Author: bugman
Date: Wed Feb 8 11:52:12 2012
New Revision: 15318
URL: http://svn.gna.org/viewcvs/relax?rev=15318&view=rev
Log:
Modified the base script for the frame order system tests to allow the state
file to be used.
If the load_state flag is set, then instead of the full loading of all the
data, the pre-created
state files in the shared data directories will be used. This is to
significantly speed up these
system tests.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=15318&r1=15317&r2=15318&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py
Wed Feb 8 11:52:12 2012
@@ -40,6 +40,7 @@
class Base_script:
# Class variables.
cone = True
+ load_state = False
def __init__(self, interpreter):
"""Execute the frame order analysis."""
@@ -51,6 +52,18 @@
# The data path.
self.data_path = BASE_PATH + self.directory
+ # Pre-created set up.
+ if self.load_state:
+ # Reset the data store.
+ self.interpreter.reset()
+
+ # Load the save file.
+ self.interpreter.state.load('frame_order', dir=self.data_path)
+
+ # New set up.
+ else:
+ self.setup()
+
# Optimise.
self.optimisation()
@@ -69,74 +82,6 @@
def optimisation(self):
"""Optimise the frame order model."""
-
- # Create the data pipe.
- self.interpreter.pipe.create(pipe_name='frame order',
pipe_type='frame order')
-
- # Read the structures.
- self.interpreter.structure.read_pdb('1J7O_1st_NH.pdb',
dir=BASE_PATH, set_mol_name='N-dom')
- self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb',
dir=BASE_PATH, set_mol_name='C-dom')
-
- # Load the spins.
- self.interpreter.structure.load_spins('@N')
- self.interpreter.structure.load_spins('@H')
-
- # Load the NH vectors.
- self.interpreter.structure.vectors(spin_id='@N', attached='H',
ave=False)
-
- # Set the values needed to calculate the dipolar constant.
- self.interpreter.value.set(1.041 * 1e-10, 'r', spin_id="@N")
- self.interpreter.value.set('15N', 'heteronuc_type', spin_id="@N")
- self.interpreter.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 not hasattr(ds, 'flag_rdc') or ds.flag_rdc:
- self.interpreter.rdc.read(align_id=ln[i],
file='rdc_%s.txt'%ln[i], dir=self.data_path, res_num_col=2, spin_name_col=5,
data_col=6, error_col=7)
-
- # The PCS.
- if not hasattr(ds, 'flag_pcs') or ds.flag_pcs:
- self.interpreter.pcs.read(align_id=ln[i],
file='pcs_%s.txt'%ln[i], dir=self.data_path, res_num_col=2, spin_name_col=5,
data_col=6, error_col=7)
-
- # The temperature and field strength.
- self.interpreter.temperature(id=ln[i], temp=303)
- self.interpreter.frq.set(id=ln[i], frq=900e6)
-
- # Load the N-domain tensors (the full tensors).
- self.interpreter.script(BASE_PATH + 'tensors.py')
-
- # Define the domains.
- self.interpreter.domain(id='N', spin_id=":1-78")
- self.interpreter.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.
- self.interpreter.align_tensor.init(tensor=red[i],
params=(0,0,0,0,0))
-
- # Set the domain info.
- self.interpreter.align_tensor.set_domain(tensor=full[i],
domain='N')
- self.interpreter.align_tensor.set_domain(tensor=red[i],
domain='C')
-
- # Specify which tensor is reduced.
- self.interpreter.align_tensor.reduction(full_tensor=full[i],
red_tensor=red[i])
-
- # Select the model.
- self.interpreter.frame_order.select_model(self.model)
-
- # Set the reference domain.
- self.interpreter.frame_order.ref_domain('N')
-
- # Set the initial pivot point.
- pivot = array([ 37.254, 0.5, 16.7465])
- self.interpreter.frame_order.pivot(pivot, fix=True)
-
- # Set the paramagnetic centre.
- self.interpreter.paramag.centre(pos=[35.934, 12.194, -4.206])
# Set the number of numerical integration points.
if hasattr(self, 'num_int_pts'):
@@ -218,6 +163,78 @@
self.interpreter.frame_order.domain_to_pdb(domain='C',
pdb='1J7P_1st_NH_rot.pdb')
+ def setup(self):
+ """Optimise the frame order model."""
+
+ # Create the data pipe.
+ self.interpreter.pipe.create(pipe_name='frame order',
pipe_type='frame order')
+
+ # Read the structures.
+ self.interpreter.structure.read_pdb('1J7O_1st_NH.pdb',
dir=BASE_PATH, set_mol_name='N-dom')
+ self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb',
dir=BASE_PATH, set_mol_name='C-dom')
+
+ # Load the spins.
+ self.interpreter.structure.load_spins('@N')
+ self.interpreter.structure.load_spins('@H')
+
+ # Load the NH vectors.
+ self.interpreter.structure.vectors(spin_id='@N', attached='H',
ave=False)
+
+ # Set the values needed to calculate the dipolar constant.
+ self.interpreter.value.set(1.041 * 1e-10, 'r', spin_id="@N")
+ self.interpreter.value.set('15N', 'heteronuc_type', spin_id="@N")
+ self.interpreter.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 not hasattr(ds, 'flag_rdc') or ds.flag_rdc:
+ self.interpreter.rdc.read(align_id=ln[i],
file='rdc_%s.txt'%ln[i], dir=self.data_path, res_num_col=2, spin_name_col=5,
data_col=6, error_col=7)
+
+ # The PCS.
+ if not hasattr(ds, 'flag_pcs') or ds.flag_pcs:
+ self.interpreter.pcs.read(align_id=ln[i],
file='pcs_%s.txt'%ln[i], dir=self.data_path, res_num_col=2, spin_name_col=5,
data_col=6, error_col=7)
+
+ # The temperature and field strength.
+ self.interpreter.temperature(id=ln[i], temp=303)
+ self.interpreter.frq.set(id=ln[i], frq=900e6)
+
+ # Load the N-domain tensors (the full tensors).
+ self.interpreter.script(BASE_PATH + 'tensors.py')
+
+ # Define the domains.
+ self.interpreter.domain(id='N', spin_id=":1-78")
+ self.interpreter.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.
+ self.interpreter.align_tensor.init(tensor=red[i],
params=(0,0,0,0,0))
+
+ # Set the domain info.
+ self.interpreter.align_tensor.set_domain(tensor=full[i],
domain='N')
+ self.interpreter.align_tensor.set_domain(tensor=red[i],
domain='C')
+
+ # Specify which tensor is reduced.
+ self.interpreter.align_tensor.reduction(full_tensor=full[i],
red_tensor=red[i])
+
+ # Select the model.
+ self.interpreter.frame_order.select_model(self.model)
+
+ # Set the reference domain.
+ self.interpreter.frame_order.ref_domain('N')
+
+ # Set the initial pivot point.
+ pivot = array([ 37.254, 0.5, 16.7465])
+ self.interpreter.frame_order.pivot(pivot, fix=True)
+
+ # Set the paramagnetic centre.
+ self.interpreter.paramag.centre(pos=[35.934, 12.194, -4.206])
+
+
def transform(self):
"""Transform the domain to the average position."""
r15318 - /branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/cam/base_script.py