Author: semor
Date: Wed Jan 9 21:38:52 2008
New Revision: 4583
URL: http://svn.gna.org/viewcvs/relax?rev=4583&view=rev
Log:
Started the shifting of the consistency tests code to the new relax design.
Followed the tips by Edward d'Auvergne in the post at:
https://mail.gna.org/public/relax-devel/2008-01/msg00012.html (Message-id:
<1199821867.8905.7.camel@localhost>)
Modified:
branches/consistency_tests_1.3/specific_fns/consistency_tests.py
Modified: branches/consistency_tests_1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/consistency_tests.py?rev=4583&r1=4582&r2=4583&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/consistency_tests.py Wed Jan
9 21:38:52 2008
@@ -38,18 +38,18 @@
"""Class containing functions specific to consistency testing."""
- def calculate(self, run=None, verbosity=1, sim_index=None):
+ def calculate(self, verbosity=1, sim_spin=None):
"""Calculation of the consistency functions."""
- # Run argument.
- self.run = run
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
# Test if the frequency has been set.
- if not hasattr(relax_data_store, 'ct_frq') or not
relax_data_store.ct_frq.has_key(self.run) or
type(relax_data_store.ct_frq[self.run]) != float:
+ if not hasattr(cdp, 'ct_frq') or not
relax_data_store.ct_frq.has_key(self.run) or
type(relax_data_store.ct_frq[self.run]) != float:
raise RelaxError, "The frequency for the run " + `self.run` + "
has not been set up."
# Test if the nucleus type has been set.
- if not hasattr(relax_data_store, 'gx'):
+ if not hasattr(cdp, 'gx'):
raise RelaxNucleusError
# Test if the sequence data is loaded.
@@ -57,9 +57,9 @@
raise RelaxNoSequenceError, self.run
# Test if the CSA, bond length, angle Theta and correlation time
values have been set.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Skip unselected residues.
- if not relax_data_store.res[self.run][i].select:
+ for spin in spin_loop(spin_id):
+ # Skip unselected spins.
+ if not spin.select:
continue
# CSA value.
@@ -67,15 +67,15 @@
raise RelaxNoValueError, "CSA"
# Bond length value.
- if not hasattr(relax_data_store.res[self.run][i], 'r') or
relax_data_store.res[self.run][i].r == None:
+ if not hasattr(cdp, 'r') or relax_data_store.res[self.run][i].r
== None:
raise RelaxNoValueError, "bond length"
# Angle Theta
- if not hasattr(self.relax.data.res[self.run][i], 'orientation')
or self.relax.data.res[self.run][i].orientation == None:
+ if not hasattr(cdp, 'orientation') or
relax_data_store.res[self.run][i].orientation == None:
raise RelaxNoValueError, "angle Theta"
# Correlation time
- if not hasattr(self.relax.data.res[self.run][i], 'tc') or
self.relax.data.res[self.run][i].tc == None:
+ if not hasattr(cdp, 'tc') or
relax_data_store.res[self.run][i].tc == None:
raise RelaxNoValueError, "correlation time"
# Frequency index.
@@ -83,12 +83,12 @@
raise RelaxError, "No relaxation data corresponding to the
frequency " + `relax_data_store.ct_frq[self.run]` + " has been loaded."
# Consistency testing.
- for i in xrange(len(relax_data_store.res[self.run])):
+ for i in xrange(len(cdp)):
# Reassign data structure.
- data = relax_data_store.res[self.run][i]
-
- # Skip unselected residues.
- if not data.select:
+ data = cdp
+
+ # Skip unselected spins.
+ if not spin.select:
continue
# Residue specific frequency index.
@@ -266,7 +266,7 @@
return 13 * 1e-9
- def num_instances(self, run=None):
+ def num_instances(self):
"""Function for returning the number of instances."""
# Arguments.
@@ -280,12 +280,12 @@
return len(relax_data_store.res[self.run])
- def overfit_deselect(self, run):
+ def overfit_deselect(self):
"""Function for deselecting residues without sufficient data to
support calculation"""
- # Test the sequence data exists:
- if not relax_data_store.res.has_key(run):
- raise RelaxNoSequenceError, run
+ # Test if the sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Loop over residue data:
for residue in relax_data_store.res[run]:
@@ -444,7 +444,8 @@
"""
__docformat__ = "plaintext"
- def set_frq(self, run=None, frq=None):
+
+ def set_frq(self, frq=None):
"""Function for selecting which relaxation data to use in the
consistency tests."""
# Run argument.
@@ -471,7 +472,7 @@
relax_data_store.ct_frq[self.run] = frq
- def set_error(self, run, instance, index, error):
+ def set_error(self, instance, spin, error):
"""Function for setting parameter errors."""
# Arguments.
@@ -490,7 +491,7 @@
relax_data_store.res[self.run][instance].f_r2_err = error
- def sim_return_param(self, run, instance, index):
+ def sim_return_param(self, instance, spin):
"""Function for returning the array of simulation parameter
values."""
# Arguments.
@@ -513,7 +514,7 @@
return relax_data_store.res[self.run][instance].f_r2_sim
- def sim_return_selected(self, run, instance):
+ def sim_return_selected(self, instance):
"""Function for returning the array of selected simulation flags."""
# Arguments.
@@ -523,7 +524,7 @@
return relax_data_store.res[self.run][instance].select_sim
- def set_selected_sim(self, run, instance, select_sim):
+ def set_selected_sim(self, instance, select_sim):
"""Function for returning the array of selected simulation flags."""
# Arguments.
@@ -533,7 +534,7 @@
relax_data_store.res[self.run][instance].select_sim = select_sim
- def sim_pack_data(self, run, i, sim_data):
+ def sim_pack_data(self, spin, sim_data):
"""Function for packing Monte Carlo simulation data."""
# Test if the simulation data already exists.
@@ -595,7 +596,7 @@
file.write("\n")
- def write_columnar_results(self, file, run):
+ def write_columnar_results(self, file):
"""Function for printing the results into a file."""
# Arguments.
@@ -689,8 +690,8 @@
index = j
# Data exists for this data type.
- ri.append(`data.relax_data[index]`)
- ri_error.append(`data.relax_error[index]`)
+ ri.append(spin)
+ ri_error.append(spin)
# No data exists for this data type.
except:
@@ -809,7 +810,7 @@
# Relaxation data and errors.
ri = []
ri_error = []
- if hasattr(self.relax.data, 'num_ri'):
+ if hasattr(relax_data_store, 'num_ri'):
for k in xrange(relax_data_store.num_ri[self.run]):
try:
# Find the residue specific data corresponding
to k.
@@ -819,8 +820,8 @@
index = l
# Data exists for this data type.
- ri.append(`data.relax_sim_data[i][index]`)
- ri_error.append(`data.relax_error[index]`)
+ ri.append(spin)
+ ri_error.append(spin)
# No data exists for this data type.
except:
r4583 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py