Author: bugman
Date: Tue May 13 23:41:56 2014
New Revision: 23162
URL: http://svn.gna.org/viewcvs/relax?rev=23162&view=rev
Log:
Replaced 'Q-factor' with 'Q factor' throughout the relax codebase.
This change to the correct notation covers code, comments, and docstrings.
Modified:
trunk/auto_analyses/stereochem_analysis.py
trunk/pipe_control/pcs.py
trunk/pipe_control/rdc.py
trunk/specific_analyses/n_state_model/api.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py
trunk/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
trunk/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
Modified: trunk/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/stereochem_analysis.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
--- trunk/auto_analyses/stereochem_analysis.py (original)
+++ trunk/auto_analyses/stereochem_analysis.py Tue May 13 23:41:56 2014
@@ -24,7 +24,7 @@
The analysis is preformed by using multiple ensembles of structures,
randomly sampled from a given
set of structures. The discrimination is performed by comparing the sets of
ensembles using NOE
-violations and RDC Q-factors.
+violations and RDC Q factors.
This script is split into multiple stages:
@@ -39,12 +39,12 @@
using the fit to first algorithm. The superimposed ensembles will be
placed into the
"ensembles_superimposed" directory. This stage is not necessary for the
NOE analysis.
- 4. The RDC Q-factor analysis.
+ 4. The RDC Q factor analysis.
5. Generation of Grace graphs.
- 6. Final ordering of ensembles using the combined RDC and NOE
Q-factors, whereby the NOE
- Q-factor is defined as::
+ 6. Final ordering of ensembles using the combined RDC and NOE Q
factors, whereby the NOE
+ Q factor is defined as::
Q^2 = U / sum(NOE_i^2),
@@ -210,7 +210,7 @@
elif self.stage == 3:
self.superimpose()
- # RDC Q-factor analysis.
+ # RDC Q factor analysis.
elif self.stage == 4:
self.rdc_analysis()
@@ -231,13 +231,13 @@
def combined_q(self):
- """Calculate the combined Q-factor.
+ """Calculate the combined Q factor.
The combined Q is defined as::
Q_total^2 = Q_NOE^2 + Q_RDC^2,
- and the NOE Q-factor as::
+ and the NOE Q factor as::
Q^2 = U / sum(NOE_i^2),
@@ -253,7 +253,7 @@
# Loop over the configurations.
for i in range(len(self.configs)):
# Print out.
- print("Creating the combined Q-factor file for configuration
'%s'." % self.configs[i])
+ print("Creating the combined Q factor file for configuration
'%s'." % self.configs[i])
# Open the NOE results file and read the data.
file = open(self.results_dir+sep+"NOE_viol_" + self.configs[i])
@@ -265,7 +265,7 @@
rdc_lines = file.readlines()
file.close()
- # The combined Q-factor file.
+ # The combined Q factor file.
out = open(self.results_dir+sep+"Q_total_%s" % self.configs[i],
'w')
out_sorted = open(self.results_dir+sep+"Q_total_%s_sorted" %
self.configs[i], 'w')
@@ -277,7 +277,7 @@
noe_viol = float(noe_lines[j].split()[1])
q_rdc = float(rdc_lines[j].split()[1])
- # The NOE Q-factor.
+ # The NOE Q factor.
q_noe = sqrt(noe_viol/self.noe_norm)
# Combined Q.
@@ -430,10 +430,10 @@
grace_curve.close()
grace_dist.close()
- # RDC Q-factors.
+ # RDC Q factors.
if access(self.results_dir+sep+"Q_factors_" + self.configs[0] +
"_sorted", F_OK):
# Print out.
- print("Generating RDC Q-factor Grace plots.")
+ print("Generating RDC Q factor Grace plots.")
# Open the Grace output files.
grace_curve = open(self.results_dir+sep+"RDC_%s_curve.agr" %
self.rdc_name, 'w')
@@ -451,7 +451,7 @@
# Add a new graph set.
data.append([])
- # Loop over the Q-factors.
+ # Loop over the Q factors.
values = []
for j in range(1, len(lines)):
# Extract the violation.
@@ -465,8 +465,8 @@
dist.append(self.generate_distribution(values,
inc=self.bucket_num, upper=self.upper_lim_rdc, lower=self.lower_lim_rdc))
# Headers.
- write_xy_header(file=grace_curve, title='%s RDC Q-factor
comparison' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[0]*n],
axis_labels=[['Ensemble (sorted)', '%s RDC Q-factor (pales format)' %
self.rdc_name]], legend_pos=[[0.3, 0.8]])
- write_xy_header(file=grace_dist, title='%s RDC Q-factor
comparison' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[1]*n],
symbol_sizes=[[0.5]*n], linestyle=[[3]*n], axis_labels=[['%s RDC Q-factor
(pales format)' % self.rdc_name, 'Frequency']], legend_pos=[[1.1, 0.8]])
+ write_xy_header(file=grace_curve, title='%s RDC Q factor
comparison' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[0]*n],
axis_labels=[['Ensemble (sorted)', '%s RDC Q factor (pales format)' %
self.rdc_name]], legend_pos=[[0.3, 0.8]])
+ write_xy_header(file=grace_dist, title='%s RDC Q factor
comparison' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[1]*n],
symbol_sizes=[[0.5]*n], linestyle=[[3]*n], axis_labels=[['%s RDC Q factor
(pales format)' % self.rdc_name, 'Frequency']], legend_pos=[[1.1, 0.8]])
# Write the data.
write_xy_data([data], file=grace_curve, graph_type='xy')
@@ -514,8 +514,8 @@
data_scaled[i].append([sqrt(noe_viol/self.noe_norm),
q_factor])
# Write the data.
- write_xy_header(file=grace_file, title='Correlation plot - %s
RDC vs. NOE' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[9]*n],
symbol_sizes=[[0.24]*n], linetype=[[0]*n], axis_labels=[['NOE violation
(Angstrom\\S2\\N)', '%s RDC Q-factor (pales format)' % self.rdc_name]],
legend_pos=[[1.1, 0.8]])
- write_xy_header(file=grace_file_scaled, title='Correlation plot
- %s RDC vs. NOE Q-factor' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[9]*n],
symbol_sizes=[[0.24]*n], linetype=[[0]*n], axis_labels=[['Normalised NOE
violation (Q = sqrt(U / \\xS\\f{}NOE\\si\\N\\S2\\N))', '%s RDC Q-factor
(pales format)' % self.rdc_name]], legend_pos=[[1.1, 0.8]])
+ write_xy_header(file=grace_file, title='Correlation plot - %s
RDC vs. NOE' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[9]*n],
symbol_sizes=[[0.24]*n], linetype=[[0]*n], axis_labels=[['NOE violation
(Angstrom\\S2\\N)', '%s RDC Q factor (pales format)' % self.rdc_name]],
legend_pos=[[1.1, 0.8]])
+ write_xy_header(file=grace_file_scaled, title='Correlation plot
- %s RDC vs. NOE Q factor' % self.rdc_name, subtitle=subtitle, sets=[n],
set_names=[self.configs], set_colours=[colours], symbols=[[9]*n],
symbol_sizes=[[0.24]*n], linetype=[[0]*n], axis_labels=[['Normalised NOE
violation (Q = sqrt(U / \\xS\\f{}NOE\\si\\N\\S2\\N))', '%s RDC Q factor
(pales format)' % self.rdc_name]], legend_pos=[[1.1, 0.8]])
write_xy_data([data], file=grace_file, graph_type='xy')
write_xy_data([data_scaled], file=grace_file_scaled,
graph_type='xy')
@@ -694,7 +694,7 @@
#grid_search(inc=4)
self.interpreter.minimise("simplex", constraints=False)
- # Store and write out the Q-factors.
+ # Store and write out the Q factors.
q_factors.append([cdp.q_rdc, ens])
out.write("%-20i%20.15f%20.15f\n" % (ens, cdp.q_rdc,
cdp.q_rdc_norm2))
Modified: trunk/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/pcs.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
--- trunk/pipe_control/pcs.py (original)
+++ trunk/pipe_control/pcs.py Tue May 13 23:41:56 2014
@@ -544,9 +544,9 @@
def q_factors(spin_id=None):
- """Calculate the Q-factors for the PCS data.
-
- @keyword spin_id: The spin ID string used to restrict the Q-factor
calculation to a subset of all spins.
+ """Calculate the Q factors for the PCS data.
+
+ @keyword spin_id: The spin ID string used to restrict the Q factor
calculation to a subset of all spins.
@type spin_id: None or str
"""
@@ -558,7 +558,7 @@
warn(RelaxWarning("No PCS data exists, Q factors cannot be
calculated."))
return
- # Q-factor dictionary.
+ # Q factor dictionary.
cdp.q_factors_pcs = {}
# Loop over the alignments.
@@ -595,7 +595,7 @@
# Sum the PCSs squared (for normalisation).
pcs2_sum = pcs2_sum + spin.pcs[align_id]**2
- # The Q-factor for the alignment.
+ # The Q factor for the alignment.
if pcs2_sum:
Q = sqrt(sse / pcs2_sum)
cdp.q_factors_pcs[align_id] = Q
@@ -611,7 +611,7 @@
warn(RelaxWarning("No back-calculated PCS data can be found for
the alignment ID '%s', skipping the PCS Q factor calculation for this
alignment." % align_id))
continue
- # The total Q-factor.
+ # The total Q factor.
cdp.q_pcs = 0.0
for id in cdp.q_factors_pcs:
cdp.q_pcs = cdp.q_pcs + cdp.q_factors_pcs[id]**2
Modified: trunk/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/rdc.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Tue May 13 23:41:56 2014
@@ -575,9 +575,9 @@
def q_factors(spin_id=None):
- """Calculate the Q-factors for the RDC data.
-
- @keyword spin_id: The spin ID string used to restrict the Q-factor
calculation to a subset of all spins.
+ """Calculate the Q factors for the RDC data.
+
+ @keyword spin_id: The spin ID string used to restrict the Q factor
calculation to a subset of all spins.
@type spin_id: None or str
"""
@@ -589,7 +589,7 @@
warn(RelaxWarning("No RDC data exists, Q factors cannot be
calculated."))
return
- # Q-factor dictonaries.
+ # Q factor dictonaries.
cdp.q_factors_rdc = {}
cdp.q_factors_rdc_norm2 = {}
@@ -683,16 +683,16 @@
if Da == 0.0:
norm = 1e-15
- # The Q-factor for the alignment.
+ # The Q factor for the alignment.
cdp.q_factors_rdc[align_id] = sqrt(sse / N / norm)
else:
cdp.q_factors_rdc[align_id] = 0.0
- # The second Q-factor definition.
+ # The second Q factor definition.
cdp.q_factors_rdc_norm2[align_id] = sqrt(sse / D2_sum)
- # The total Q-factor.
+ # The total Q factor.
cdp.q_rdc = 0.0
cdp.q_rdc_norm2 = 0.0
for id in cdp.q_factors_rdc:
Modified: trunk/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/api.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/api.py (original)
+++ trunk/specific_analyses/n_state_model/api.py Tue May 13 23:41:56
2014
@@ -161,11 +161,11 @@
# Store the back-calculated data.
minimise_bc_data(model)
- # Calculate the RDC Q-factors.
+ # Calculate the RDC Q factors.
if 'rdc' in data_types:
rdc.q_factors()
- # Calculate the PCS Q-factors.
+ # Calculate the PCS Q factors.
if 'pcs' in data_types:
pcs.q_factors()
@@ -568,14 +568,14 @@
# Statistical analysis.
if sim_index == None and ('rdc' in data_types or 'pcs' in
data_types):
- # Get the final back calculated data (for the Q-factor and
+ # Get the final back calculated data (for the Q factor and
minimise_bc_data(model)
- # Calculate the RDC Q-factors.
+ # Calculate the RDC Q factors.
if 'rdc' in data_types:
rdc.q_factors()
- # Calculate the PCS Q-factors.
+ # Calculate the PCS Q factors.
if 'pcs' in data_types:
pcs.q_factors()
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/rotor2/pcs_only/ave_pos_back_calc.py
Tue May 13 23:41:56 2014
@@ -64,7 +64,7 @@
rdc.write(align_id=id, file='ave_pos_rdc_%s.txt'%id, bc=True, force=True)
pcs.write(align_id=id, file='ave_pos_pcs_%s.txt'%id, bc=True, force=True)
-# Calculate Q-factors.
+# Calculate Q factors.
rdc.calc_q_factors()
pcs.calc_q_factors()
Modified: trunk/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
(original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py Tue
May 13 23:41:56 2014
@@ -55,7 +55,7 @@
# Back calc.
self._execute_uf(uf_name='rdc.back_calc')
-# Q-factors.
+# Q factors.
self._execute_uf(uf_name='rdc.calc_q_factors')
# Correlation plots.
Modified:
trunk/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py?rev=23162&r1=23161&r2=23162&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
(original)
+++
trunk/test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
Tue May 13 23:41:56 2014
@@ -23,7 +23,7 @@
The analysis is preformed by using multiple ensembles of structures,
randomly sampled from a given
set of structures. The discrimination is performed by comparing the sets of
ensembles using NOE
-violations and RDC Q-factors.
+violations and RDC Q factors.
This script is split into multiple stages:
@@ -38,7 +38,7 @@
using the fit to first algorithm. The superimposed ensembles will be
placed into the
"ensembles_superimposed" directory. This stage is not necessary for the
NOE analysis.
- 4. The RDC Q-factor analysis.
+ 4. The RDC Q factor analysis.
5. Generation of Grace graphs.
"""
r23162 - in /trunk: auto_analyses/ pipe_control/ specific_analyses/n_state_model/ test_suite/shared_data/frame_order/cam/rot...