Author: bugman
Date: Fri Feb 6 15:32:12 2015
New Revision: 27603
URL: http://svn.gna.org/viewcvs/relax?rev=27603&view=rev
Log:
Updated the relative stereochemistry auto-analysis to use the relax library
plotting API.
Modified:
trunk/auto_analyses/stereochem_analysis.py
Modified: trunk/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/stereochem_analysis.py?rev=27603&r1=27602&r2=27603&view=diff
==============================================================================
--- trunk/auto_analyses/stereochem_analysis.py (original)
+++ trunk/auto_analyses/stereochem_analysis.py Fri Feb 6 15:32:12 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2010-2014 Edward d'Auvergne
#
+# Copyright (C) 2010-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -58,9 +58,9 @@
import sys
# relax module imports.
-from pipe_control.grace import write_xy_data, write_xy_header
from lib.periodic_table import periodic_table
from lib.physical_constants import dipolar_constant
+from lib.plotting.api import write_xy_data, write_xy_header
from prompt.interpreter import Interpreter
from lib.errors import RelaxError
from lib.io import mkdir_nofail
@@ -410,12 +410,12 @@
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)']], 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']], legend_pos=[[1.1, 0.8]])
+ write_xy_header(format='grace', 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)']], legend_pos=[[0.3, 0.8]])
+ write_xy_header(format='grace', 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']], 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')
+ write_xy_data(format='grace', data=[data], file=grace_curve,
graph_type='xy')
+ write_xy_data(format='grace', data=[dist], file=grace_dist,
graph_type='xy')
# Close the files.
grace_curve.close()
@@ -456,12 +456,12 @@
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(format='grace', 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(format='grace', 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')
- write_xy_data([dist], file=grace_dist, graph_type='xy')
+ write_xy_data(format='grace', data=[data], file=grace_curve,
graph_type='xy')
+ write_xy_data(format='grace', data=[dist], file=grace_dist,
graph_type='xy')
# Close the files.
grace_curve.close()
@@ -505,10 +505,10 @@
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_data([data], file=grace_file, graph_type='xy')
- write_xy_data([data_scaled], file=grace_file_scaled,
graph_type='xy')
+ write_xy_header(format='grace', 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(format='grace', 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(format='grace', data=[data], file=grace_file,
graph_type='xy')
+ write_xy_data(format='grace', data=[data_scaled],
file=grace_file_scaled, graph_type='xy')
def noe_viol(self):
r27603 - /trunk/auto_analyses/stereochem_analysis.py