Hi Edward. How should I handle the value.write function?
I was thinking of adding w_eff and Delta_omega as parameters, like these commits: r22409 - /trunk/specific_analyses/relax_disp/api.py http://www.mail-archive.com/relax-commits@gna.org/msg20031.html r22411 - /trunk/specific_analyses/relax_disp/api.py http://www.mail-archive.com/relax-commits@gna.org/msg20033.html If I was about to use the value.write function, how should I initialize a call to the function to calculate theta, Delta_omega? Best Troels 2014-03-07 12:26 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Hi Troels, > > One consideration you need to make for the functions of the relax > library is that these are independent of the relax data store and the > pipe_control package (used to manipulate the data store) and the > specific_analyses package. I.e. you should be able to use all > functions without the rest of relax, hence it could be distributed > with other GPL v3+ NMR software. Here you have used a number of > pipe_control.mol_res_spin and specific_analyses.relax_disp.disp_data > functions. Therefore this indicates that the code would be better > located in the specific_analyses.relax_disp.disp_data module. A > calc_tilt_angle() function in the relax library would essentially need > to take all its data as arguments (spin-lock field and offset and > chemical shift) and return the tilt angle. > > The other problem is the storing of theta in the spin containers. > This should not be done as the user can change the(spin-lock field, > offset, or chemical shift and hence the tilt angle theta will change. > It is much better to generate theta when needed by the > relax_disp.plot_disp_curves user function, and then not store it (so > it is destroyed automatically by Python). Such non-permanent > parameters are used extensively throughout relax, especially in the > N-state or ensemble analysis code. > > Regards, > > Edward > > > On 7 March 2014 11:42, <tlin...@nmr-relax.com> wrote: > > Author: tlinnet > > Date: Fri Mar 7 11:42:36 2014 > > New Revision: 22427 > > > > URL: http://svn.gna.org/viewcvs/relax?rev=22427&view=rev > > Log: > > Added lib.rotating_frame module containing functions related to rotating > frame NMR calculations. > > > > Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace > graphs production for R1rho analysis with R2_eff as function of Omega_eff. > > > > Added: > > trunk/lib/rotating_frame.py > > > > Added: trunk/lib/rotating_frame.py > > URL: > http://svn.gna.org/viewcvs/relax/trunk/lib/rotating_frame.py?rev=22427&view=auto > > > ============================================================================== > > --- trunk/lib/rotating_frame.py (added) > > +++ trunk/lib/rotating_frame.py Fri Mar 7 11:42:36 2014 > > @@ -0,0 +1,77 @@ > > > +############################################################################### > > +# > # > > +# Copyright (C) 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/>. > # > > +# > # > > > +############################################################################### > > + > > +# Module docstring. > > +"""Module containing functions related to rotating frame NMR > calculations.""" > > + > > +# Python module imports. > > +from os import sep > > + > > +# relax module imports. > > +from pipe_control.mol_res_spin import find_index, get_spin_ids, > index_molecule, index_residue, return_spin, spin_loop > > +from specific_analyses.relax_disp.disp_data import loop_exp_frq_offset, > return_offset_data, return_param_key_from_data, return_spin_lock_nu1 > > + > > +def calc_tilt_angle(): > > + # Get the field count > > + field_count = cdp.spectrometer_frq_count > > + > > + # Get the spin_lock_field points > > + spin_lock_nu1 = return_spin_lock_nu1(ref_flag=False) > > + > > + # Initialize data containers > > + all_spin_ids = get_spin_ids() > > + > > + # Containers for only selected spins > > + cur_spin_ids = [] > > + cur_spins = [] > > + for curspin_id in all_spin_ids: > > + # Get the spin > > + curspin = return_spin(curspin_id) > > + > > + # Check if is selected > > + if curspin.select == True: > > + cur_spin_ids.append(curspin_id) > > + cur_spins.append(curspin) > > + > > + # The offset and R1 data. > > + chemical_shifts, offsets, tilt_angles = > return_offset_data(spins=cur_spins, spin_ids=cur_spin_ids, > field_count=field_count, fields=spin_lock_nu1) > > + > > + # Loop over the index of spins, then exp_type, frq, offset > > + print("Printing the following") > > + print("exp_type curspin_id frq offset{ppm} > offsets[ei][si][mi][oi]{rad/s} ei mi oi si di cur_spin.chemical_shift{ppm} > chemical_shifts[ei][si][mi]{rad/s} spin_lock_nu1{Hz} > tilt_angles[ei][si][mi][oi]{rad}") > > + for si in range(len(cur_spin_ids)): > > + theta_spin_dic = dict() > > + curspin_id = cur_spin_ids[si] > > + cur_spin = cur_spins[si] > > + for exp_type, frq, offset, ei, mi, oi in > loop_exp_frq_offset(return_indices=True): > > + # Loop over the dispersion points. > > + spin_lock_fields = spin_lock_nu1[ei][mi][oi] > > + for di in range(len(spin_lock_fields)): > > + print("%-8s %-10s %11.1f %8.4f %12.5f %i %i %i %i > %i %7.3f %12.5f %12.5f %12.5f"%(exp_type, curspin_id, frq, offset, > offsets[ei][si][mi][oi], ei, mi, oi, si, di, cur_spin.chemical_shift, > chemical_shifts[ei][si][mi], spin_lock_fields[di], > tilt_angles[ei][si][mi][oi][di])) > > + dic_key = return_param_key_from_data(exp_type=exp_type, > frq=frq, offset=offset, point=spin_lock_fields[di]) > > + theta_spin_dic["%s"%(dic_key)] = > tilt_angles[ei][si][mi][oi][di] > > + # Store the data > > + cur_spin.theta = theta_spin_dic > > + > > + print("\nThe theta data now resides in") > > + for curspin, mol_name, res_num, res_name, spin_id in > spin_loop(full_info=True, return_id=True, skip_desel=True): > > + spin_index = find_index(selection=spin_id, global_index=False) > > + print("%s cdp.mol[%i].res[%i].spin[%i].theta"%(spin_id, > spin_index[0], spin_index[1], spin_index[2])) > > > > > > _______________________________________________ > > relax (http://www.nmr-relax.com) > > > > This is the relax-commits mailing list > > relax-comm...@gna.org > > > > 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 > relax-devel@gna.org > > 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 >
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