Author: bugman
Date: Wed Dec 10 14:12:18 2014
New Revision: 27055
URL: http://svn.gna.org/viewcvs/relax?rev=27055&view=rev
Log:
Some more fixes for the Structure.test_align_molecules system test.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/st
Author: bugman
Date: Wed Dec 10 15:53:34 2014
New Revision: 27056
URL: http://svn.gna.org/viewcvs/relax?rev=27056&view=rev
Log:
Change to the Structure.test_align system test.
The molecules argument for the structure.align user function has been changed
to match the models
argument, in that it n
Author: bugman
Date: Wed Dec 10 15:56:46 2014
New Revision: 27057
URL: http://svn.gna.org/viewcvs/relax?rev=27057&view=rev
Log:
Implemented the new molecules argument for the structure.align user function.
In addition to accepting the new argument, the user function backend has been
redesigned f
Author: bugman
Date: Wed Dec 10 16:37:18 2014
New Revision: 27058
URL: http://svn.gna.org/viewcvs/relax?rev=27058&view=rev
Log:
Created the Structure.test_rmsd_molecules system test.
This will be used to implement a new molecules argument for the structure.rmsd
user function so that
the RMSD bet
Author: bugman
Date: Wed Dec 10 17:03:24 2014
New Revision: 27059
URL: http://svn.gna.org/viewcvs/relax?rev=27059&view=rev
Log:
Implemented the new molecules argument for the structure.rmsd user function.
This allows the RMSD between different molecules rather than different models
to be calcula
Author: bugman
Date: Wed Dec 10 17:07:08 2014
New Revision: 27060
URL: http://svn.gna.org/viewcvs/relax?rev=27060&view=rev
Log:
Removed some temporary printouts from the structure.align user function.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main
Author: bugman
Date: Wed Dec 10 17:20:19 2014
New Revision: 27061
URL: http://svn.gna.org/viewcvs/relax?rev=27061&view=rev
Log:
Created the Structure.test_displacement_molecules system test.
This will be used to implement the new molecules argument for the
structure.displacement user
function.
Author: bugman
Date: Wed Dec 10 17:34:55 2014
New Revision: 27062
URL: http://svn.gna.org/viewcvs/relax?rev=27062&view=rev
Log:
Implemented the molecules argument for the structure.displacement user function.
This allows the displacements (translations and rotations) to be calculated
between dif
Author: bugman
Date: Wed Dec 10 18:53:48 2014
New Revision: 27063
URL: http://svn.gna.org/viewcvs/relax?rev=27063&view=rev
Log:
Created the Structure.test_find_pivot system test.
This is to check the structure.find_pivot user function as this algorithm is
currently not being
checked in the test
Author: bugman
Date: Wed Dec 10 18:57:14 2014
New Revision: 27064
URL: http://svn.gna.org/viewcvs/relax?rev=27064&view=rev
Log:
Created the Structure.test_find_pivot_molecules system test.
This will be used to implement support for a molecules argument in the
structure.find_pivot user
function s
Author: bugman
Date: Thu Dec 11 08:37:45 2014
New Revision: 27065
URL: http://svn.gna.org/viewcvs/relax?rev=27065&view=rev
Log:
Increased the precision of pivot optimisation in the
Structure.test_find_pivot_molecules system test.
Modified:
trunk/test_suite/system_tests/structure.py
Modifie
Author: bugman
Date: Thu Dec 11 08:41:07 2014
New Revision: 27066
URL: http://svn.gna.org/viewcvs/relax?rev=27066&view=rev
Log:
Implemented the molecules argument for the structure.find_pivot user function.
This allows the motional pivot optimisation between different molecules rather
than diffe
Author: bugman
Date: Thu Dec 11 08:58:36 2014
New Revision: 27067
URL: http://svn.gna.org/viewcvs/relax?rev=27067&view=rev
Log:
Shifted the atomic assembly code from the structure.align user function into
its own function.
The new function assemble_coordinates() of the pipe_control.structure.mai
Author: bugman
Date: Thu Dec 11 09:04:35 2014
New Revision: 27068
URL: http://svn.gna.org/viewcvs/relax?rev=27068&view=rev
Log:
Changed the argument order for the structure.align user function.
The standardised order will now be pipes, models, molecules, atom_id, etc.
Modified:
trunk/pipe_c
Author: bugman
Date: Thu Dec 11 09:25:06 2014
New Revision: 27069
URL: http://svn.gna.org/viewcvs/relax?rev=27069&view=rev
Log:
Converted the structure.find_pivot user function to the new
pipes/models/molecules/atom_id design.
This allows the motional pivot algorithm to work on atomic coordinate
===
--- trunk/lib/structure/internal/coordinates.py (added)
+++ trunk/lib/structure/internal/coordinates.py Thu Dec 11 09:44:53 2014
@@ -0,0 +1,140 @@
+###
+#
Author: bugman
Date: Thu Dec 11 09:49:08 2014
New Revision: 27071
URL: http://svn.gna.org/viewcvs/relax?rev=27071&view=rev
Log:
Tooltip standardisation for the structure.align and structure.find_pivot user
functions.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_function
Author: bugman
Date: Thu Dec 11 10:02:23 2014
New Revision: 27072
URL: http://svn.gna.org/viewcvs/relax?rev=27072&view=rev
Log:
Comment fix.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_contro
Author: bugman
Date: Thu Dec 11 10:20:56 2014
New Revision: 27073
URL: http://svn.gna.org/viewcvs/relax?rev=27073&view=rev
Log:
The coordinate assembly function now returns list of unique IDs.
This is for each structural object, model and molecule.
Modified:
trunk/lib/structure/internal/coo
Author: bugman
Date: Thu Dec 11 10:33:05 2014
New Revision: 27074
URL: http://svn.gna.org/viewcvs/relax?rev=27074&view=rev
Log:
Changed the structure ID strings returned by the assemble_coord_array()
function.
This is from the lib.structure.internal.coordinates module. The structural
object na
Author: bugman
Date: Thu Dec 11 10:38:43 2014
New Revision: 27075
URL: http://svn.gna.org/viewcvs/relax?rev=27075&view=rev
Log:
More improvements for the structure ID strings returned by the
assemble_coord_array() function.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: tr
Author: bugman
Date: Thu Dec 11 10:43:48 2014
New Revision: 27076
URL: http://svn.gna.org/viewcvs/relax?rev=27076&view=rev
Log:
More improvements for the structure ID strings returned by the
assemble_coord_array() function.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: tr
Author: bugman
Date: Thu Dec 11 10:48:26 2014
New Revision: 27077
URL: http://svn.gna.org/viewcvs/relax?rev=27077&view=rev
Log:
Converted the internal structural displacement object to use unique IDs rather
than model numbers.
This allows the object to be much more flexible in what types of stru
Author: bugman
Date: Thu Dec 11 10:50:16 2014
New Revision: 27078
URL: http://svn.gna.org/viewcvs/relax?rev=27078&view=rev
Log:
Converted the structure.displacement user function to the new
pipes/models/molecules/atom_id design.
This allows the displacements to be calculated between atomic coord
Author: bugman
Date: Thu Dec 11 10:55:53 2014
New Revision: 27080
URL: http://svn.gna.org/viewcvs/relax?rev=27080&view=rev
Log:
Updated the Structure.test_displacement_molecules system test.
This is for the changes to the structure.displacement user function.
Modified:
trunk/test_suite/syst
Author: bugman
Date: Thu Dec 11 10:55:24 2014
New Revision: 27079
URL: http://svn.gna.org/viewcvs/relax?rev=27079&view=rev
Log:
Another refinement for the structure ID strings returned by the
assemble_coord_array() function.
Modified:
trunk/lib/structure/internal/coordinates.py
Modified: t
Author: bugman
Date: Thu Dec 11 11:03:54 2014
New Revision: 27081
URL: http://svn.gna.org/viewcvs/relax?rev=27081&view=rev
Log:
Docstring spelling fixes for the steady-state NOE and relaxation curve-fitting
auto-analyses.
Modified:
trunk/auto_analyses/noe.py
trunk/auto_analyses/relax_fi
Author: bugman
Date: Thu Dec 11 11:20:03 2014
New Revision: 27082
URL: http://svn.gna.org/viewcvs/relax?rev=27082&view=rev
Log:
Converted the structure.rmsd user function to the new
pipes/models/molecules/atom_id design.
This allows the RMSD calculation to work on atomic coordinates from differe
Author: bugman
Date: Thu Dec 11 11:34:24 2014
New Revision: 27083
URL: http://svn.gna.org/viewcvs/relax?rev=27083&view=rev
Log:
Created the internal structural object model_list() method.
This is to simplify the assembly of a list of all current models in the
structural object.
Modified:
t
Author: bugman
Date: Thu Dec 11 11:37:33 2014
New Revision: 27084
URL: http://svn.gna.org/viewcvs/relax?rev=27084&view=rev
Log:
Converted the structure.superimpose user function to the new
pipes/models/molecules/atom_id design.
The user function arguments have not changed, however the backend no
Author: bugman
Date: Thu Dec 11 11:42:40 2014
New Revision: 27085
URL: http://svn.gna.org/viewcvs/relax?rev=27085&view=rev
Log:
Documentation fix for the assemble_coord_array() function.
The return values for lib.structure.internal.coordinates.assemble_coord_array()
were incorrectly
documented.
Author: bugman
Date: Thu Dec 11 11:46:04 2014
New Revision: 27086
URL: http://svn.gna.org/viewcvs/relax?rev=27086&view=rev
Log:
Modified the Structure.test_bug_22070_structure_superimpose_after_deletion
system test.
This now calls the structure.align user function after calling the
structure.su
Author: bugman
Date: Thu Dec 11 11:49:26 2014
New Revision: 27087
URL: http://svn.gna.org/viewcvs/relax?rev=27087&view=rev
Log:
Fixes for the structure.superimpose and structure.align user functions.
The fit_to_mean() and fit_to_first() functions of lib.structure.superimpose
where being incorrec
Author: bugman
Date: Thu Dec 11 12:25:03 2014
New Revision: 27088
URL: http://svn.gna.org/viewcvs/relax?rev=27088&view=rev
Log:
Code refactorisation for the structure.align user function backend.
The looping over data pipes, model numbers, and molecule names, skipping those
that don't match the
Author: bugman
Date: Thu Dec 11 13:13:19 2014
New Revision: 27089
URL: http://svn.gna.org/viewcvs/relax?rev=27089&view=rev
Log:
Some docstring expansions for the pipe_control.structure.main module functions.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structu
Author: bugman
Date: Thu Dec 11 13:40:41 2014
New Revision: 27090
URL: http://svn.gna.org/viewcvs/relax?rev=27090&view=rev
Log:
Refactored the descriptions of a number of structure user functions.
This includes the structure.align, structure.displacement,
structure.find_pivot, structure.rmsd and
Author: bugman
Date: Thu Dec 11 16:00:21 2014
New Revision: 27091
URL: http://svn.gna.org/viewcvs/relax?rev=27091&view=rev
Log:
Changed the design of the
lib.structure.internal.coordinates.assemble_coord_array() function.
The elements_flag argument has been renamed to seq_info_flag. If this is
Author: bugman
Date: Thu Dec 11 16:03:42 2014
New Revision: 27092
URL: http://svn.gna.org/viewcvs/relax?rev=27092&view=rev
Log:
Fix for the structure.align user function if no data pipes are supplied.
The pipes list was no longer being created as it was shifted to the
assemble_coordinates() func
Author: bugman
Date: Thu Dec 11 16:23:46 2014
New Revision: 27093
URL: http://svn.gna.org/viewcvs/relax?rev=27093&view=rev
Log:
Bug fix for the lib.arg_check.is_int_list() function for checking a list of
lists.
This is used to check user function arguments, but was causing a RelaxError to
be ra
Author: bugman
Date: Thu Dec 11 17:13:55 2014
New Revision: 27094
URL: http://svn.gna.org/viewcvs/relax?rev=27094&view=rev
Log:
Converted the structure.web_of_motion user function to the new
pipe/model/molecule/atom_id design.
This allows the web of motion representation to work on atomic coordi
Author: bugman
Date: Thu Dec 11 17:27:20 2014
New Revision: 27095
URL: http://svn.gna.org/viewcvs/relax?rev=27095&view=rev
Log:
Fix for the IDs returned by
lib.structure.internal.coordinates.assemble_coord_array().
The list of unique structure IDs was being incorrectly constructed if multiple
m
Author: bugman
Date: Thu Dec 11 17:27:46 2014
New Revision: 27096
URL: http://svn.gna.org/viewcvs/relax?rev=27096&view=rev
Log:
Fix for the Structure.test_displacement system test for the
assemble_coord_array() function bugfix.
Modified:
trunk/test_suite/system_tests/structure.py
Modified:
Author: bugman
Date: Thu Dec 11 17:28:11 2014
New Revision: 27097
URL: http://svn.gna.org/viewcvs/relax?rev=27097&view=rev
Log:
Removed a debugging printout.
Modified:
trunk/lib/arg_check.py
Modified: trunk/lib/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/arg_check.py?rev=2
Author: bugman
Date: Thu Dec 11 18:55:25 2014
New Revision: 27098
URL: http://svn.gna.org/viewcvs/relax?rev=27098&view=rev
Log:
Modified the Structure.test_align system test to show a failure of the
structure.align user function.
The alignment causes all atoms in the structural object to be tran
Author: bugman
Date: Thu Dec 11 19:01:54 2014
New Revision: 27099
URL: http://svn.gna.org/viewcvs/relax?rev=27099&view=rev
Log:
Modified the Structure.test_superimpose_fit_to_mean system test.
This is also to demonstrate a bug, this time in the structure.superimpose user
function, in which
the a
Author: bugman
Date: Thu Dec 11 19:10:37 2014
New Revision: 27100
URL: http://svn.gna.org/viewcvs/relax?rev=27100&view=rev
Log:
Modified some system tests of the structure.align and structure.superimpose
user functions.
The displace_id argument has been introduced for both of these user function
Author: bugman
Date: Thu Dec 11 19:37:46 2014
New Revision: 27101
URL: http://svn.gna.org/viewcvs/relax?rev=27101&view=rev
Log:
Added the displace_id argument to the structure.align and structure.superimpose
user functions.
This gives both of these user functions finer control over which atoms a
Author: bugman
Date: Thu Dec 11 19:38:25 2014
New Revision: 27102
URL: http://svn.gna.org/viewcvs/relax?rev=27102&view=rev
Log:
Fixes for the Structure.test_superimpose_fit_to_mean system test for the
displace_id argument.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trun
Author: bugman
Date: Fri Dec 12 10:48:40 2014
New Revision: 27103
URL: http://svn.gna.org/viewcvs/relax?rev=27103&view=rev
Log:
Modified the Structure.test_align_molecules system test to catch a bug.
This is the failure of the displace_id argument of the structure.align user
function when the
mo
Author: bugman
Date: Fri Dec 12 10:52:24 2014
New Revision: 27104
URL: http://svn.gna.org/viewcvs/relax?rev=27104&view=rev
Log:
Fix for the displace_id and molecules arguments of the structure.align user
function.
The atom ID used for the translations and rotations is now properly constructed
f
Author: bugman
Date: Fri Dec 12 11:41:11 2014
New Revision: 27105
URL: http://svn.gna.org/viewcvs/relax?rev=27105&view=rev
Log:
Changes for water in the PDB file created by the structure.write_pdb user
function.
The waters with the residue name 'HOH' are no longer output to HET records.
Modifi
Author: bugman
Date: Fri Dec 12 12:08:20 2014
New Revision: 27106
URL: http://svn.gna.org/viewcvs/relax?rev=27106&view=rev
Log:
Improvement for the structure.read_pdb user function.
The helix and sheet secondary structure reading now takes the real_mol argument
into account to
avoid reading in t
Author: bugman
Date: Fri Dec 12 12:22:03 2014
New Revision: 27107
URL: http://svn.gna.org/viewcvs/relax?rev=27107&view=rev
Log:
Improvement for the merge argument of the structure.read_pdb user function.
This argument is now overridden if the molecule to merge to does not exist.
This allows the
Author: bugman
Date: Fri Dec 12 12:22:47 2014
New Revision: 27108
URL: http://svn.gna.org/viewcvs/relax?rev=27108&view=rev
Log:
Fix for the selective secondary structure reading of the structure.read_pdb
user function.
The molecule index needs to incremented by 1 to be the molecule number.
Mod
Author: bugman
Date: Fri Dec 12 15:36:01 2014
New Revision: 27109
URL: http://svn.gna.org/viewcvs/relax?rev=27109&view=rev
Log:
Large improvement for the PDB molecule identification code.
This affects the structure.read_pdb user function. Now the chain ID code, if
present in the PDB
file, is be
Author: bugman
Date: Fri Dec 12 16:06:47 2014
New Revision: 27110
URL: http://svn.gna.org/viewcvs/relax?rev=27110&view=rev
Log:
Expanded the displace_id argument for the structure.align user function.
This can now be a list of atom IDs, so that any atoms can be rotated together
with the structur
Author: bugman
Date: Fri Dec 12 21:48:16 2014
New Revision: 27111
URL: http://svn.gna.org/viewcvs/relax?rev=27111&view=rev
Log:
Fix for the Noe.test_bug_21562_noe_replicate_fail system test.
This is for the changed behaviour of the structure.read_pdb user function. The
problem is that the
PDB f
Author: bugman
Date: Mon Dec 15 18:44:42 2014
New Revision: 27112
URL: http://svn.gna.org/viewcvs/relax?rev=27112&view=rev
Log:
Expanded the description of the structure.rmsd user function.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structure.py
URL:
http://
Author: bugman
Date: Tue Dec 16 09:10:28 2014
New Revision: 27113
URL: http://svn.gna.org/viewcvs/relax?rev=27113&view=rev
Log:
Changed the paragraph ordering in the documentation of a number of the
structure user functions.
This includes the structure.align, structure.displacement, and
structu
Author: bugman
Date: Tue Dec 16 09:11:58 2014
New Revision: 27114
URL: http://svn.gna.org/viewcvs/relax?rev=27114&view=rev
Log:
Fix for the prompt examples documentation for the structure.align user function.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structu
Author: bugman
Date: Tue Dec 16 09:15:35 2014
New Revision: 27115
URL: http://svn.gna.org/viewcvs/relax?rev=27115&view=rev
Log:
Improved the sizing layout of the structure.align user function GUI dialog.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structure.py
Author: bugman
Date: Tue Dec 16 09:19:19 2014
New Revision: 27116
URL: http://svn.gna.org/viewcvs/relax?rev=27116&view=rev
Log:
Improved the sizing layout of the structure.superimpose user function GUI
dialog.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/struc
Author: bugman
Date: Tue Dec 16 09:26:34 2014
New Revision: 27117
URL: http://svn.gna.org/viewcvs/relax?rev=27117&view=rev
Log:
Merged revisions 27044,27052-27116 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r27044 | bugman | 2014-12-09 14:59:51 +0100 (Tue, 09 Dec 20
Author: bugman
Date: Tue Dec 16 10:01:56 2014
New Revision: 27118
URL: http://svn.gna.org/viewcvs/relax?rev=27118&view=rev
Log:
Merged revisions 26907,26925,26956,26964-26989 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
r26907 | bugman | 2014-12-03 08:50:18 +0100 (We
Author: bugman
Date: Thu Dec 18 09:11:29 2014
New Revision: 27119
URL: http://svn.gna.org/viewcvs/relax?rev=27119&view=rev
Log:
Created the Structure.test_atomic_fluctuations system test.
This will be used to implement the idea of the structure.atomic_fluctuations
user function.
Modified:
Author: bugman
Date: Thu Dec 18 09:51:58 2014
New Revision: 27120
URL: http://svn.gna.org/viewcvs/relax?rev=27120&view=rev
Log:
Small fix for the new Structure.test_atomic_fluctuations system test.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/
Author: bugman
Date: Thu Dec 18 10:00:31 2014
New Revision: 27121
URL: http://svn.gna.org/viewcvs/relax?rev=27121&view=rev
Log:
Another small fix for the Structure.test_atomic_fluctuations system test.
The matrix diagonal was incorrect.
Modified:
trunk/test_suite/system_tests/structure.py
Author: bugman
Date: Thu Dec 18 10:03:26 2014
New Revision: 27122
URL: http://svn.gna.org/viewcvs/relax?rev=27122&view=rev
Log:
Implemented the structure.atomic_fluctuations user function.
This is loosely based on the structure.web_of_motion user function and is
related to it. The user
function
Author: bugman
Date: Thu Dec 18 10:33:09 2014
New Revision: 27123
URL: http://svn.gna.org/viewcvs/relax?rev=27123&view=rev
Log:
Created 4 unit tests for the lib.io.swap_extension function.
This is in preparation for implementing the function.
Modified:
trunk/test_suite/unit_tests/_lib/test_
Author: bugman
Date: Thu Dec 18 10:35:22 2014
New Revision: 27124
URL: http://svn.gna.org/viewcvs/relax?rev=27124&view=rev
Log:
Implemented the lib.io.swap_extension() function.
This is confirmed to be fully functional by its four unit tests.
Modified:
trunk/lib/io.py
Modified: trunk/lib/i
--- trunk/lib/software/__init__.py (original)
+++ trunk/lib/plotting/__init__.py Thu Dec 18 11:05:44 2014
@@ -1,6 +1,6 @@
###
#
Author: bugman
Date: Thu Dec 18 11:15:34 2014
New Revision: 27126
URL: http://svn.gna.org/viewcvs/relax?rev=27126&view=rev
Log:
Created the Structure.test_atomic_fluctuations_gnuplot system test.
This checks the operation of the structure.atomic_fluctuations user function
when the output format
lib/plotting/api.py Thu Dec 18 12:05:07 2014
@@ -0,0 +1,53 @@
+###
+# #
+# Copyright (C) 2014 Edward d'Auvergne#
+# #
+#
unk/lib/plotting/gnuplot.py Thu Dec 18 12:07:24 2014
@@ -0,0 +1,55 @@
+###
+# #
+# Copyright (C) 2014 Edward d'Auvergne#
+#
Author: bugman
Date: Thu Dec 18 12:13:07 2014
New Revision: 27129
URL: http://svn.gna.org/viewcvs/relax?rev=27129&view=rev
Log:
Enabled the gnuplot format for the structure.atomic_fluctuations user function.
This uses the plotting API correlation_matrix() function for visualisation.
The change
Author: bugman
Date: Thu Dec 18 12:23:42 2014
New Revision: 27130
URL: http://svn.gna.org/viewcvs/relax?rev=27130&view=rev
Log:
Shifted the matrix output of the structure.atomic_fluctuations user function
into lib.plotting.text.
The new lib.plotting.text module will be used by the relax library
Author: bugman
Date: Thu Dec 18 12:25:01 2014
New Revision: 27131
URL: http://svn.gna.org/viewcvs/relax?rev=27131&view=rev
Log:
More simplifications for the structure.atomic_fluctuations user function
backend.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/stru
Author: bugman
Date: Thu Dec 18 12:28:49 2014
New Revision: 27132
URL: http://svn.gna.org/viewcvs/relax?rev=27132&view=rev
Log:
Fix for the structure.atomic_fluctuations user function backend.
The pipe_control.structure.main.atomic_fluctuations() function no longer opens
the output file.
Modif
Author: bugman
Date: Thu Dec 18 12:30:37 2014
New Revision: 27133
URL: http://svn.gna.org/viewcvs/relax?rev=27133&view=rev
Log:
The gnuplot correlation_matrix() plotting API function now creates a text file
of the data.
The lib.plotting.gnuplot.correlation_matrix() function now calls the
lib.plo
Author: bugman
Date: Thu Dec 18 16:08:32 2014
New Revision: 27134
URL: http://svn.gna.org/viewcvs/relax?rev=27134&view=rev
Log:
Significantly expanded the gnuplot script from via the correlation_matrix()
plotting API function.
This is for the structure.atomic_fluctuations user function. The out
Author: bugman
Date: Thu Dec 18 16:17:41 2014
New Revision: 27135
URL: http://svn.gna.org/viewcvs/relax?rev=27135&view=rev
Log:
Improvement in the comments from the gnuplot correlation_matrix() plotting API
function.
Modified:
trunk/lib/plotting/gnuplot.py
Modified: trunk/lib/plotting/gnup
Author: bugman
Date: Thu Dec 18 16:45:24 2014
New Revision: 27136
URL: http://svn.gna.org/viewcvs/relax?rev=27136&view=rev
Log:
Updated the Structure.test_atomic_fluctuations_gnuplot system test.
This is for the gnuplot correlation_matrix() plotting API changes which affect
the
structure.atomic_
Author: bugman
Date: Thu Dec 18 16:46:11 2014
New Revision: 27137
URL: http://svn.gna.org/viewcvs/relax?rev=27137&view=rev
Log:
Docstring fixes for the Structure.test_atomic_fluctuations_gnuplot system test.
This was pointing to the structure.rmsd user function instead of
structure.atomic_fluctu
Author: bugman
Date: Thu Dec 18 18:07:19 2014
New Revision: 27138
URL: http://svn.gna.org/viewcvs/relax?rev=27138&view=rev
Log:
Fixes and improvements for the gnuplot correlation_matrix() plotting API
function.
This is for the structure.atomic_fluctuations user function. The "pm3d map"
plot ty
Author: bugman
Date: Thu Dec 18 18:55:27 2014
New Revision: 27139
URL: http://svn.gna.org/viewcvs/relax?rev=27139&view=rev
Log:
Forced the gnuplot correlation_matrix plot to be square.
This is for the correlation_matrix() plotting API function used by the new
structure.atomic_fluctuations user fu
Author: bugman
Date: Thu Dec 18 18:57:38 2014
New Revision: 27140
URL: http://svn.gna.org/viewcvs/relax?rev=27140&view=rev
Log:
Updated the Structure.test_atomic_fluctuations_gnuplot system test.
This is for the changes of the gnuplot correlation_matrix() plotting API
function used by the
struct
Author: bugman
Date: Fri Dec 19 10:49:00 2014
New Revision: 27141
URL: http://svn.gna.org/viewcvs/relax?rev=27141&view=rev
Log:
Docstring fix for the Structure.test_atomic_fluctuations system test.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/
Author: bugman
Date: Fri Dec 19 10:49:22 2014
New Revision: 27142
URL: http://svn.gna.org/viewcvs/relax?rev=27142&view=rev
Log:
Another docstring fix for the Structure.test_atomic_fluctuations system test.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/syste
Author: bugman
Date: Fri Dec 19 11:01:02 2014
New Revision: 27143
URL: http://svn.gna.org/viewcvs/relax?rev=27143&view=rev
Log:
Created the Structure.test_atomic_fluctuations_angle system test.
This will be used to implement the mapping of inter-atomic vector angular
fluctuations between
structu
Author: bugman
Date: Fri Dec 19 11:23:46 2014
New Revision: 27144
URL: http://svn.gna.org/viewcvs/relax?rev=27144&view=rev
Log:
Implemented angular fluctuations for the structure.atomic_fluctuations user
function.
This adds the measure argument to the user function to allow either the default
o
Author: bugman
Date: Fri Dec 19 11:49:07 2014
New Revision: 27145
URL: http://svn.gna.org/viewcvs/relax?rev=27145&view=rev
Log:
Clean ups and speed ups of the structure.atomic_fluctuations user function.
Duplicate calculations are now avoided, as the SD matrix is symmetric.
Modified:
trunk/
Author: bugman
Date: Fri Dec 19 15:10:42 2014
New Revision: 27146
URL: http://svn.gna.org/viewcvs/relax?rev=27146&view=rev
Log:
Description improvements and GUI layout fixes for the
structure.atomic_fluctuations user function.
Modified:
trunk/user_functions/structure.py
Modified: trunk/use
Author: bugman
Date: Fri Dec 19 16:42:53 2014
New Revision: 27147
URL: http://svn.gna.org/viewcvs/relax?rev=27147&view=rev
Log:
Added the 'parallax shift' measure to the structure.atomic_fluctuations user
function.
The parallax shift is defined as the length of the average vector minus the
inte
Author: bugman
Date: Fri Dec 19 19:31:23 2014
New Revision: 27148
URL: http://svn.gna.org/viewcvs/relax?rev=27148&view=rev
Log:
Updated the gnuplot scripts to be executable.
These are the scripts created by the gnuplot specific correlation_matrix()
plotting API function.
The file is made executa
Author: bugman
Date: Mon Dec 22 09:09:57 2014
New Revision: 27149
URL: http://svn.gna.org/viewcvs/relax?rev=27149&view=rev
Log:
Created the Structure.test_atomic_fluctuations_parallax system test.
This is to demonstrate that the parallax shift fluctuations are not implemented
correctly.
Modifi
Author: bugman
Date: Mon Dec 22 09:19:50 2014
New Revision: 27151
URL: http://svn.gna.org/viewcvs/relax?rev=27151&view=rev
Log:
Proper implementation of the 'parallax shift' for the
structure.atomic_fluctuations user function.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/
Author: bugman
Date: Mon Dec 22 09:19:13 2014
New Revision: 27150
URL: http://svn.gna.org/viewcvs/relax?rev=27150&view=rev
Log:
Fix for the Structure.test_atomic_fluctuations_parallax system test.
The distance shifts need to be numbers, not vectors.
Modified:
trunk/test_suite/system_tests/s
Author: bugman
Date: Mon Dec 22 10:56:15 2014
New Revision: 27152
URL: http://svn.gna.org/viewcvs/relax?rev=27152&view=rev
Log:
Improved the structure.atomic_fluctuations user function documentation.
The fluctuation categories are now better explained. And the 'parallax shift'
option is now
ava
Author: bugman
Date: Tue Dec 23 11:07:45 2014
New Revision: 27153
URL: http://svn.gna.org/viewcvs/relax?rev=27153&view=rev
Log:
Fix for the parallax shift description in the structure.atomic_fluctuations
user function.
The parallax shift is not quite orthogonal to the distance fluctuations.
Mo
Author: bugman
Date: Fri Jan 9 14:17:13 2015
New Revision: 27156
URL: http://svn.gna.org/viewcvs/relax?rev=27156&view=rev
Log:
More redirects for the relax HTML manual at
http://www.nmr-relax.com/manual/index.html.
This is required as the latex2html program used to build the manual has been
mo
701 - 800 of 22585 matches
Mail list logo
