Author: bugman
Date: Fri Jan 27 11:40:15 2012
New Revision: 15275
URL: http://svn.gna.org/viewcvs/relax?rev=15275&view=rev
Log:
Updated the rigid frame order model system test script.
This now matches the
/test_suite/shared_data/frame_order/cam/rigid/frame_order.py script.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py?rev=15275&r1=15274&r2=15275&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py
Fri Jan 27 11:40:15 2012
@@ -5,13 +5,14 @@
from os import sep
# relax module imports.
-from generic_fns.structure.mass import centre_of_mass
+from data import Relax_data_store; ds = Relax_data_store()
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 + 'rigid'
class Analysis:
@@ -21,40 +22,75 @@
# Optimise.
self.optimisation()
- # The rotation matrix.
- R = zeros((3, 3), float64)
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
- print("Rotation matrix:\n%s\n" % R)
- R = transpose(R)
- print("Inverted rotation:\n%s\n" % R)
-
# Load the original structure.
self.original_structure()
# Domain transformation.
- self.transform(R, array([ 37.254, 0.5, 16.7465]))
+ self.transform()
+
+ # Display in pymol.
+ self.pymol_display()
+
+ # Save the state.
+ state.save('devnull', force=True)
def optimisation(self):
"""Optimise the frame order model."""
- # The file paths.
- PATH_N_DOM = DATA_PATH
- PATH_C_DOM = PATH_N_DOM+sep+'rigid'+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=":80-148")
# 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.
@@ -63,17 +99,32 @@
# Set the reference domain.
frame_order.ref_domain('N')
+ # Set the initial 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=4.3434999280669997, param='ave_pos_alpha')
+ value.set(val=0.43544332764249905, param='ave_pos_beta')
+ value.set(val=3.8013235235956007, param='ave_pos_gamma')
+ calc()
+ print("\nchi2: %s" % cdp.chi2)
+
# Optimise.
- grid_search(inc=3)
- 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)
@@ -86,20 +137,47 @@
pipe.create(pipe_name='orig pos', pipe_type='frame order')
# Load the structure.
- structure.read_pdb(DATA_PATH+'1J7P_1st_NH.pdb')
-
- # Store the centre of mass.
- cdp.CoM = centre_of_mass()
+ structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=BASE_PATH)
- def transform(self, R, pivot):
+ def pymol_display(self):
+ """Display the results in PyMOL."""
+
+ # Switch back to the main data pipe.
+ pipe.switch('frame order')
+
+ # Load the PDBs of the 2 domains.
+ structure.read_pdb('1J7O_1st_NH.pdb', dir='..')
+ structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..')
+
+ # Create the cone PDB file.
+ #frame_order.cone_pdb(file='cone.pdb', force=True)
+
+ # Set the domains.
+ frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
+ frame_order.domain_to_pdb(domain='C', pdb='1J7P_1st_NH_rot.pdb')
+
+
+
+ def transform(self):
"""Transform the domain to the average position."""
+
+ # Switch back to the main data pipe.
+ pipe.switch('frame order')
+
+ # The rotation matrix.
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, R)
+ print("Rotation matrix:\n%s\n" % R)
+ R = transpose(R)
+ print("Inverted rotation:\n%s\n" % R)
+ pivot = cdp.pivot
# Create a special data pipe for the average rigid body position.
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('1J7P_1st_NH_rot.pdb', dir=BASE_PATH)
# Rotate all atoms.
structure.rotate(R=R, origin=pivot)
@@ -107,9 +185,6 @@
# Write out the new PDB.
structure.write_pdb('devnull')
- # Store the centre of mass.
- cdp.CoM = centre_of_mass()
-
# Execute the analysis.
Analysis()
r15275 - /branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/rigid.py