Hi Troels, If you add this OpenDX mapping functionally to a new system test - which would be awesome as it is not currently tested - then you might want to set ds.dx_inc to 2 or 3. Keeping the tests as fast as possible would be the goal. You can not load the files into OpenDX to check them in the system test, but you can check for their exact contents.
Cheers, Edward On 8 May 2014 02:44, <[email protected]> wrote: > 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) > > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
