Author: tlinnet
Date: Thu May 8 02:44:16 2014
New Revision: 23074
URL: http://svn.gna.org/viewcvs/relax?rev=23074&view=rev
Log:
Fix for script for the visualising the spin dynamics point which generated
the data.
This is to the script, which can visualize the synthetic CPMG data.
sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014)
B14 model - 2-site exact solution model for all time scales.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging
Modified:
trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
Modified: trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py?rev=23074&r1=23073&r2=23074&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py Thu
May 8 02:44:16 2014
@@ -1,3 +1,23 @@
+###############################################################################
+#
#
+# Copyright (C) 2013-2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program 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 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
# Script for calculating synthetics CPMG data.
# Python module imports.
@@ -147,7 +167,7 @@
ds.opendx = True
if not hasattr(ds, 'dx_inc'):
- ds.dx_inc = 70
+ ds.dx_inc = 50
# The set r2eff err.
if not hasattr(ds, 'r2eff_err'):
@@ -311,20 +331,34 @@
if ds.opendx:
# First switch pipe, since dx.map will go through parameters and end
up a "bad" place. :-)
pipe_name_MODEL_MAP = "%s_%s_map"%(pipe_name, model_analyse)
- pipe.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL_MAP,
bundle_to = pipe_bundle)
+ pipe.copy(pipe_from=pipe_name, pipe_to=pipe_name_MODEL_MAP, bundle_to
= pipe_bundle)
pipe.switch(pipe_name=pipe_name_MODEL_MAP)
+ # Copy R2eff, but not the original parameters
+ value.copy(pipe_from=pipe_name_r2eff, pipe_to=pipe_name_MODEL_MAP,
param='r2eff')
+
+ # Then select model.
+ relax_disp.select_model(model=model_analyse)
+
+ # Define dx parameters
dx_params = ['dw', 'pA', 'kex']
- for cur_spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
- cur_spin_id = spin_id
+ for res_name, res_num, spin_name, params in cur_spins:
+ cur_spin_id = ":%i@%s"%(res_num, spin_name)
+ cur_spin = return_spin(cur_spin_id)
dx_point = []
+
+ # Now get the parameters.
for dx_param in dx_params:
- set_val = getattr(cur_spin, dx_param)
- dx_point.append( set_val )
-
+ set_value = float(params[dx_param ])
+ dx_point.append(set_value)
+
+ print("Params for dx map is")
+ print(dx_params)
+ print("Point param for dx map is")
+ print(dx_point)
file_name_map = "map%s" % (cur_spin_id .replace('#',
'_').replace(':', '_').replace('@', '_'))
file_name_point = "point%s" % (cur_spin_id .replace('#',
'_').replace(':', '_').replace('@', '_'))
- dx.map(params=dx_params, map_type='Iso3D', spin_id=":1@N",
inc=ds.dx_inc, lower=None, upper=None, axis_incs=5,
file_prefix=file_name_map, dir=ds.resdir, point=dx_point,
point_file=file_name_point, remap=None)
+ dx.map(params=dx_params, map_type='Iso3D', spin_id=cur_spin_id,
inc=ds.dx_inc, lower=None, upper=None, axis_incs=5,
file_prefix=file_name_map, dir=ds.resdir, point=dx_point,
point_file=file_name_point, remap=None)
#vp_exec: A flag specifying whether to execute the visual program
automatically at start-up.
#dx.execute(file_prefix=file_name, dir=ds.resdir, dx_exe='dx',
vp_exec=True)
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Re: r23074 - /trunk/test_suite/system_tests/scripts/relax_disp/cpmg_synthetic.py