r11145 - /1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py -- April 27, 2010 - 16:08

Author: bugman
Date: Tue Apr 27 16:08:02 2010
New Revision: 11145

URL: http://svn.gna.org/viewcvs/relax?rev=11145&view=rev
Log:
Wrote a script for testing the missing RDC and PCS data.

This uses the N-state model with N=1, so direct testing of the single state 
to 4 tensors.


Added:
    1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
      - copied, changed from r11098, 
1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py

Copied: 
1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py (from 
r11098, 1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py)
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py?p2=1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py&p1=1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py&r1=11098&r2=11145&rev=11145&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py 
(original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py 
Tue Apr 27 16:08:02 2010
@@ -3,34 +3,21 @@
 # Python module imports.
 import __main__
 from os import sep
-import sys
-
-# relax imports.
-from data import Relax_data_store; ds = Relax_data_store()
-from specific_fns.setup import n_state_model_obj
 
 
 # Path of the files.
-str_path = __main__.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
-data_path = __main__.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'align_data'
+str_path = __main__.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'dna'
+data_path = __main__.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'missing_data'
 
 # Create the data pipe.
-pipe.create('lactose', 'N-state')
+pipe.create('missing_data_test', 'N-state')
 
-# Load the structures.
-NUM_STR = 4
-for i in range(NUM_STR):
-    structure.read_pdb(file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, 
parser='internal', set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
+# Load the structure.
+structure.read_pdb(file='LE_trunc.pdb', dir=str_path, set_mol_name='LE')
 
 # Load the sequence information.
-structure.load_spins(spin_id=':UNK@C*', combine_models=False, ave_pos=False)
-structure.load_spins(spin_id=':UNK@H*', combine_models=False, ave_pos=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')
+structure.load_spins(spin_id='@C*', combine_models=False, ave_pos=False)
+structure.load_spins(spin_id='@H*', combine_models=False, ave_pos=False)
 
 # Load the CH vectors for the C atoms.
 structure.vectors(spin_id='@C*', attached='H*', ave=False)
@@ -46,51 +33,29 @@
 # Load the RDCs and PCSs.
 for i in xrange(len(align_list)):
     # The RDC.
-    rdc.read(align_id=align_list[i], file='rdc.txt', dir=data_path, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=1, data_col=i+3, error_col=None)
-    rdc.read(align_id=align_list[i], file='rdc_err.txt', dir=data_path, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=1, data_col=None, error_col=i+3)
-    rdc.display(align_id=align_list[i])
+    if i != 1:
+        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)
+        rdc.display(align_id=align_list[i])
 
     # The PCS.
-    pcs.read(align_id=align_list[i], file='pcs.txt', dir=data_path, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=1, data_col=i+2, error_col=None)
-    pcs.read(align_id=align_list[i], file='pcs_err.txt', dir=data_path, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=1, data_col=None, error_col=i+2)
-    pcs.display(align_id=align_list[i])
+    if i != 2:
+        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)
+        pcs.display(align_id=align_list[i])
 
     # The temperature.
     temperature(id=align_list[i], temp=298)
 
     # The frequency.
-    frq.set(id=align_list[i], frq=900.015 * 1e6)
+    frq.set(id=align_list[i], frq=799.75376122 * 1e6)
 
-# Create a data pipe for the aligned tag structures.
-pipe.create('tag', 'N-state')
-
-# Load all the tag structures.
-NUM_TAG = 10
-for i in range(NUM_TAG):
-    structure.read_pdb(file='tag_MCMM4_'+repr(i+1), dir=str_path, 
parser='internal', set_model_num=i+1, set_mol_name='tag')
-
-# Load the lanthanide atoms.
-structure.load_spins(spin_id='@C1', combine_models=False, ave_pos=False)
-
-# Switch back to the main analysis data pipe.
-pipe.switch('lactose')
-
-# Calculate the paramagnetic centre (from the structures in the 'tag' data 
pipe).
-pcs.centre(atom_id=':4@C1', pipe='tag')
+# Set the paramagnetic centre.
+pcs.centre([1, 2, -30])
 
 # Set up the model.
-n_state_model.select_model(model='population')
-
-# Set to equal probabilities.
-for j in xrange(NUM_STR):
-    value.set(1.0/NUM_STR, 'p'+repr(j))
+n_state_model.select_model(model='fixed')
 
 # Minimisation.
-minimise('bfgs', constraints=True, max_iter=5)
-
-# Calculate the AIC value.
-k, n, chi2 = n_state_model_obj.model_statistics()
-ds[ds.current_pipe].aic = chi2 + 2.0*k
+minimise('bfgs', constraints=True)
 
 # Write out a results file.
 results.write('devnull', force=True)