Author: bugman
Date: Fri Oct 2 11:41:42 2015
New Revision: 27939
URL: http://svn.gna.org/viewcvs/relax?rev=27939&view=rev
Log:
Merged revisions
24433-24436,24441-24444,24449-24451,24455,24457-24459,24461-24499,24504,24506,24509
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
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r24433 | bugman | 2014-07-03 15:04:20 +0200 (Thu, 03 Jul 2014) | 8 lines
Redesign of the average domain position part of the frame_order.pdb_model
user function.
The Monte Carlo simulations are now represented. If the file root is set
to the default of
'ave_pos', then these will be placed in the file 'ave_pos.pdb', or a
compressed version. Each
simulation is in a different model, matching the geometric representation
'*_sim.pdb' files. The
original structure is copied for each model, and then rotated to the MC
simulation average position.
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r24434 | bugman | 2014-07-03 15:25:47 +0200 (Thu, 03 Jul 2014) | 6 lines
Change all of the domain user function calls in the frame order CaM test
data scripts.
The domains are now identified by the molecule name rather than the range
of residues. This allows
non-protein atoms, for example the Ca2+ atoms, to be rotated to the average
domain position as well.
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r24435 | bugman | 2014-07-03 15:44:41 +0200 (Thu, 03 Jul 2014) | 8 lines
The PyMOL disable command is now used by the pymol.frame_order user
function.
This is to first disable all PyMOL objects prior to loading anything, to
hide the original
structures and any previous frame order representations, and then to hide
all of the Monte Carlo
simulation representations. This is to simplify the picture initially
presented to the user while
still allowing all elements to be easily found.
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r24436 | bugman | 2014-07-03 15:45:01 +0200 (Thu, 03 Jul 2014) | 3 lines
Removed a debugging printout.
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r24441 | bugman | 2014-07-03 17:16:15 +0200 (Thu, 03 Jul 2014) | 3 lines
The pymol.frame_order user function now centers and zooms on all objects.
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r24442 | bugman | 2014-07-03 17:48:36 +0200 (Thu, 03 Jul 2014) | 7 lines
Simplified the PyMOL view commands in all of the CaM test data optimisation
scripts.
The pymol.view user function is not necessary as the PyMOL GUI will be
launched by the
pymol.frame_order user function. And the pymol.command user function call
for running the 'hide
all' command is also now redundant.
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r24443 | bugman | 2014-07-03 17:55:53 +0200 (Thu, 03 Jul 2014) | 6 lines
Removed all remaining uncompressed PDB files from the CaM test data
directories.
These were complicating the debugging of the pymol.frame_order user
function, as they were being
loaded on top of the compressed versions.
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r24444 | bugman | 2014-07-03 17:58:05 +0200 (Thu, 03 Jul 2014) | 5 lines
Removed some rotation files from the CaM frame order test data directories.
These files are no longer of any use and just take up large amounts of room
for nothing.
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r24449 | bugman | 2014-07-04 10:34:56 +0200 (Fri, 04 Jul 2014) | 12 lines
Added titles to the frame order geometric representation PDB files from
frame_order.pdb_model.
These are in the form of special Ti atoms placed 40 Angstrom away from the
pivot along the z-axis of
the system, or shifted 3 more Angstrom for the Monte Carlo simulations.
These are used to label the
alternative representations or the Monte Carlo simulation representations.
The residue type is set
to TLE and this has been registered in the internal structural object.
The pymol.frame_order user function now calls the represent_titles()
function to select these atoms,
hide them, and then add a long descriptive title. The atom name is used to
distinguish between
different titles.
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r24450 | bugman | 2014-07-04 10:47:05 +0200 (Fri, 04 Jul 2014) | 12 lines
Changed the alternative representation names for the frame order geometric
objects.
The aim is to put both representations on a more equal footing, as they are
identical solutions.
Hence the inverted representation might be the correct representation of
the domain motions. So
instead of calling these 'positive' and 'negative', the 'A' and 'B'
notation will be used.
This affects the names of the files produced by the frame_order.pdb_model
user function as well as
the internal titles. Instead of ending the files with "*_pos.*" and
""*_neg.*", these have been
changed to "*_A.*" and ""*_B.*". The atoms used for the titles have also
been renamed, and the
pymol.frame_order user function now labels the titles using the 'A' and 'B'
notation.
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r24451 | bugman | 2014-07-04 11:02:51 +0200 (Fri, 04 Jul 2014) | 7 lines
Changes to the rotor object in the frame order geometric representations.
For the isotropic and pseudo-elliptic cone models, the rotor is now halved.
Instead of having two
axes radiating from the central pivot and terminating in the propeller
blades, now only the positive
axis is shown lying in the centre of the cone.
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r24455 | bugman | 2014-07-04 12:00:51 +0200 (Fri, 04 Jul 2014) | 6 lines
Fixes for the MC simulation rotor objects in the frame order geometric
representation.
The axes of the Monte Carlo simulation rotors objects were being set to the
original values and not
to the simulation values.
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r24457 | bugman | 2014-07-04 15:19:18 +0200 (Fri, 04 Jul 2014) | 5 lines
Fixes for the titles in the frame order geometric representation from
frame_order.pdb_model.
There were a few bugs for a number of the frame order models preventing
this code from working.
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r24458 | bugman | 2014-07-04 15:25:04 +0200 (Fri, 04 Jul 2014) | 3 lines
Added the geometric module to the specific_analyses.frame_order package
__all__ list.
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r24459 | bugman | 2014-07-04 15:38:30 +0200 (Fri, 04 Jul 2014) | 16 lines
Redesign of the geometric representation of the cone structural objects to
allow for models.
The old representation was not compatible with the PDB model concept
whereby each model must have
the same number of atoms. To handle this situation, the cone objects have
been simplified.
Specifically the cone cap.
The old behaviour was to remove all points outside of the cone when
creating the cone cap, and then
to stitch the cap to the cone edge in a subsequent step. Now the behaviour
is that all points
outside of the distribution are shifted to the cone edge. This avoids the
need to stitch the cap to
the edge. This behaviour means that all cones with the same inc value will
have the same number of
atoms.
The cones for the pseudo-ellipses are not as nice as the latitudinal lines
are not strait at the
cone edge, but at least creating multiple models with different cone sizes
is now possible.
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r24461 | bugman | 2014-07-05 14:39:55 +0200 (Sat, 05 Jul 2014) | 5 lines
Bug fix for the y-axis rotation matrix for the double rotor Sobol'
integration points.
The matrix was inverted.
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r24462 | bugman | 2014-07-05 15:53:30 +0200 (Sat, 05 Jul 2014) | 17 lines
Reverted r24332 as this was incorrect - the data input was wrong, not the
frame order matrix.
The command used was:
svn merge -r24332:r24331 .
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r24332 | bugman | 2014-06-26 16:29:46 +0200 (Thu, 26 Jun 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/lib/frame_order/double_rotor.py
Fix for the double rotor frame order matrix assembly function.
The rotations where applied in reverse, hence the 2nd degree frame order
matrix was the Kronecker
product transpose of the correct form.
.....
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r24463 | bugman | 2014-07-05 19:06:09 +0200 (Sat, 05 Jul 2014) | 9 lines
Converted all frame order target function data structures to float64.
This affects the vector data structures used for the PCS numeric
integration. The float32
structures added for speed do not actually increase the speed. For the
double rotor model, 10
target function calls took the pcs_pivot_motion_double_rotor() function
44.936 seconds using float32
and 44.105 seconds using all float64. The cumulative time is also longer.
This must be because
other parts are float64, and therefore type conversions are happening
during target function calls.
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r24464 | bugman | 2014-07-05 20:29:37 +0200 (Sat, 05 Jul 2014) | 3 lines
Updated the frame order system test chi-squared values for the fix of
r24461.
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r24465 | bugman | 2014-07-05 20:37:38 +0200 (Sat, 05 Jul 2014) | 6 lines
Fixes for the double rotor frame order system tests for the CaM synthetic
data.
The torsion angles needed to be swapped and the pivot point changed from
the C terminal domain CoM
to the N domain CoM.
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r24466 | bugman | 2014-07-05 20:46:51 +0200 (Sat, 05 Jul 2014) | 5 lines
More fixes for the double rotor frame order system tests for the CaM
synthetic data.
The eigensystem was inverted.
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r24467 | bugman | 2014-07-05 20:47:53 +0200 (Sat, 05 Jul 2014) | 5 lines
Updated the chi2 check for the large angle double rotor frame order system
tests.
This is needed for the eigenframe fix.
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r24468 | bugman | 2014-07-05 20:51:40 +0200 (Sat, 05 Jul 2014) | 5 lines
Updates for the frame order system tests for the float32 to float64 change
(r24463).
Some chi-squared values have slightly changed.
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r24469 | bugman | 2014-07-05 23:10:54 +0200 (Sat, 05 Jul 2014) | 6 lines
The CaM frame order test data optimisation scripts now save more state
files.
The state of the true dynamics and the fixed pivot optimisation results are
now stored as well.
This might be useful for extracting these results without redoing the
calculations.
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r24470 | bugman | 2014-07-05 23:18:19 +0200 (Sat, 05 Jul 2014) | 5 lines
The script for representing the frame order dynamics for the CaM test data
has been updated.
The domains of the system are now defined.
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r24471 | bugman | 2014-07-07 09:34:02 +0200 (Mon, 07 Jul 2014) | 13 lines
Changed the CaM frame order test data superimposition values.
Because the domains are now defined via the molecule name rather than the
residue numbers, the
centroid of rotation set to the CoM has been shifted as now the Ca2+ ions
are included in the CoM
calculation. Therefore the superimpose.py script has been updated to not
delete the Ca atoms (this
reverts r23354).
All of the frame order optimisation scripts have been updated with the new
rotation Euler angles and
translation vector. To match this, the system test base script for the CaM
frame order test data
has also had its rotations and translations updates, and the domain user
function call changed to
use molecule names.
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r24472 | bugman | 2014-07-07 09:58:19 +0200 (Mon, 07 Jul 2014) | 5 lines
Updated all of the CaM frame order system test chi-squared values.
These have changed slightly due to the rotation and translation changes
(r24471).
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r24473 | bugman | 2014-07-07 16:28:29 +0200 (Mon, 07 Jul 2014) | 5 lines
Added support for the 'pivot_disp' frame order parameter to the grid search.
This is required for the double rotor model.
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r24474 | bugman | 2014-07-07 16:57:24 +0200 (Mon, 07 Jul 2014) | 6 lines
Changed some of the default values for the frame order auto-analysis.
The number of Sobol' quasi-random integration points were far too low to
obtain any reasonable
results.
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r24475 | bugman | 2014-07-07 18:20:15 +0200 (Mon, 07 Jul 2014) | 6 lines
Simplified the PyMOL visualisation relax script created by the frame order
auto-analysis.
This now consists of a single pymol.frame_order user function call. The
other pymol user function
calls were unnecessary.
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r24476 | bugman | 2014-07-08 11:26:46 +0200 (Tue, 08 Jul 2014) | 5 lines
Added the full optimisation results for the large angle double rotor frame
order model.
This is for the CaM test data using the new frame_order.py optimisation
script.
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r24477 | bugman | 2014-07-08 11:36:31 +0200 (Tue, 08 Jul 2014) | 3 lines
Removal of some accidentally committed debugging code.
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r24478 | bugman | 2014-07-08 12:08:28 +0200 (Tue, 08 Jul 2014) | 7 lines
Added model support for the rotor geometric object.
This is the structural object used in the frame order analysis to create
PDB representations of
rotor motions. The number of atoms created for the rotor is now constant,
allowing for models
whereby the atom number and connectivity must be preserved between all
models.
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r24479 | bugman | 2014-07-08 12:17:48 +0200 (Tue, 08 Jul 2014) | 6 lines
Changed the grid search pivot displacement frame order parameter.
Instead of searching from 0 to 50 Angstroms, the search is now from 10 to
50. This is to avoid the
edge case of pivot_disp = 0.0 from which the optimisation cannot escape.
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r24480 | bugman | 2014-07-08 14:21:23 +0200 (Tue, 08 Jul 2014) | 7 lines
Speed up of the PCS component of the rigid frame order model.
The lanthanide to atom vectors are now being calculated outside of the
alignment tensor and spin
loops, as well as the inverse vector lengths to the 5th power. This
increases the speed by a factor
of 1.216 (from 38.133 to 31.368 seconds for 23329 calls of the func_rigid()
target function).
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r24481 | bugman | 2014-07-08 15:57:43 +0200 (Tue, 08 Jul 2014) | 5 lines
Added the full optimisation results for the rigid frame order model.
This is for the CaM test data using the new frame_order.py optimisation
script.
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r24482 | bugman | 2014-07-08 17:07:24 +0200 (Tue, 08 Jul 2014) | 7 lines
Numpy <= 1.6 fixes for the frame order PCS code.
The numpy.linalg.norm function does not have an axis argument in numpy 1.6,
therefore the
lib.compat.norm() function is now used instead. This function was created
exactly for this axis
argument problem.
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r24483 | bugman | 2014-07-09 10:03:17 +0200 (Wed, 09 Jul 2014) | 8 lines
Created the new specific_analyses.frame_order.variables module.
This currently contains variables for all of the frame order model names,
as well as various lists
of these models. The rest of the frame order specific analysis code as
well as the frame order user
functions have been converted to use these model variables exclusively
rather than having the
model name strings hardcoded throughout the codebase.
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r24484 | bugman | 2014-07-09 10:05:34 +0200 (Wed, 09 Jul 2014) | 5 lines
Added the full optimisation results for the double rotor test data.
This is for the CaM frame order test data using the new frame_order.py
optimisation script.
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r24485 | bugman | 2014-07-09 10:40:09 +0200 (Wed, 09 Jul 2014) | 3 lines
Added a script for profiling the target function calls of the
pseudo-ellipse frame order model.
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r24486 | bugman | 2014-07-09 10:59:03 +0200 (Wed, 09 Jul 2014) | 5 lines
Added a timeit script and log file showing how numpy.cos() is 10 times
slower than math.cos().
This is for single floats.
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r24487 | bugman | 2014-07-09 11:39:08 +0200 (Wed, 09 Jul 2014) | 9 lines
Shifted the calculation of the theta_max cone opening for the
pseudo-ellipse outside of all loops.
This is infrastructure change for potentially eliminating all of the
looping for the PCS numeric
integration in the future. It however slightly speeds up the
pseudo-ellipse frame order model.
Using 500 target function calls in the profiling_pseudo_ellipse.py script in
test_suite/shared_data/frame_order/timings/, the time spent in the
pcs_pivot_motion_full_qrint()
function decreases from 20.849 to 20.719 seconds.
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r24488 | bugman | 2014-07-09 11:52:30 +0200 (Wed, 09 Jul 2014) | 6 lines
Converted the torsionless pseudo-ellipse model to also use the
tmax_pseudo_ellipse_array() function.
This allows the calculation of the pseudo-elliptic cone opening theta_max
to be shifted outside of
all loops.
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r24489 | bugman | 2014-07-09 11:59:05 +0200 (Wed, 09 Jul 2014) | 5 lines
Created a profiling script and log file for the isotropic cone frame order
model.
This shows where the slow points of the model are, using 2000 target
function calls.
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r24490 | bugman | 2014-07-09 12:02:55 +0200 (Wed, 09 Jul 2014) | 7 lines
Increased the function call number to 500 in the pseudo-ellipse frame order
model profiling script.
The profiling log file has also been added to show where the slowness is -
specifically that the
numeric PCS integration takes almost the same amount of time as the RDC
frame order matrix
construction using the scipy.integrate.quad() function.
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r24491 | bugman | 2014-07-09 12:04:11 +0200 (Wed, 09 Jul 2014) | 3 lines
Removal of unused imports from the lib.frame_order.rotor module as
identified using pylint.
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r24492 | bugman | 2014-07-09 14:23:48 +0200 (Wed, 09 Jul 2014) | 3 lines
Added the new variables module to the specific_analyses.frame_order package
__all__ list.
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r24493 | bugman | 2014-07-09 14:59:32 +0200 (Wed, 09 Jul 2014) | 5 lines
Created the specific_analyses.frame_order.checks.check_pivot() function.
This is to check that the pivot point has been set.
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r24494 | bugman | 2014-07-09 14:59:58 +0200 (Wed, 09 Jul 2014) | 3 lines
The frame order grid search is now checking if the pivot point has been set.
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r24495 | bugman | 2014-07-09 15:31:21 +0200 (Wed, 09 Jul 2014) | 7 lines
Modified the specific_analyses.frame_order.parameters.update_model()
function.
The pivot parameters are now set to 0.0 if they do not currently exist.
They were previously
excluded from this initialisation, but this is required for the frame order
models if the pivot is
not initially fixed at a give location in the PDB space.
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r24496 | bugman | 2014-07-09 16:20:51 +0200 (Wed, 09 Jul 2014) | 3 lines
Added a profiling script and log file for the free rotor frame order model.
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r24497 | bugman | 2014-07-09 16:36:14 +0200 (Wed, 09 Jul 2014) | 5 lines
Added the log file which should have been committed at r24496.
The number of function calls has also been decreased to 100.
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r24498 | bugman | 2014-07-09 17:09:10 +0200 (Wed, 09 Jul 2014) | 7 lines
Updated the frame order optimisation results for the CaM isotropic cone
test data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository and the
old ones removed.
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r24499 | bugman | 2014-07-09 17:19:52 +0200 (Wed, 09 Jul 2014) | 7 lines
Modified the script for recreating the frame order PDB representation and
displaying it in PyMOL.
The state loading, domain redefinition, and representation creation parts
have all been removed, as
these will soon all be redundant as the frame order analysis for all models
is being redone. All
that remains are the pymol.frame_order() function calls for displaying all
the representations.
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r24504 | bugman | 2014-07-09 19:52:00 +0200 (Wed, 09 Jul 2014) | 5 lines
The pivot point parameters in the frame order analysis are no longer scaled
by 100.
This is to match the average domain position translation which is also not
scaled.
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r24506 | bugman | 2014-07-10 10:36:20 +0200 (Thu, 10 Jul 2014) | 8 lines
The specific_analyses.frame_order.variables module is now used throughout
the frame order code.
[... 505 lines stripped ...]
r27939 - in /trunk: ./ auto_analyses/ lib/frame_order/ lib/structure/ lib/structure/internal/ lib/structure/represent/ pipe_...