Author: bugman
Date: Thu Oct 1 19:49:46 2015
New Revision: 27917
URL: http://svn.gna.org/viewcvs/relax?rev=27917&view=rev
Log:
Merged revisions 23208-23211 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23208 | bugman | 2014-05-16 16:36:45 +0200 (Fri, 16 May 2014) | 7 lines
Updated the CaM frame order test model superimposition script.
The structure.superimpose user function is now correctly called. The
output log file has been added
to the repository as it contains the correct translation and Euler rotation
information needed for
the test models.
........
r23209 | bugman | 2014-05-16 16:55:55 +0200 (Fri, 16 May 2014) | 6 lines
Parameter update for the isotropic cone CaM frame order test model
optimisation script.
The Euler angles for the rotation about the motional pivot have been
replaced by the translation
vector and Euler angle CoM rotation parameters.
........
r23210 | bugman | 2014-05-17 18:03:44 +0200 (Sat, 17 May 2014) | 1 line
Removed an unused import and an extra blank line.
........
r23211 | bugman | 2014-05-17 18:03:46 +0200 (Sat, 17 May 2014) | 5 lines
Fix for a number of the frame order models which do not have parameter
constraints.
The linear_constraint() function was returning A, b = [], [] for these
models, but these empty numpy
arrays were causing the minfx library (https://gna.org/projects/minfx/) to
fail. These values are
now caught and the constraint algorithm turned off in the minimise()
specific API method.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/superimpose.log
- copied unchanged from r23211,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log
Modified:
trunk/ (props changed)
trunk/specific_analyses/frame_order/api.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/superimpose.py
Propchange: trunk/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Oct 1 19:49:46 2015
@@ -1 +1 @@
-/branches/frame_order_cleanup:1-23195,23197-23205
+/branches/frame_order_cleanup:1-23195,23197-23205,23208-23211
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27917&r1=27916&r2=27917&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/api.py (original)
+++ trunk/specific_analyses/frame_order/api.py Thu Oct 1 19:49:46 2015
@@ -29,9 +29,11 @@
from minfx.grid import grid_point_array
from numpy import float64, zeros
from re import search
+from warnings import warn
# relax module imports.
from lib.errors import RelaxError, RelaxNoModelError
+from lib.warnings import RelaxWarning
from pipe_control import pipes
from pipe_control.interatomic import interatomic_loop, return_interatom
from pipe_control.mol_res_spin import return_spin, spin_loop
@@ -505,6 +507,16 @@
if constraints:
A, b = linear_constraints(scaling_matrix=scaling_matrix[0])
+ # No constraints.
+ if len(A) == 0:
+ warn(RelaxWarning("The '%s' model parameters are not
constrained, turning the linear constraint algorithm off." % cdp.model))
+ constraints = False
+
+ # Pop out the log barrier algorithm.
+ if min_algor == 'Log barrier':
+ min_algor = min_options[0]
+ min_options = min_options[1:]
+
# Grid search.
if search('^[Gg]rid', min_algor):
results = grid_point_array(func=model.func, args=(),
points=min_options, verbosity=verbosity)
Modified: trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py?rev=27917&r1=27916&r2=27917&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
(original)
+++ trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
Thu Oct 1 19:49:46 2015
@@ -3,12 +3,10 @@
# Python module imports.
from numpy import array
-# relax module imports.
-from lib.geometry.rotations import reverse_euler_zyz
-
# The real parameter values.
-AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA =
reverse_euler_zyz(4.3434999280669997, 0.43544332764249905, 3.8013235235956007)
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -21.269217407269576,
-3.122610661328414, -2.400652421655998]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [ 5.623469076122531,
0.435439405668396, 5.081265529106499]
AXIS_THETA = 0.96007997859534299767
AXIS_PHI = 4.03227550621962294031
CONE_THETA = 0.6
@@ -85,6 +83,9 @@
frame_order.quad_int(flag=False)
# Check the minimum.
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
value.set(param='ave_pos_beta', val=AVE_POS_BETA)
value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
@@ -108,7 +109,6 @@
frame_order.pivot(pivot, fix=False)
minimise('simplex', constraints=True)
-
# Test Monte Carlo simulations.
monte_carlo.setup(number=5)
monte_carlo.create_data()
Modified: trunk/test_suite/shared_data/frame_order/cam/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/superimpose.py?rev=27917&r1=27916&r2=27917&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/superimpose.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/superimpose.py Thu Oct 1
19:49:46 2015
@@ -8,7 +8,7 @@
structure.read_pdb('1J7P_1st_NH_rot.pdb', set_mol_name='C-dom',
set_model_num=2)
# Superimpose.
-structure.superimpose(method='fit to first', centre='CoM')
+structure.superimpose(method='fit to first', centre_type='CoM')
# Save the result.
structure.write_pdb('superimpose.pdb', force=True)
r27917 - in /trunk: ./ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/ test_suite/shared_data/frame_o...