r5019 - /1.3/sample_scripts/diff_min.py -- February 19, 2008 - 11:50

Author: bugman
Date: Tue Feb 19 11:50:03 2008
New Revision: 5019

URL: http://svn.gna.org/viewcvs/relax?rev=5019&view=rev
Log:
Converted the diff_min.py sample script to the new relax design.


Modified:
    1.3/sample_scripts/diff_min.py

Modified: 1.3/sample_scripts/diff_min.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/diff_min.py?rev=5019&r1=5018&r2=5019&view=diff
==============================================================================
--- 1.3/sample_scripts/diff_min.py (original)
+++ 1.3/sample_scripts/diff_min.py Tue Feb 19 11:50:03 2008
@@ -1,8 +1,8 @@
 # Script for model-free analysis.
 
-# Set the run names (also the names of preset model-free models).
-#runs = ['m1']
-runs = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
+# Set the data pipe names (also the names of preset model-free models).
+#pipes = ['m1']
+pipes = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
 
 # Nuclei type
 nuclei('N')
@@ -14,35 +14,35 @@
 print "#####################################"
 print "\n\n\n"
 
-for name in runs:
-    # Create the run.
-    run.create(name, 'mf')
+for name in pipes:
+    # Create the data pipe.
+    pipe.create(name, 'mf')
 
     # Load the sequence.
-    sequence.read(name, 'noe.500.out')
+    sequence.read('noe.500.out')
 
     # Load a PDB file.
-    structure.read_pdb(name, 'example.pdb')
+    structure.read_pdb('example.pdb')
 
     # Load the relaxation data.
-    relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
-    relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out')
-    relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out')
-    relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out')
-    relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out')
-    relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out')
+    relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
+    relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
+    relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
+    relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
+    relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
+    relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
 
     # Setup other values.
-    diffusion_tensor.init(name, (1e-8, 1.0, 60, 290), param_types=1, 
spheroid_type='oblate', fixed=1)
-    value.set(name, 1.02 * 1e-10, 'bond_length')
-    value.set(name, -172 * 1e-6, 'csa')
+    diffusion_tensor.init((1e-8, 1.0, 60, 290), param_types=1, 
spheroid_type='oblate', fixed=1)
+    value.set(1.02 * 1e-10, 'bond_length')
+    value.set(-172 * 1e-6, 'csa')
 
     # Select the model-free model.
-    model_free.select_model(run=name, model=name)
+    model_free.select_model(model=name)
 
     # Minimise.
-    grid_search(name, inc=5)
-    minimise('newton', run=name)
+    grid_search(inc=5)
+    minimise('newton')
 
 # Minimise the diffusion tensor parameters.
 print "\n\n\n\n\n"
@@ -51,19 +51,23 @@
 print "###########################################"
 print "\n\n\n"
 
-for name in runs:
+# Loop over the data pipes.
+for name in pipes:
+    # Switch to the data pipe.
+    pipe.switch(name)
+
     # Unfix the diffusion tensor.
-    fix(name, 'diff', fixed=0)
+    fix('diff', fixed=0)
 
     # Fix all model-free paremeter values.
-    fix(name, 'all_res')
+    fix('all_res')
 
     # Minimise.
-    grid_search(name, inc=5)
-    minimise('newton', run=name, max_iter=5000)
+    grid_search(inc=5)
+    minimise('newton', max_iter=5000)
 
     # Write the results.
-    results.write(run=name, file='results', force=1)
+    results.write(file='results', force=1)
 
 # Save the program state.
 state.save('save', force=1)