Author: bugman
Date: Fri Mar 4 15:04:16 2011
New Revision: 12797
URL: http://svn.gna.org/viewcvs/relax?rev=12797&view=rev
Log:
Added a sample script for creating plots of experimental verses back
calculated relaxation data.
Added:
1.3/sample_scripts/model_free/grace_ri_data_correlation.py
Added: 1.3/sample_scripts/model_free/grace_ri_data_correlation.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/grace_ri_data_correlation.py?rev=12797&view=auto
==============================================================================
--- 1.3/sample_scripts/model_free/grace_ri_data_correlation.py (added)
+++ 1.3/sample_scripts/model_free/grace_ri_data_correlation.py Fri Mar 4
15:04:16 2011
@@ -1,0 +1,178 @@
+###############################################################################
+#
#
+# Copyright (C) 2011 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+"""Script for creating correlations plots of experimental verses back
calculated relaxation data."""
+
+
+# relax module imports.
+from generic_fns.mol_res_spin import spin_loop
+from generic_fns.relax_data import num_frq
+
+
+def grace_header(file):
+ """Generate the Grace header text."""
+
+ # A4, portrait.
+ file.write("@page size 595, 842\n")
+
+ # Graph data.
+ world = ["0, 0, 400, 3", "0, 0, 400, 20", "0, 0, 400, 1"]
+ view = ["@ view 0.100000, 0.876456, 0.950000, 1.264685", "@ view
0.100000, 0.488228, 0.950000, 0.876456", "@ view 0.100000, 0.100000,
0.950000, 0.488228"]
+ x_label = ["", "", "Residue number"]
+ x_ticklabel = ["off", "off", "on"]
+ y_label = ["R\s1\N (rad.s\S-1\N)", "R\s2\N (rad.s\S-1\N)", "Steady-state
NOE"]
+ legend = ["on", "off", "off"]
+
+ # The data labels.
+ data_legend = [[], [], []]
+ for ri_id in cdp.ri_ids:
+ # The graph numbers.
+ if cdp.ri_type[ri_id] == 'R1':
+ g_index = 0
+ elif cdp.ri_type[ri_id] == 'R2':
+ g_index = 1
+ elif cdp.ri_type[ri_id] == 'NOE':
+ g_index = 2
+
+ # Frequency string.
+ string = '%i MHz' % (cdp.frq[ri_id]/1e6)
+
+ # The label.
+ data_legend[g_index].append("%s Exp. data" % string)
+ data_legend[g_index].append("%s BC. data" % string)
+
+ # Loop over the graphs.
+ for i in range(3):
+ # Show all graphs.
+ file.write("@g%s hidden false\n" % i)
+
+ # Specific graph.
+ file.write("@with g%s\n" % i)
+
+ # World.
+ file.write("@ world %s\n" % world[i])
+
+ # Arrange graphs.
+ file.write("%s\n" % view[i])
+
+ # X-axis setting.
+ file.write("@ xaxis bar linewidth 0.5\n")
+ file.write("@ xaxis tick major 50\n")
+ file.write("@ xaxis tick minor ticks 4\n")
+ file.write("@ xaxis tick major size 0.5\n")
+ file.write("@ xaxis tick major linewidth 0.5\n")
+ file.write("@ xaxis tick minor linewidth 0.5\n")
+ file.write("@ xaxis tick minor size 0.250000\n")
+ file.write("@ xaxis ticklabel %s\n" % x_ticklabel[i])
+ file.write("@ xaxis ticklabel char size 0.74\n")
+ file.write("@ xaxis label \"%s\"\n" % x_label[i])
+
+ # Y-axis setting.
+ file.write("@ yaxis bar linewidth 0.5\n")
+ file.write("@ yaxis tick major size 0.5\n")
+ file.write("@ yaxis tick major linewidth 0.5\n")
+ file.write("@ yaxis tick minor linewidth 0.5\n")
+ file.write("@ yaxis tick minor size 0.250000\n")
+ file.write("@ yaxis ticklabel char size 0.74\n")
+ file.write("@ yaxis label \"%s\"\n" % y_label[i])
+
+ # Legend and frame.
+ file.write("@ legend %s\n" % legend[i])
+ file.write("@ legend 0.3, 0.8\n")
+ file.write("@ legend box linewidth 0.5\n")
+ file.write("@ legend char size 0.76\n")
+ file.write("@ frame linewidth 0.5\n")
+
+ # Data set settings.
+ for j in range(len(data_legend[i])):
+ # Changing values.
+ colour = j/2 + 1
+ linestyle = j%2
+ if j%2:
+ symbol = 9
+ else:
+ symbol = 2
+
+ # Symbol info.
+ file.write("@ s%s symbol %s\n" % (j, symbol))
+ file.write("@ s%s symbol size 0.25\n" % j)
+ file.write("@ s%s symbol color %s\n" % (j, colour))
+ file.write("@ s%s symbol fill color %s\n" % (j, colour))
+ file.write("@ s%s symbol fill pattern 0\n" % j)
+ file.write("@ s%s symbol linewidth 0.5\n" % j)
+
+ # Line info.
+ file.write("@ s%s line linestyle %s\n" % (j, linestyle))
+ file.write("@ s%s line linewidth 0.5\n" % j)
+ file.write("@ s%s line color %s\n" % (j, colour))
+ file.write("@ s%s errorbar color %s\n" % (j, colour))
+
+ # Error bars.
+ file.write("@ s%s errorbar size 0.25\n" % j)
+ file.write("@ s%s errorbar linewidth 0.5\n" % j)
+ file.write("@ s%s errorbar riser linestyle 2\n" % j)
+ file.write("@ s%s errorbar riser linewidth 0.5\n" % j)
+ file.write("@ s%s legend \"%s\"\n" % (j, data_legend[i][j]))
+
+
+# Load the relax state.
+state.load('results', dir='.')
+
+# Back calculate the relaxation data.
+relax_data.back_calc()
+
+# Open the correlation plot file.
+file = open('corr_plot.agr', 'w')
+
+# Generate the header.
+grace_header(file)
+
+# Init.
+s_count = [0, 0, 0]
+
+# Loop over the relaxation data.
+for ri_id in cdp.ri_ids:
+ # The graph numbers.
+ if cdp.ri_type[ri_id] == 'R1':
+ g_index = 0
+ elif cdp.ri_type[ri_id] == 'R2':
+ g_index = 1
+ elif cdp.ri_type[ri_id] == 'NOE':
+ g_index = 2
+
+ # The experimental data.
+ file.write('@target G%s.S%s\n@type xydy\n' % (g_index, s_count[g_index]))
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ file.write('%s %s %s\n' % (res_num, spin.ri_data[ri_id],
spin.ri_data_err[ri_id]))
+ file.write('&\n')
+
+ # Increment the set counter.
+ s_count[g_index] += 1
+
+ # The back-calculated data.
+ file.write('@target G%s.S%s\n@type xy\n' % (g_index, s_count[g_index]))
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ file.write('%s %s\n' % (res_num, spin.ri_data_bc[ri_id]))
+ file.write('&\n')
+
+ # Increment the set counter.
+ s_count[g_index] += 1
r12797 - /1.3/sample_scripts/model_free/grace_ri_data_correlation.py