Author: semor
Date: Fri Jan 11 18:02:57 2008
New Revision: 4650
URL: http://svn.gna.org/viewcvs/relax?rev=4650&view=rev
Log:
Continued the shifting of the consistency tests code to the new relax design
started at r4583.
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=4650&r1=4649&r2=4650&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.3/specific_fns/consistency_tests.py Fri Jan
11 18:02:57 2008
@@ -49,7 +49,7 @@
raise RelaxError, "The frequency has not been set up."
# Test if the sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
+ if not cdp.res.has_key:
raise RelaxNoSequenceError, self.run
# Test if the CSA, bond length, angle Theta and correlation time
values have been set.
@@ -76,8 +76,8 @@
raise RelaxNoValueError, "correlation time"
# Frequency index.
- if relax_data_store.ct_frq[self.run] not in
relax_data_store.frq[self.run]:
- raise RelaxError, "No relaxation data corresponding to the
frequency " + `relax_data_store.ct_frq[self.run]` + " has been loaded."
+ if cdp.ct_frq not in cdp.frq:
+ raise RelaxError, "No relaxation data corresponding to the
frequency " + `cdp.ct_frq` + " has been loaded."
# Consistency testing.
for spin in spin_loop(spin_id):
@@ -91,7 +91,7 @@
# Residue specific frequency index.
frq_index = None
for j in xrange(data.num_frq):
- if data.frq[j] == relax_data_store.ct_frq[self.run]:
+ if data.frq[j] == cdp.ct_frq:
frq_index = j
if frq_index == None:
continue
@@ -129,7 +129,7 @@
continue
# Initialise the function to calculate.
- self.ct = Consistency(frq=relax_data_store.ct_frq[self.run],
gx=relax_data_store.gx, gh=relax_data_store.gh, mu0=relax_data_store.mu0,
h_bar=relax_data_store.h_bar)
+ self.ct = Consistency(frq=cdp.ct_frq, gx=relax_data_store.gx,
gh=relax_data_store.gh, mu0=relax_data_store.mu0,
h_bar=relax_data_store.h_bar)
# Calculate the consistency tests values.
j0, f_eta, f_r2 = self.ct.func(orientation=data.orientation,
tc=data.tc, r=data.r, csa=data.csa, r1=r1, r2=r2, noe=noe)
@@ -270,11 +270,11 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
+ if not cdp.res.has_key:
return 0
# Return the number of residues.
- return len(relax_data_store.res[self.run])
+ return len(cdp.res)
def overfit_deselect(self):
@@ -445,28 +445,28 @@
def set_frq(self, frq=None):
"""Function for selecting which relaxation data to use in the
consistency tests."""
- # Run argument.
- self.run = run
-
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
# Test if the run exists.
if not self.run in relax_data_store.run_names:
raise RelaxNoPipeError, self.run
# Test if the run type is set to 'ct'.
- function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
+ function_type = relax_data_store.run_types[cdp.run_names.index]
if function_type != 'ct':
raise RelaxFuncSetupError,
self.relax.specific_setup.get_string(function_type)
# Test if the frequency has been set.
- if hasattr(relax_data_store, 'ct_frq') and
relax_data_store.ct_frq.has_key(self.run):
- raise RelaxError, "The frequency for the run " + `self.run` + "
has already been set."
+ if hasattr(cdp, 'ct_frq'):
+ raise RelaxError, "The frequency for the run has already been
set."
# Create the data structure if it doesn't exist.
- if not hasattr(relax_data_store, 'ct_frq'):
- relax_data_store.ct_frq = {}
+ if not hasattr(cdp, 'ct_frq'):
+ cdp.ct_frq = {}
# Set the frequency.
- relax_data_store.ct_frq[self.run] = frq
+ cdp.ct_frq = frq
def set_error(self, instance, spin, error):
@@ -477,15 +477,15 @@
# Return J(0) sim data.
if index == 0:
- relax_data_store.res[self.run][instance].j0_err = error
+ cdp.res[instance].j0_err = error
# Return F_eta sim data.
if index == 1:
- relax_data_store.res[self.run][instance].f_eta_err = error
+ cdp.res[instance].f_eta_err = error
# Return F_R2 sim data.
if index == 2:
- relax_data_store.res[self.run][instance].f_r2_err = error
+ cdp.res[instance].f_r2_err = error
def sim_return_param(self, instance, spin):
@@ -495,20 +495,20 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Skip unselected residues.
- if not relax_data_store.res[self.run][instance].select:
+ if not cdp.res[instance].select:
return
# Return J(0) sim data.
if index == 0:
- return relax_data_store.res[self.run][instance].j0_sim
+ return cdp.res[instance].j0_sim
# Return F_eta sim data.
if index == 1:
- return relax_data_store.res[self.run][instance].f_eta_sim
+ return cdp.res[instance].f_eta_sim
# Return F_R2 sim data.
if index == 2:
- return relax_data_store.res[self.run][instance].f_r2_sim
+ return cdp.res[instance].f_r2_sim
def sim_return_selected(self, instance):
@@ -518,7 +518,7 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Multiple instances.
- return relax_data_store.res[self.run][instance].select_sim
+ return cdp.res[instance].select_sim
def set_selected_sim(self, instance, select_sim):
@@ -528,7 +528,7 @@
cdp = relax_data_store[relax_data_store.current_pipe]
# Multiple instances.
- relax_data_store.res[self.run][instance].select_sim = select_sim
+ cdp.res[instance].select_sim = select_sim
def sim_pack_data(self, spin, sim_data):
@@ -604,7 +604,7 @@
raise RelaxNoPipeError, self.run
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
+ if not cdp.res.has_key:
raise RelaxNoSequenceError, self.run
@@ -615,9 +615,9 @@
ri = []
ri_error = []
if hasattr(relax_data_store, 'num_ri'):
- for i in xrange(relax_data_store.num_ri[self.run]):
- ri.append('Ri_(' + relax_data_store.ri_labels[self.run][i] +
"_" +
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][i]]
+ ")")
- ri_error.append('Ri_error_(' +
relax_data_store.ri_labels[self.run][i] + "_" +
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][i]]
+ ")")
+ for i in xrange(cdp.num_ri):
+ ri.append('Ri_(' + cdp.ri_labels[i] + "_" +
cdp.frq_labels[cdp.remap_table[i]] + ")")
+ ri_error.append('Ri_error_(' + cdp.ri_labels[i] + "_" +
cdp.frq_labels[cdp.remap_table[i]] + ")")
# Write the header line.
self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', data_set='Data_set', nucleus='Nucleus',
wH='Proton_frq_(MHz)', j0='J(0)', f_eta='F_eta', f_r2='F_R2',
r='Bond_length_(A)', csa='CSA_(ppm)', orientation='Angle_Theta_(degrees)',
tc='Correlation_time_(ns)', ri_labels='Ri_labels', remap_table='Remap_table',
frq_labels='Frq_labels', frq='Frequencies', ri=ri, ri_error=ri_error)
@@ -630,14 +630,14 @@
nucleus = self.relax.generic.nuclei.find_nucleus()
# The proton frequency in MHz.
- wH = relax_data_store.ct_frq[self.run] / 1e6
+ wH = cdp.ct_frq / 1e6
# Relaxation data setup.
try:
- ri_labels = replace(`relax_data_store.ri_labels[self.run]`, ' ',
'')
- remap_table = replace(`relax_data_store.remap_table[self.run]`,
' ', '')
- frq_labels = replace(`relax_data_store.frq_labels[self.run]`, '
', '')
- frq = replace(`relax_data_store.frq[self.run]`, ' ', '')
+ ri_labels = replace(`cdp.ri_labels`, ' ', '')
+ remap_table = replace(`cdp.remap_table`, ' ', '')
+ frq_labels = replace(`cdp.frq_labels`, ' ', '')
+ frq = replace(`cdp.frq`, ' ', '')
except AttributeError:
ri_labels = `None`
remap_table = `None`
@@ -645,9 +645,9 @@
frq = `None`
# Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
+ for i in xrange(len(cdp.res)):
# Reassign data structure.
- data = relax_data_store.res[self.run][i]
+ data = cdp.res[i]
# J(0).
j0 = None
@@ -677,13 +677,13 @@
# Relaxation data and errors.
ri = []
ri_error = []
- if hasattr(relax_data_store, 'num_ri'):
- for i in xrange(relax_data_store.num_ri[self.run]):
+ if hasattr(cdp, 'num_ri'):
+ for i in xrange(cdp.num_ri):
try:
# Find the residue specific data corresponding to i.
index = None
for j in xrange(data.num_ri):
- if data.ri_labels[j] ==
relax_data_store.ri_labels[self.run][i] and
data.frq_labels[data.remap_table[j]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][i]]:
+ if data.ri_labels[j] == cdp.ri_labels[i] and
data.frq_labels[data.remap_table[j]] == cdp.frq_labels[cdp.remap_table[i]]:
index = j
# Data exists for this data type.
@@ -703,15 +703,15 @@
#########
# Skip this section and the next if no simulations have been setup.
- if not hasattr(relax_data_store, 'sim_state'):
+ if not hasattr(cdp, 'sim_state'):
return
- elif relax_data_store.sim_state[self.run] == 0:
+ elif cdp.sim_state == 0:
return
# Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
+ for i in xrange(len(cdp.res)):
# Reassign data structure.
- data = relax_data_store.res[self.run][i]
+ data = cdp.res[i]
# J(0).
j0 = None
@@ -751,7 +751,7 @@
# Relaxation data and errors.
ri = []
ri_error = []
- for i in xrange(relax_data_store.num_ri[self.run]):
+ for i in xrange(cdp.num_ri):
ri.append(None)
ri_error.append(None)
@@ -763,11 +763,11 @@
####################
# Loop over the simulations.
- for i in xrange(relax_data_store.sim_number[self.run]):
+ for i in xrange(cdp.sim_number):
# Loop over the sequence.
- for j in xrange(len(relax_data_store.res[self.run])):
+ for j in xrange(len(cdp.res)):
# Reassign data structure.
- data = relax_data_store.res[self.run][j]
+ data = cdp.res[j]
# J(0).
j0 = None
@@ -807,13 +807,13 @@
# Relaxation data and errors.
ri = []
ri_error = []
- if hasattr(relax_data_store, 'num_ri'):
- for k in xrange(relax_data_store.num_ri[self.run]):
+ if hasattr(cdp, 'num_ri'):
+ for k in xrange(cdp.num_ri):
try:
# Find the residue specific data corresponding
to k.
index = None
for l in xrange(data.num_ri):
- if data.ri_labels[l] ==
relax_data_store.ri_labels[self.run][k] and
data.frq_labels[data.remap_table[l]] ==
relax_data_store.frq_labels[self.run][relax_data_store.remap_table[self.run][k]]:
+ if data.ri_labels[l] == cdp.ri_labels[k] and
data.frq_labels[data.remap_table[l]] == cdp.frq_labels[cdp.remap_table[k]]:
index = l
# Data exists for this data type.
r4650 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py