Author: bugman
Date: Fri Mar 22 17:03:52 2013
New Revision: 18989
URL: http://svn.gna.org/viewcvs/relax?rev=18989&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18033:18034
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18035:18036
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18036:18037
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18037:18038
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18041:18042
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18070:18071
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18085:18086
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18033:18034
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18034 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18035:18036
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18036 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18036:18037
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18037 into '.':
U test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18037:18038
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18038 into '.':
A
test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/full_analysis.py
A
test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/full_analysis.py
A test_suite/shared_data/frame_order/cam/rotor_2_state/full_analysis.py
A test_suite/shared_data/frame_order/cam/rotor2/full_analysis.py
A test_suite/shared_data/frame_order/cam/free_rotor2/full_analysis.py
A test_suite/shared_data/frame_order/cam/rigid/full_analysis.py
A test_suite/shared_data/frame_order/cam/iso_cone/full_analysis.py
A test_suite/shared_data/frame_order/cam/pseudo_ellipse2/full_analysis.py
A
test_suite/shared_data/frame_order/cam/iso_cone_torsionless/full_analysis.py
A
test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/full_analysis.py
A test_suite/shared_data/frame_order/cam/rotor/full_analysis.py
A
test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/full_analysis.py
A test_suite/shared_data/frame_order/cam/free_rotor/full_analysis.py
A test_suite/shared_data/frame_order/cam/pseudo_ellipse/full_analysis.py
[edau@localhost relax-trunk]$ svn merge -r18041:18042
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18042 into '.':
U test_suite/system_tests/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18070:18071
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18071 into '.':
U test_suite/system_tests/align_tensor.py
[edau@localhost relax-trunk]$ svn merge -r18085:18086
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18086 into '.':
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$
Added:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/free_rotor/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/free_rotor2/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/iso_cone/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/rigid/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rigid/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/rotor/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotor/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotor2/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/full_analysis.py
- copied unchanged from r18038,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/rotor_2_state/full_analysis.py
Modified:
trunk/auto_analyses/frame_order.py
trunk/specific_fns/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
trunk/test_suite/system_tests/align_tensor.py
trunk/test_suite/system_tests/frame_order.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=18989&r1=18988&r2=18989&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 17:03:52 2013
@@ -85,6 +85,12 @@
# Execution lock.
status.exec_lock.acquire(pipe_bundle, mode='auto-analysis')
+ # Initial printout.
+ text = "# Frame order auto-analysis #"
+ print("\n\n\n\n\n\n\n" + "#"*len(text))
+ print("%s" % text)
+ print("#"*len(text))
+
# Store the args.
self.data_pipe_full = data_pipe_full
self.data_pipe_subset = data_pipe_subset
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=18989&r1=18988&r2=18989&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 17:03:52 2013
@@ -497,11 +497,11 @@
cone = Iso_cone(cone_theta)
# Create the positive and negative cones.
- geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=cdp.pivot, R=R_pos, inc=inc,
distribution='regular')
+ geometric.create_cone_pdb(mol=mol, cone=cone,
start_res=mol.res_num[-1]+1, apex=cdp.pivot, R=R_pos, inc=inc,
distribution='regular', axis_flag=False)
# The negative.
if neg_cone:
- geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=cdp.pivot, R=R_neg, inc=inc,
distribution='regular')
+ geometric.create_cone_pdb(mol=mol_neg, cone=cone,
start_res=mol_neg.res_num[-1]+1, apex=cdp.pivot, R=R_neg, inc=inc,
distribution='regular', axis_flag=False)
# Create the PDB file.
@@ -1450,9 +1450,9 @@
if eigen_gamma != None:
cdp.eigen_gamma_sim[sim_index] = wrap_angles(eigen_gamma,
cdp.eigen_gamma-pi, cdp.eigen_gamma+pi)
if axis_theta != None:
- cdp.axis_theta_sim[sim_index] = axis_theta
+ cdp.axis_theta_sim[sim_index] = wrap_angles(axis_theta,
cdp.axis_theta-pi, cdp.axis_theta+pi)
if axis_phi != None:
- cdp.axis_phi_sim[sim_index] = axis_phi
+ cdp.axis_phi_sim[sim_index] = wrap_angles(axis_phi,
cdp.axis_phi-pi, cdp.axis_phi+pi)
# Cone parameters.
if cone_theta != None:
@@ -1493,9 +1493,9 @@
if eigen_gamma != None:
cdp.eigen_gamma = wrap_angles(eigen_gamma, 0.0, 2.0*pi)
if axis_theta != None:
- cdp.axis_theta = axis_theta
+ cdp.axis_theta = wrap_angles(axis_theta, 0.0, 2.0*pi)
if axis_phi != None:
- cdp.axis_phi = axis_phi
+ cdp.axis_phi = wrap_angles(axis_phi, 0.0, 2.0*pi)
# Cone parameters.
if cone_theta != None:
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py?rev=18989&r1=18988&r2=18989&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
Fri Mar 22 17:03:52 2013
@@ -108,9 +108,9 @@
value.set(param='eigen_alpha', val=3.14159265358979311600)
value.set(param='eigen_beta', val=0.96007997859534310869)
value.set(param='eigen_gamma', val=4.03227550621962294031)
- value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0)
- value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0)
- value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0)
+ value.set(param='cone_theta_x', val=30.0 * 2.0 * pi / 360.0) #
0.52359877559829882
+ value.set(param='cone_theta_y', val=50.0 * 2.0 * pi / 360.0) #
0.87266462599716477
+ value.set(param='cone_sigma_max', val=60.0 * 2.0 * pi / 360.0) #
1.0471975511965976
calc()
print("\nchi2: %s" % repr(cdp.chi2))
Modified: trunk/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/align_tensor.py?rev=18989&r1=18988&r2=18989&view=diff
==============================================================================
--- trunk/test_suite/system_tests/align_tensor.py (original)
+++ trunk/test_suite/system_tests/align_tensor.py Fri Mar 22 17:03:52 2013
@@ -100,7 +100,7 @@
self.interpreter.pipe.create('copy test', 'N-state')
# Initialise one tensor.
- self.interpreter.align_tensor.init(tensor='orig',
params=self.tensors_full[0], param_types=0)
+ self.interpreter.align_tensor.init(tensor='orig', align_id='test',
params=self.tensors_full[0], param_types=0)
# Copy the tensor.
self.interpreter.align_tensor.copy(tensor_from='orig',
tensor_to='new')
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=18989&r1=18988&r2=18989&view=diff
==============================================================================
--- trunk/test_suite/system_tests/frame_order.py (original)
+++ trunk/test_suite/system_tests/frame_order.py Fri Mar 22 17:03:52 2013
@@ -99,7 +99,7 @@
del status.flag_pcs
- def check_chi2(self, chi2=0.0, places=8):
+ def check_chi2(self, chi2=0.0, places=1):
"""Check the function evaluation."""
# Switch back to the original pipe.
@@ -108,8 +108,22 @@
# Get the debugging message.
self.mesg = self.mesg_opt_debug()
+ # Scale the chi2 values down.
+ if chi2 > 1000.0:
+ chi2 = chi2 / 1000.0
+ chi2_fit = cdp.chi2 / 1000.0
+ elif chi2 > 100.0:
+ chi2 = chi2 / 100.0
+ chi2_fit = cdp.chi2 / 100.0
+ elif chi2 > 10.0:
+ chi2 = chi2 / 10.0
+ chi2_fit = cdp.chi2 / 10.0
+ else:
+ chi2 = chi2
+ chi2_fit = cdp.chi2
+
# Check the chi2 value.
- self.assertAlmostEqual(cdp.chi2, chi2, places, msg=self.mesg)
+ self.assertAlmostEqual(chi2_fit, chi2, places, msg=self.mesg)
def flags(self, rdc=True, pcs=True, opt=False):
r18989 - in /trunk: auto_analyses/ specific_fns/ test_suite/shared_data/frame_order/cam/free_rotor/ test_suite/shared_data/f...