r14837 - /1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py -- October 12, 2011 - 15:18

Author: bugman
Date: Wed Oct 12 15:18:25 2011
New Revision: 14837

URL: http://svn.gna.org/viewcvs/relax?rev=14837&view=rev
Log:
Created a system test script for checking one type of algorithm for Ln3+ 
position optimisation.


Added:
    1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
      - copied, changed from r14836, 
1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py

Copied: 1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py 
(from r14836, 
1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py)
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?p2=1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py&p1=1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py&r1=14836&r2=14837&rev=14837&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py 
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py Wed 
Oct 12 15:18:25 2011
@@ -1,4 +1,4 @@
-"""Script for testing the Monte Carlo simulations of fitting an alignment 
tensor to RDCs and PCSs."""
+"""Script for testing the lanthanide position optimisation using RDCs and 
PCSs."""
 
 # Python module imports.
 from os import sep
@@ -11,47 +11,71 @@
 
 
 # Path of the alignment data and structure.
-DATA_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'monte_carlo_testing'
-STRUCT_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'sphere'
+DATA_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'population_model'
+STRUCT_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
 
 # Create the data pipe.
-pipe.create('MC test', 'N-state')
+pipe.create('Ln3+ opt', 'N-state')
 
-# Load the test structure.
-structure.read_pdb(file='sphere', dir=STRUCT_PATH)
+# Load the structures.
+for i in range(1, 4):
+    structure.read_pdb(file='lactose_MCMM4_S1_%i.pdb' % i, dir=STRUCT_PATH, 
set_model_num=i, set_mol_name='LE')
 
 # Load the spins.
-structure.load_spins()
+structure.load_spins(spin_id=':UNK@C*', ave_pos=False)
+structure.load_spins(spin_id=':UNK@H*', ave_pos=False)
 
-# Load the NH vectors.
-structure.vectors(spin_id='@N', attached='H', ave=False)
+# Deselect the CH2 protons (the rotation of these doesn't work in the model, 
but the carbon doesn't move).
+deselect.spin(spin_id=':UNK@H6')
+deselect.spin(spin_id=':UNK@H7')
+deselect.spin(spin_id=':UNK@H17')
+deselect.spin(spin_id=':UNK@H18')
+
+# Load the CH vectors.
+structure.vectors(spin_id='@C*', attached='H*', ave=False)
 
 # Set the values needed to calculate the dipolar constant.
-value.set(1.041 * 1e-10, 'bond_length', spin_id="@N")
-value.set('15N', 'heteronucleus', spin_id="@N")
-value.set('1H', 'proton', spin_id="@N")
-
-# RDCs.
-rdc.read(align_id='synth', file='synth_rdc', dir=DATA_PATH, mol_name_col=1, 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, 
error_col=7)
-
-# PCSs.
-pcs.read(align_id='synth', file='synth_pcs', dir=DATA_PATH, mol_name_col=1, 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, 
error_col=7)
+value.set(1.10 * 1e-10, 'bond_length', spin_id="@C*")
+value.set('13C', 'heteronucleus', spin_id="@C*")
+value.set('1H', 'proton', spin_id="@C*")
 
 # Set the paramagnetic centre.
-paramag.centre(pos=[10.0, 0.0, 0.0])
+paramag.centre([ -14.8,    0.9,    0.2])
 
-# The temperature.
-temperature(id='synth', temp=303)
+# File list.
+align_list = ['Dy', 'Tb', 'Tm', 'Er']
 
-# The frequency.
-frq.set(id='synth', frq=600.0 * 1e6)
+# Load the RDCs and PCSs.
+for i in xrange(len(align_list)):
+    # The RDC.
+    rdc.read(align_id=align_list[i], file='missing_rdc_%i' % i, 
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, 
spin_num_col=None, spin_name_col=5, data_col=6, error_col=None)
 
-# Set up the model.
-n_state_model.select_model(model='fixed')
+    # The PCS.
+    pcs.read(align_id=align_list[i], file='missing_pcs_%i' % i, 
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, 
spin_num_col=None, spin_name_col=5, data_col=6, error_col=None)
 
-# Minimisation.
-grid_search(inc=3)
-minimise('simplex', constraints=False, max_iter=500)
+    # The temperature.
+    temperature(id=align_list[i], temp=298)
+
+    # The frequency.
+    frq.set(id=align_list[i], frq=799.75376122 * 1e6)
+
+    # Set up the model.
+    n_state_model.select_model('fixed')
+
+    # Minimisation.
+    grid_search(inc=3)
+    minimise('newton', constraints=False)
+
+    # Fix the tensor.
+    align_tensor.fix(id=align_list[i])
+
+# Optimise the Ln3+ position.
+paramag.centre(fix=False)
+minimise('simplex', constraints=False)
+
+# Optimise everything.
+align_tensor.fix(fixed=False)
+minimise('simplex', constraints=False)
 
 # Monte Carlo simulations.
 monte_carlo.setup(3)