Author: bugman
Date: Thu Jan 26 13:59:28 2012
New Revision: 15266
URL: http://svn.gna.org/viewcvs/relax?rev=15266&view=rev
Log:
Reactivated the Frame_order.test_cam_free_rotor2 system test using the new
analysis design.
Modified:
branches/frame_order_testing/test_suite/system_tests/frame_order.py
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
Modified: branches/frame_order_testing/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/frame_order.py?rev=15266&r1=15265&r2=15266&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/frame_order.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/frame_order.py Thu
Jan 26 13:59:28 2012
@@ -189,46 +189,25 @@
self.assertAlmostEqual(cdp.chi2, 13.8, 1, msg=self.mesg)
- def fixme_test_cam_free_rotor2(self):
+ def test_cam_free_rotor2(self):
"""Test the second free rotor frame order model of CaM."""
+ # Setup.
+ ds.flag_rdc = True
+ ds.flag_pcs = True
+ ds.flag_opt = False
+
# Execute the script.
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'free_rotor2.py')
- # The base data.
- pivot = array([ 37.254, 0.5, 16.7465])
- com = array([ 26.83678091, -12.37906417, 28.34154128])
- pivot_com_axis = com - pivot
- rot_axis = array([ 0.62649633, 0.77455282, -0.08700742])
-
- # The average position CoM.
- ave_pivot_com_axis = ds['ave pos'].CoM - pivot
-
- # The projection of the CoMs onto the rotation axis.
- orig_proj = dot(pivot_com_axis, rot_axis)
- ave_proj = dot(ave_pivot_com_axis, rot_axis)
-
- # Check that the projections are equal.
- self.assertAlmostEqual(orig_proj, ave_proj, 0)
-
- # The rotation axis.
+ # Switch back to the original pipe.
self.interpreter.pipe.switch('frame order')
- spherical_vect = zeros(3, float64)
- spherical_vect[0] = 1.0
- spherical_vect[1] = cdp.axis_theta
- spherical_vect[2] = cdp.axis_phi
- cart_vect = zeros(3, float64)
- spherical_to_cartesian(spherical_vect, cart_vect)
- print("\nReal rotation axis: %s" % repr(rot_axis))
- print("Fitted rotation axis: %s" % repr(cart_vect))
-
- # The dot product.
- angle = acos(dot(cart_vect, rot_axis))
- if angle > pi/2:
- angle = acos(dot(cart_vect, -rot_axis))
-
- # Check the angle.
- self.assertAlmostEqual(angle, 0.0, 2)
+
+ # Get the debugging message.
+ self.mesg = self.mesg_opt_debug()
+
+ # Check the chi2 value.
+ self.assertAlmostEqual(cdp.chi2, 0.0, 1, msg=self.mesg)
def fixme_test_cam_iso_cone_free_rotor(self):
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py?rev=15266&r1=15265&r2=15266&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
Thu Jan 26 13:59:28 2012
@@ -5,13 +5,15 @@
from os import sep
# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.structure.mass import centre_of_mass
from maths_fns.rotation_matrix import euler_to_R_zyz
from status import Status; status = Status()
# Some variables.
-DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep
+BASE_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'+sep
+DATA_PATH = BASE_PATH + 'free_rotor2'
class Analysis:
@@ -38,23 +40,59 @@
def optimisation(self):
"""Optimise the frame order model."""
- # The file paths.
- PATH_N_DOM = DATA_PATH
- PATH_C_DOM = PATH_N_DOM+sep+'free_rotor2'+sep
-
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
- # Load the tensors.
- script(PATH_N_DOM + 'tensors.py')
- script(PATH_C_DOM + 'tensors.py')
+ # Read the structures.
+ structure.read_pdb('1J7O_1st_NH.pdb', dir=BASE_PATH,
set_mol_name='N-dom')
+ structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=BASE_PATH,
set_mol_name='C-dom')
+
+ # Load the spins.
+ structure.load_spins('@N')
+ structure.load_spins('@H')
+
+ # Load the NH vectors.
+ structure.vectors(spin_id='@N', attached='H', ave=False)
+
+ # Set the values needed to calculate the dipolar constant.
+ value.set(1.041 * 1e-10, 'r', spin_id="@N")
+ value.set('15N', 'heteronuc_type', spin_id="@N")
+ value.set('1H', 'proton_type', spin_id="@N")
+
+ # Loop over the alignments.
+ ln = ['dy', 'tb', 'tm', 'er']
+ for i in range(len(ln)):
+ # Load the RDCs.
+ if ds.flag_rdc:
+ rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i],
dir=DATA_PATH, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+
+ # The PCS.
+ if ds.flag_pcs:
+ pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i],
dir=DATA_PATH, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+
+ # The temperature and field strength.
+ temperature(id=ln[i], temp=303)
+ frq.set(id=ln[i], frq=900e6)
+
+ # Load the N-domain tensors (the full tensors).
+ script(BASE_PATH + 'tensors.py')
+
+ # Define the domains.
+ domain(id='N', spin_id=":1-78")
+ domain(id='C', spin_id=":80-144")
# The tensor domains and reductions.
full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom']
red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
for i in range(len(full)):
+ # Initialise the reduced tensor.
+ align_tensor.init(tensor=red[i], params=(0,0,0,0,0))
+
+ # Set the domain info.
align_tensor.set_domain(tensor=full[i], domain='N')
align_tensor.set_domain(tensor=red[i], domain='C')
+
+ # Specify which tensor is reduced.
align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
# Select the model.
@@ -63,22 +101,33 @@
# Set the reference domain.
frame_order.ref_domain('N')
- # Set the parameters to that after a 21 increment grid search (for a
massive speed up).
- value.set(val=2.2143, param='ave_pos_beta')
- value.set(val=0.897, param='ave_pos_gamma')
- value.set(val=1.570, param='axis_theta')
- value.set(val=1.1968, param='axis_phi')
+ # The pivot point.
+ pivot = array([ 37.254, 0.5, 16.7465])
+ frame_order.pivot(pivot, fix=True)
+
+ # Set the paramagnetic centre.
+ paramag.centre(pos=[35.934, 12.194, -4.206])
+
+ # Check the minimum.
+ value.set(val=2.5534876110153948, param='ave_pos_beta')
+ value.set(val=0.47194843111649976, param='ave_pos_gamma')
+ value.set(val=1.6573281536701425, param='axis_theta')
+ value.set(val=0.89246262623423234, param='axis_phi')
+ calc()
+ print("\nchi2: %s" % cdp.chi2)
# Optimise.
- minimise('simplex', constraints=False)
+ if ds.flag_opt:
+ grid_search(inc=11)
+ minimise('simplex', constraints=False)
- # Test Monte Carlo simulations.
- monte_carlo.setup(number=3)
- monte_carlo.create_data()
- monte_carlo.initial_values()
- minimise('simplex', constraints=False)
- eliminate()
- monte_carlo.error_analysis()
+ # Test Monte Carlo simulations.
+ monte_carlo.setup(number=3)
+ monte_carlo.create_data()
+ monte_carlo.initial_values()
+ minimise('simplex', constraints=False)
+ eliminate()
+ monte_carlo.error_analysis()
# Write the results.
results.write('devnull', dir=None, force=True)
@@ -91,7 +140,7 @@
pipe.create(pipe_name='orig pos', pipe_type='frame order')
# Load the structure.
- structure.read_pdb(DATA_PATH+'1J7P_1st_NH.pdb')
+ structure.read_pdb(BASE_PATH+'1J7P_1st_NH.pdb')
# Store the centre of mass.
cdp.CoM = centre_of_mass()
@@ -104,7 +153,7 @@
pipe.create(pipe_name='ave pos', pipe_type='frame order')
# Load the structure.
- structure.read_pdb(DATA_PATH+'1J7P_1st_NH_rot.pdb')
+ structure.read_pdb(BASE_PATH+'1J7P_1st_NH_rot.pdb')
# Rotate all atoms.
structure.rotate(R=R, origin=pivot)
r15266 - in /branches/frame_order_testing/test_suite/system_tests: frame_order.py scripts/frame_order/cam/free_rotor2.py