Author: bugman
Date: Mon Feb 22 13:39:46 2010
New Revision: 10815
URL: http://svn.gna.org/viewcvs/relax?rev=10815&view=rev
Log:
Stereochem_analysis.grace_plots() now uses the new write_xy_header() &
write_xy_data() fns.
Modified:
1.3/auto_analyses/stereochem_analysis.py
Modified: 1.3/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/stereochem_analysis.py?rev=10815&r1=10814&r2=10815&view=diff
==============================================================================
--- 1.3/auto_analyses/stereochem_analysis.py (original)
+++ 1.3/auto_analyses/stereochem_analysis.py Mon Feb 22 13:39:46 2010
@@ -55,6 +55,7 @@
# relax module imports.
from generic_fns import pipes
+from generic_fns.grace import write_xy_data, write_xy_header
from generic_fns.selection import spin_loop
from physical_constants import dipolar_constant, g1H, g13C
from prompt.interpreter import Interpreter
@@ -184,6 +185,24 @@
def grace_plots(self):
"""Generate grace plots of the results."""
+ # The number of configs.
+ n = len(self.configs)
+
+ # The colours for the different configs.
+ defaults = [4, 2] # Blue and red.
+ colours = []
+ for i in range(n):
+ # Default colours.
+ if i < len(defaults):
+ colours.append(defaults[i])
+
+ # Otherwise black!
+ else:
+ colours.append(0)
+
+ # Subtitle for all graphs.
+ subtitle = '%s ensembles of %s' % (self.num_ens, self.num_models)
+
# NOE violations.
if access(self.results_dir+sep+"NOE_viol_" + self.configs[0] +
"_sorted", F_OK):
# Print out.
@@ -193,74 +212,38 @@
grace_curve = open(self.results_dir+sep+"NOE_viol_curve.agr",
'w')
grace_dist = open(self.results_dir+sep+"NOE_viol_dist.agr", 'w')
- # S-curve header.
- colours = [4, 2] # Blue and red.
- grace_curve.write("@version 50121\n")
- grace_curve.write("@page size 842, 595\n") # A4.
- grace_curve.write("@with g0\n")
- grace_curve.write("@ world 0, 0, %s, 200\n" % self.num_ens)
- grace_curve.write("@ view 0.150000, 0.150000, 1.28, 0.85\n")
- grace_curve.write("@ title \"NOE violation comparison\"\n")
- grace_curve.write("@ subtitle \"%s ensembles of %s\"\n" %
(self.num_ens, self.num_models))
- grace_curve.write("@ xaxis label \"Ensemble (sorted)\"\n")
- grace_curve.write("@ yaxis label \"NOE violation
(Angstrom\S2\N)\"\n")
- grace_curve.write("@ legend 0.3, 0.8\n")
- for i in range(len(self.configs)):
- grace_curve.write("@ s%s line color %s\n" % (i,
colours[i]))
- grace_curve.write("@ s%s legend \"%s\"\n" % (i,
self.configs[i]))
-
- # Distribution header.
- colours = [4, 2] # Blue and red.
- grace_dist.write("@version 50121\n")
- grace_dist.write("@page size 842, 595\n") # A4.
- grace_dist.write("@with g0\n")
- grace_dist.write("@ world 0, 0, 200, 0.2\n")
- grace_dist.write("@ view 0.150000, 0.150000, 1.28, 0.85\n")
- grace_dist.write("@ title \"NOE violation comparison\"\n")
- grace_dist.write("@ subtitle \"%s ensembles of %s\"\n" %
(self.num_ens, self.num_models))
- grace_dist.write("@ xaxis label \"NOE violation
(Angstrom\S2\N)\"\n")
- grace_dist.write("@ yaxis label \"Frequency\"\n")
- grace_dist.write("@ legend 1.1, 0.8\n")
- for i in range(len(self.configs)):
- grace_dist.write("@ s%s symbol 1\n" % i)
- grace_dist.write("@ s%s symbol size 0.5\n" % i)
- grace_dist.write("@ s%s symbol color %s\n" % (i,
colours[i]))
- grace_dist.write("@ s%s line linestyle 3\n" % i)
- grace_dist.write("@ s%s line color %s\n" % (i,
colours[i]))
- grace_dist.write("@ s%s legend \"%s\"\n" % (i,
self.configs[i]))
-
# Loop over the configurations.
- for i in range(len(self.configs)):
- # Header.
- grace_curve.write("@target G0.S"+repr(i)+"\n@type xy\n")
- grace_dist.write("@target G0.S"+repr(i)+"\n@type xy\n")
-
+ data = []
+ dist = []
+ for i in range(n):
# Open the results file and read the data.
file = open(self.results_dir+sep+"NOE_viol_" +
self.configs[i] + "_sorted")
lines = file.readlines()
file.close()
+ # Add a new graph set.
+ data.append([])
+
# Loop over the ensembles and extract the NOE violation.
noe_viols = []
- for i in range(1, len(lines)):
+ for j in range(1, len(lines)):
# Extract the violation.
- viol = float(split(lines[i])[1])
+ viol = float(split(lines[j])[1])
noe_viols.append(viol)
- # Write the data.
- grace_curve.write("%-8s%-30s\n" % (i, viol))
+ # Add to the data structure.
+ data[i].append([j, viol])
# Calculate the R distribution.
- dist = self.generate_distribution(noe_viols,
inc=self.bucket_num, upper=self.upper_lim_noe, lower=self.lower_lim_noe)
-
- # Loop over the distribution bins.
- for i in range(len(dist)):
- # Write the data.
- grace_dist.write("%s %s\n" % (dist[i][0], dist[i][1]))
-
- # End of data.
- grace_curve.write("&\n")
- grace_dist.write("&\n")
+ dist.append(self.generate_distribution(noe_viols,
inc=self.bucket_num, upper=self.upper_lim_noe, lower=self.lower_lim_noe))
+
+ # Headers.
+ write_xy_header(file=grace_curve, title='NOE violation
comparison', subtitle=subtitle, sets=n, set_names=self.configs,
set_colours=colours, symbols=[0]*n, axis_labels=['Ensemble (sorted)', 'NOE
violation (Angstrom\S2\N)'], axis_min=[0, 0], axis_max=[self.num_ens, 200],
legend_pos=[0.3, 0.8])
+ write_xy_header(file=grace_dist, title='NOE violation
comparison', subtitle=subtitle, sets=n, set_names=self.configs,
set_colours=colours, symbols=[1]*n, symbol_sizes=[0.5]*n, linestyle=[3]*n,
axis_labels=['NOE violation (Angstrom\S2\N)', 'Frequency'], axis_min=[0, 0],
axis_max=[200, 0.2], legend_pos=[1.1, 0.8])
+
+ # Write the data.
+ write_xy_data([data], file=grace_curve, graph_type='xy')
+ write_xy_data([dist], file=grace_dist, graph_type='xy')
# Close the files.
grace_curve.close()
@@ -275,79 +258,42 @@
grace_curve = open(self.results_dir+sep+"RDC_%s_curve.agr" %
self.rdc_name, 'w')
grace_dist = open(self.results_dir+sep+"RDC_%s_dist.agr" %
self.rdc_name, 'w')
- # S-curve header.
- colours = [4, 2] # Blue and red.
- grace_curve.write("@version 50121\n")
- grace_curve.write("@page size 842, 595\n") # A4.
- grace_curve.write("@with g0\n")
- grace_curve.write("@ world 0, 0, %s, 2\n" % self.num_ens)
- grace_curve.write("@ view 0.150000, 0.150000, 1.28, 0.85\n")
- grace_curve.write("@ title \"%s RDC Q-factor comparison\"\n"
% self.rdc_name)
- grace_curve.write("@ subtitle \"%s ensembles of %s\"\n" %
(self.num_ens, self.num_models))
- grace_curve.write("@ xaxis label \"Ensemble (sorted)\"\n")
- grace_curve.write("@ yaxis label \"%s RDC Q-factor (pales
format)\"\n" % self.rdc_name)
- grace_curve.write("@ legend 0.3, 0.8\n")
- for i in range(len(self.configs)):
- grace_curve.write("@ s%s line color %s\n" % (i,
colours[i]))
- grace_curve.write("@ s%s legend \"%s\"\n" % (i,
self.configs[i]))
-
- # Distribution header.
- colours = [4, 2] # Blue and red.
- grace_dist.write("@version 50121\n")
- grace_dist.write("@page size 842, 595\n") # A4.
- grace_dist.write("@with g0\n")
- grace_dist.write("@ world 0, 0, 2, 0.2\n")
- grace_dist.write("@ view 0.150000, 0.150000, 1.28, 0.85\n")
- grace_dist.write("@ title \"%s RDC Q-factor comparison\"\n" %
self.rdc_name)
- grace_dist.write("@ subtitle \"%s ensembles of %s\"\n" %
(self.num_ens, self.num_models))
- grace_dist.write("@ xaxis label \"%s RDC Q-factor (pales
format)\"\n" % self.rdc_name)
- grace_dist.write("@ yaxis label \"Frequency\"\n")
- grace_dist.write("@ legend 1.1, 0.8\n")
- for i in range(len(self.configs)):
- grace_dist.write("@ s%s symbol 1\n" % i)
- grace_dist.write("@ s%s symbol size 0.5\n" % i)
- grace_dist.write("@ s%s symbol color %s\n" % (i,
colours[i]))
- grace_dist.write("@ s%s line linestyle 3\n" % i)
- grace_dist.write("@ s%s line color %s\n" % (i,
colours[i]))
- grace_dist.write("@ s%s legend \"%s\"\n" % (i,
self.configs[i]))
-
# Loop over the configurations.
- for i in range(len(self.configs)):
- # Grace headers.
- grace_curve.write("@target G0.S%s\n@type xy\n" % i)
- grace_dist.write("@target G0.S%s\n@type xy\n" % i)
-
+ data = []
+ dist = []
+ for i in range(n):
# Open the results file and read the data.
file = open(self.results_dir+sep+"Q_factors_" +
self.configs[i] + "_sorted")
lines = file.readlines()
file.close()
+ # Add a new graph set.
+ data.append([])
+
# Loop over the Q-factors.
values = []
- for i in range(1, len(lines)):
+ for j in range(1, len(lines)):
# Extract the violation.
- value = float(split(lines[i])[1])
+ value = float(split(lines[j])[1])
values.append(value)
- # Write the data.
- grace_curve.write("%-8s%-30s\n" % (i, value))
+ # Add to the data structure.
+ data[i].append([j, value])
# Calculate the R distribution.
- dist = self.generate_distribution(values,
inc=self.bucket_num, upper=self.upper_lim_rdc, lower=self.lower_lim_rdc)
-
- # Loop over the distribution bins.
- for i in range(len(dist)):
- # Write the data.
- grace_dist.write("%s %s\n" % (dist[i][0], dist[i][1]))
-
- # End of data.
- grace_curve.write("&\n")
- grace_dist.write("&\n")
+ 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], axis_min=[0, 0], axis_max=[self.num_ens, 2], 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'], axis_min=[0, 0], axis_max=[2, 0.2],
legend_pos=[1.1, 0.8])
+
+ # Write the data.
+ write_xy_data([data], file=grace_curve, graph_type='xy')
+ write_xy_data([dist], file=grace_dist, graph_type='xy')
# Close the files.
grace_curve.close()
grace_dist.close()
-
# NOE-RDC correlation plot.
if access(self.results_dir+sep+"NOE_viol_" + self.configs[0] +
"_sorted", F_OK) and access(self.results_dir+sep+"Q_factors_" +
self.configs[0] + "_sorted", F_OK):
@@ -357,35 +303,16 @@
# Open the Grace output files.
grace_file = open(self.results_dir+sep+"correlation_plot.agr",
'w')
- # Grace header.
- colours = [4, 2] # Blue and red.
- grace_file.write("@version 50121\n")
- grace_file.write("@page size 842, 595\n") # A4.
- grace_file.write("@with g0\n")
- grace_file.write("@ world 0, 0, %s, %s\n" %
(noe_viols[-1]+10, values[-1]+0.1))
- grace_file.write("@ view 0.150000, 0.150000, 1.28, 0.85\n")
- grace_file.write("@ title \"Correlation plot - RDC vs.
NOE\"\n")
- grace_file.write("@ subtitle \"%s ensembles of %s\"\n" %
(self.num_ens, self.num_models))
- grace_file.write("@ xaxis label \"NOE violation
(Angstrom\S2\N)\"\n")
- grace_file.write("@ yaxis label \"%s RDC Q-factors (pales
format)\"\n" % self.rdc_name)
- grace_file.write("@ legend 1.1, 0.8\n")
+ # Grace data.
+ data = []
for i in range(len(self.configs)):
- grace_file.write("@ s%s symbol 9\n" % i)
- grace_file.write("@ s%s symbol size 0.24\n" % i)
- grace_file.write("@ s%s symbol color %s\n" % (i,
colours[i]))
- grace_file.write("@ s%s symbol linewidth 0.5\n" % i)
- grace_file.write("@ s%s line type 0\n" % i)
- grace_file.write("@ s%s legend \"%s\"\n" % (i,
self.configs[i]))
-
- # Grace data.
- for i in range(len(self.configs)):
- # Grace header.
- grace_file.write("@target G0.S%s\n@type xy\n" % i)
-
# Open the NOE results file and read the data.
file = open(self.results_dir+sep+"NOE_viol_" +
self.configs[i])
noe_lines = file.readlines()
file.close()
+
+ # Add a new graph set.
+ data.append([])
# Open the RDC results file and read the data.
file = open(self.results_dir+sep+"Q_factors_" +
self.configs[i])
@@ -398,11 +325,12 @@
noe_viol = float(split(noe_lines[j])[1])
q_factor = float(split(rdc_lines[j])[1])
- # Write the xy pair.
- grace_file.write("%s %s\n" % (noe_viol, q_factor))
-
- # End of data.
- grace_file.write('&\n')
+ # Add the xy pair.
+ data[i].append([noe_viol, 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],
axis_min=[0, 0], axis_max=[noe_viols[-1]+10, values[-1]+0.1],
legend_pos=[1.1, 0.8])
+ write_xy_data([data], file=grace_file, graph_type='xy')
def noe_viol(self):
r10815 - /1.3/auto_analyses/stereochem_analysis.py