Author: bugman
Date: Mon Dec 14 17:53:08 2009
New Revision: 10095
URL: http://svn.gna.org/viewcvs/relax?rev=10095&view=rev
Log:
Added a catch for bug #14941 (https://gna.org/bugs/index.php?14941) to the
relax system tests.
This uses truncated data (first 2 residues), also randomised, to reproduce
the bug.
Added:
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/local_tm_trunc.bz2
(with props)
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/sphere_trunc.bz2
(with props)
1.3/test_suite/system_tests/scripts/model_free/
1.3/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
Modified:
1.3/test_suite/system_tests/model_free.py
1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
Added:
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/local_tm_trunc.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/local_tm_trunc.bz2?rev=10095&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/local_tm_trunc.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/sphere_trunc.bz2
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/sphere_trunc.bz2?rev=10095&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
1.3/test_suite/shared_data/model_free/bug_14941_local_tm_global_selection/sphere_trunc.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Modified: 1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=10095&r1=10094&r2=10095&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Mon Dec 14 17:53:08 2009
@@ -164,6 +164,13 @@
# Execute the script.
self.relax.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_14872_unicode_selection.py')
+
+
+ def test_bug_14941_local_tm_global_selection(self):
+ """Test catching bug #14941, the local tm global model selection
problem as submitted by Mikaela Stewart (mikaela dot stewart att gmail dot
com)."""
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_14941_local_tm_global_selection.py')
def test_bugs_12582_12591_12607(self):
Added:
1.3/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py?rev=10095&view=auto
==============================================================================
---
1.3/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
(added)
+++
1.3/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
Mon Dec 14 17:53:08 2009
@@ -1,0 +1,31 @@
+"""This system test catches the local tm global model selection bug
submitted by Mikaela Stewart (mikaela dot stewart att gmail dot com).
+
+The bug is:
+ - Bug #14941 (https://gna.org/bugs/?14941).
+"""
+
+# Python module imports.
+from os import sep
+import sys
+
+
+# Path of the files.
+path = sys.path[-1] +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'bug_14941_local_tm_global_selection'
+
+# Local tm data.
+pipe.create(pipe_name='local_tm', pipe_type='mf')
+results.read(file='local_tm_trunc', dir=path)
+
+# Sphere data.
+pipe.create(pipe_name='sphere', pipe_type='mf')
+results.read(file='sphere_trunc', dir=path)
+
+# Model selection.
+model_selection(method='AIC', modsel_pipe='final', pipes=['local_tm',
'sphere'])
+results.write(file='devnull', dir=None, compress_type=1, force=True)
+
+# Monte Carlo simulation setup.
+monte_carlo.setup(number=200)
+monte_carlo.create_data(method='back_calc')
+monte_carlo.initial_values()
+
Modified: 1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py?rev=10095&r1=10094&r2=10095&view=diff
==============================================================================
--- 1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py (original)
+++ 1.3/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py Mon Dec 14
17:53:08 2009
@@ -58,6 +58,10 @@
# Print out.
print("\n\n# Checking the %s() and %s() conversions.\n" %
(euler_to_R.__name__, R_to_euler.__name__))
+
+ # A small number.
+ epsilon = 1e-15
+
# End angles.
if alpha_end == None:
alpha_end = alpha_start
@@ -71,6 +75,11 @@
print(("\talpha: %s" % alpha_start))
print(("\tbeta: %s" % beta_start))
print(("\tgamma: %s\n" % gamma_start))
+ print("End angles:")
+ print(("\talpha: %s" % alpha_end))
+ print(("\tbeta: %s" % beta_end))
+ print(("\tgamma: %s\n" % gamma_end))
+
# Generate the rotation matrix.
euler_to_R(alpha_start, beta_start, gamma_start, R)
@@ -86,15 +95,38 @@
print(("\tgamma: %s\n" % gamma_new))
# Wrap the angles.
- alpha_new = wrap_angles(alpha_new, 0, 2*pi)
- beta_new = wrap_angles(beta_new, 0, 2*pi)
- gamma_new = wrap_angles(gamma_new, 0, 2*pi)
+ alpha_new = wrap_angles(alpha_new, 0-epsilon, 2*pi-epsilon)
+ beta_new = wrap_angles(beta_new, 0-epsilon, 2*pi-epsilon)
+ gamma_new = wrap_angles(gamma_new, 0-epsilon, 2*pi-epsilon)
# Print out.
print("New angles (wrapped):")
print(("\talpha: %s" % alpha_new))
print(("\tbeta: %s" % beta_new))
print(("\tgamma: %s\n" % gamma_new))
+
+ # Second solution required!
+ if abs(beta_end - beta_new) > 1e-7:
+ # Collapse the multiple beta solutions.
+ if beta_new < pi:
+ alpha_new = alpha_new + pi
+ beta_new = pi - beta_new
+ gamma_new = gamma_new + pi
+ else:
+ alpha_new = alpha_new + pi
+ beta_new = 3*pi - beta_new
+ gamma_new = gamma_new + pi
+
+ # Wrap the angles.
+ alpha_new = wrap_angles(alpha_new, 0-epsilon, 2*pi-epsilon)
+ beta_new = wrap_angles(beta_new, 0-epsilon, 2*pi-epsilon)
+ gamma_new = wrap_angles(gamma_new, 0-epsilon, 2*pi-epsilon)
+
+ # Print out.
+ print("New angles (second solution):")
+ print(("\talpha: %s" % alpha_new))
+ print(("\tbeta: %s" % beta_new))
+ print(("\tgamma: %s\n" % gamma_new))
# Checks.
self.assertAlmostEqual(alpha_end, alpha_new)
@@ -570,13 +602,15 @@
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 0.0,
0.0, 0.0)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
0.0, 0.0)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 0.0,
1.0, 0.0)
- self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 0.0,
0.0, 1.0, alpha_end=1.0, gamma_end=0.0)
+ self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 0.0,
0.0, 1.0)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
1.0, 0.0)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 0.0,
1.0, 1.0)
- self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
0.0, 1.0, alpha_end=2.0, gamma_end=0.0)
+ self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
0.0, 1.0)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
1.0, 1.0)
- self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
pi/2, 0.5, alpha_end=0.5, gamma_end=0.0)
+ self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
pi/2, 0.5)
self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
pi, 0.5)
+ self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
-pi/2, 0.5, beta_end=-pi/2+2*pi)
+ self.check_return_conversion(euler_zxy_to_R, R_to_euler_zxy, 1.0,
1.5*pi, 0.5, beta_end=pi/2)
def test_R_to_euler_zxz(self):
@@ -600,6 +634,7 @@
"""Test the rotation matrix to zyx Euler angle conversion."""
# Check random numbers, then the problematic angles.
+ self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 5.0,
2.0, 1.0)
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx,
uniform(0, 2*pi), uniform(0, pi), uniform(0, 2*pi))
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 0.0,
0.0, 0.0)
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
0.0, 0.0)
@@ -610,7 +645,7 @@
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
0.0, 1.0)
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
1.0, 1.0)
self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
pi/2, 0.5)
- self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
pi, 0.5)
+ self.check_return_conversion(euler_zyx_to_R, R_to_euler_zyx, 1.0,
pi, 0.5, alpha_end=1.0+pi, beta_end=0.0, gamma_end=0.5+pi)
def test_R_to_euler_zyz(self):
r10095 - in /1.3/test_suite: shared_data/model_free/bug_14941_local_tm_global_selection/ system_tests/ system_tests/scripts/...