11230 .
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r11233 | bugman | 2010-06-11 15:47:25 +0200 (Fri, 11 Jun 2010) | 5 lines
The PyMOL module pymol.cmd is now available within the pymol user function class.
This is accessible as pymol.cmd from the prompt/script interface.
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r11236 | bugman | 2010-06-12 17:33:38 +0200 (Sat, 12 Jun 2010) | 14 lines
Merged r11234 from the 1.3.5 tag into the 1.3 line.
The command used was:
svn merge -r11233:11234 svn+ssh://bugman@.../svn/relax/tags/1.3.5 .
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r11234 | bugman | 2010-06-12 17:23:16 +0200 (Sat, 12 Jun 2010) | 3 lines
Changed paths:
M /tags/1.3.5/scons/manuals.py
Excluded minfx from the API manual compilation.
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r11240 | bugman | 2010-06-12 18:17:47 +0200 (Sat, 12 Jun 2010) | 6 lines
Manually merged the 1.3.5 CHANGES file back into the main line.
The command used was:
svn merge -r11225:11226 svn+ssh://bugman@.../svn/relax/tags/1.3.5 .
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