Author: bugman
Date: Wed Jan 25 10:02:19 2012
New Revision: 15243
URL: http://svn.gna.org/viewcvs/relax?rev=15243&view=rev
Log:
Reactivated and converted the Frame_order.test_cam_free_rotor() system test
to the new 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_rotor.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=15243&r1=15242&r2=15243&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 Wed
Jan 25 10:02:19 2012
@@ -161,7 +161,7 @@
setattr(cdp, param, curr)
- def fixme_test_cam_free_rotor(self):
+ def test_cam_free_rotor(self):
"""Test the free rotor frame order model of CaM."""
# Execute the script.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py?rev=15243&r1=15242&r2=15243&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
Wed Jan 25 10:02:19 2012
@@ -11,7 +11,8 @@
# 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_rotor'
class Analysis:
@@ -38,23 +39,57 @@
def optimisation(self):
"""Optimise the frame order model."""
- # The file paths.
- PATH_N_DOM = DATA_PATH
- PATH_C_DOM = PATH_N_DOM+sep+'free_rotor'+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.
+ 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.
+ 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)):
+ # Initalise 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.
@@ -63,17 +98,32 @@
# Set the reference domain.
frame_order.ref_domain('N')
+ # 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.
+ cdp.ave_pos_beta = 1.1838868514111507
+ cdp.ave_pos_gamma = 0.35219976958846927
+ cdp.axis_theta = 2.1815126749944502
+ cdp.axis_phi = 0.89068285262982982
+ calc()
+ print("\nchi2: %s" % cdp.chi2)
+
# Optimise.
- grid_search(inc=11)
- minimise('simplex', constraints=False)
+ #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)
@@ -86,7 +136,7 @@
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()
@@ -99,7 +149,7 @@
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)
r15243 - in /branches/frame_order_testing/test_suite/system_tests: frame_order.py scripts/frame_order/cam/free_rotor.py