Author: tlinnet
Date: Fri Mar 7 13:21:37 2014
New Revision: 22442
URL: http://svn.gna.org/viewcvs/relax?rev=22442&view=rev
Log:
Removed lib.test_rotating_frame.py and the associated unittest.
Regarding sr #3124, (https://gna.org/support/index.php?3124) - Grace graphs
production for R1rho analysis with R2_eff as function of Omega_eff.
This is in response to
http://www.mail-archive.com/relax-devel@xxxxxxx/msg05080.html.
Removed:
trunk/lib/rotating_frame.py
trunk/test_suite/unit_tests/_lib/test_rotating_frame.py
Modified:
trunk/lib/__init__.py
trunk/test_suite/unit_tests/_lib/__init__.py
Modified: trunk/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=22442&r1=22441&r2=22442&view=diff
==============================================================================
--- trunk/lib/__init__.py (original)
+++ trunk/lib/__init__.py Fri Mar 7 13:21:37 2014
@@ -46,7 +46,6 @@
'periodic_table',
'physical_constants',
'regex',
- 'rotating_frame',
'selection',
'software',
'spectral_densities',
Removed: trunk/lib/rotating_frame.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/rotating_frame.py?rev=22441&view=auto
==============================================================================
--- trunk/lib/rotating_frame.py (original)
+++ trunk/lib/rotating_frame.py (removed)
@@ -1,94 +0,0 @@
-###############################################################################
-#
#
-# 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.
-Some of the calculations mentioned in the
U{manual<http://www.nmr-relax.com/manual/Dispersion_model_summary.html>}
-"""
-
-# 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_rotating_frame_params():
- """Calculates and return dictionaries of rotating frame parameters,
calculated from:
- - The spectrometer frequency.
- - The spin-lock or hard pulse offset.
- - The dispersion point data (the spin-lock field strength in Hz).
-
- The return will be dictionaries stored for each spin,
- - spin.Domega - The average resonance offset in the rotating frame (
Domega = w_{pop_ave} - w_rf ) [rad/s]
- - spin.theta - Rotating frame tilt angle ( theta = arctan(w_1 / Omega) )
[rad]
- - spin.w_eff - Effective field in rotating frame ( w_eff = sqrt( Omega^2
+ w_1^2 ) ) [rad/s]
-
- Calculations are mentioned in the
U{manual<http://www.nmr-relax.com/manual/Dispersion_model_summary.html>}
-
- The dictionary keys are generated with:
- return_param_key_from_data() from module
specific_analyses.relax_disp.disp_data.
- """
- # 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, Delta_omega, w_eff =
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]))
Modified: trunk/test_suite/unit_tests/_lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/__init__.py?rev=22442&r1=22441&r2=22442&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/__init__.py (original)
+++ trunk/test_suite/unit_tests/_lib/__init__.py Fri Mar 7 13:21:37
2014
@@ -39,6 +39,5 @@
'test_io',
'test_mathematics',
'test_regex',
- 'test_rotating_frame',
'test_selection'
]
Removed: trunk/test_suite/unit_tests/_lib/test_rotating_frame.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/test_rotating_frame.py?rev=22441&view=auto
==============================================================================
--- trunk/test_suite/unit_tests/_lib/test_rotating_frame.py (original)
+++ trunk/test_suite/unit_tests/_lib/test_rotating_frame.py (removed)
@@ -1,56 +0,0 @@
-###############################################################################
-#
#
-# 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.
-"""Unit tests of the lib.rotating_frame module."""
-
-# Python module imports.
-from os import sep
-
-# relax module imports.
-from lib.rotating_frame import calc_rotating_frame_params
-from lib.errors import RelaxError
-from pipe_control import state
-from pipe_control.mol_res_spin import spin_loop
-from test_suite.unit_tests.base_classes import UnitTestCase
-from status import Status; status = Status()
-
-
-class Test_rotating_frame(UnitTestCase):
- """Unit tests for the functions of the 'lib.rotating_frame' module."""
-
- def test_calc_rotating_frame_params(self):
- """Unit test of the calc_tilt_angle() function for R1rho setup.
-
- This uses the data of the saved state attached to U{bug
#21344<https://gna.org/bugs/?21344>}.
- """
-
- # Load the state.
- statefile = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21344_trunc.bz2'
- state.load_state(statefile, force=True)
-
- # Use calc_tilt_angle function
- calc_rotating_frame_params()
-
- # Test the existence of
- for curspin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=False):
- print(curspin, mol_name, res_num, res_name, spin_id)
- self.assert_(hasattr(curspin, 'theta'))
r22442 - in /trunk: lib/ test_suite/unit_tests/_lib/