Author: bugman
Date: Sat May 24 09:32:21 2014
New Revision: 23397
URL: http://svn.gna.org/viewcvs/relax?rev=23397&view=rev
Log:
Change for how the CaM frame order system test scripts handle the average
domain position rotation.
The trick of pre-rotating the 3D coordinates was used to solve the {a, b, g}
-> {0, b', g'} angle
conversion problem in the rotor models no longer works now that the average
domain position
mechanics has been simplified. Instead, high precision optimised b' and g'
values are now set, and
the ave_pos_alpha value set to None.
The high precision parameters were obtained with the frame_order.py script
located in the directory
test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target
function was modified so
that the translation vector is hard-coded to [-20.859750185691549,
-2.450606987447843,
-2.191854570352916] and the axis theta and phi angles to
0.96007997859534299767 and
4.0322755062196229403. These parameters were then commented out for the
model in the module
specific_analyses.frame_order.parameters so only b' and g' were optimised.
Iterative optimisation
was used with increasing precision, ending up with high precision using
10,000 Sobol' points.
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Sat May 24 09:32:21 2014
@@ -253,15 +253,6 @@
self._execute_uf(uf_name='structure.read_pdb',
file='1J7O_1st_NH.pdb', dir=BASE_PATH, set_mol_name='N-dom')
self._execute_uf(uf_name='structure.read_pdb',
file='1J7P_1st_NH_rot.pdb', dir=BASE_PATH, set_mol_name='C-dom')
- # Solve the {a, b, g} -> {0, b', g'} angle conversion problem in the
rotor models by pre-rotating the domain!
- if self.MODEL in ['free rotor', 'iso cone, free rotor']:
- # The rotation matrix.
- R = zeros((3, 3), float64)
- euler_to_R_zyz(self.AVE_POS_ALPHA, self.AVE_POS_BETA,
self.AVE_POS_GAMMA, R)
-
- # Rotate.
- self._execute_uf(uf_name='structure.rotate', R=R,
atom_id='#C-dom')
-
# Set up the 15N and 1H spins.
self._execute_uf(uf_name='structure.load_spins', spin_id='@N',
ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id='@H',
ave_pos=False)
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
Sat May 24 09:32:21 2014
@@ -31,6 +31,9 @@
# Set up some class variables.
DIRECTORY = 'free_rotor'
MODEL = 'free rotor'
+ AVE_POS_ALPHA = None
+ AVE_POS_BETA = 0.19740471457956135
+ AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.9600799785953431
AXIS_PHI = 4.0322755062196229
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
Sat May 24 09:32:21 2014
@@ -31,6 +31,9 @@
# Set up some class variables.
DIRECTORY = 'free_rotor2'
MODEL = 'free rotor'
+ AVE_POS_ALPHA = None
+ AVE_POS_BETA = 0.19740471457956135
+ AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.69828059079619353433
AXIS_PHI = 4.03227550621962294031
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
Sat May 24 09:32:21 2014
@@ -31,6 +31,9 @@
# Set up some class variables.
DIRECTORY = 'free_rotor_missing_data'
MODEL = 'free rotor'
+ AVE_POS_ALPHA = None
+ AVE_POS_BETA = 0.19740471457956135
+ AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.9600799785953431
AXIS_PHI = 4.0322755062196229
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
Sat May 24 09:32:21 2014
@@ -32,6 +32,9 @@
# Set up some class variables.
DIRECTORY = 'iso_cone_free_rotor'
MODEL = 'iso cone, free rotor'
+ AVE_POS_ALPHA = None
+ AVE_POS_BETA = 0.19740471457956135
+ AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.96007997859534299767
AXIS_PHI = 4.03227550621962294031
CONE_S1 = iso_cone_theta_to_S(1.0)
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py?rev=23397&r1=23396&r2=23397&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
(original)
+++
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
Sat May 24 09:32:21 2014
@@ -32,6 +32,9 @@
# Set up some class variables.
DIRECTORY = 'iso_cone_free_rotor2'
MODEL = 'iso cone, free rotor'
+ AVE_POS_ALPHA = None
+ AVE_POS_BETA = 0.19740471457956135
+ AVE_POS_GAMMA = 4.6622313104265416
AXIS_THETA = 0.69828059079619353433
AXIS_PHI = 4.03227550621962294031
CONE_S1 = iso_cone_theta_to_S(1.2)
r23397 - /branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/