Source Code for Module lib.nmr

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module containing functions related to basic NMR concepts.""" 
 24   
 25  # Python module imports. 
 26  from math import atan2, pi, sqrt 
 27   
 28  # relax module imports. 
 29  from lib.periodic_table import periodic_table 
 30   
 31   
 32 -def frequency_to_Hz(frq=None, B0=None, isotope=None): 
 33      """Convert the given frequency from ppm to Hertz units. 
 34   
 35      @keyword frq:       The frequency in ppm. 
 36      @type frq:          float 
 37      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 38      @type B0:           float 
 39      @keyword isotope:   The isotope type of the nucleus of interest. 
 40      @type isotope:      str 
 41      @return:            The frequency in Hertz. 
 42      @rtype:             float 
 43      """ 
 44   
 45      # Convert and return. 
 46      return frq * B0 / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio(isotope) * 1e-6 
 47   
 48   
 49 -def frequency_to_ppm(frq=None, B0=None, isotope=None): 
 50      """Convert the given frequency from Hertz to ppm units. 
 51   
 52      @keyword frq:       The frequency in Hertz. 
 53      @type frq:          float 
 54      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 55      @type B0:           float 
 56      @keyword isotope:   The isotope type of the nucleus of interest. 
 57      @type isotope:      str 
 58      @return:            The frequency in ppm. 
 59      @rtype:             float 
 60      """ 
 61   
 62      # Convert and return. 
 63      return frq / B0 * periodic_table.gyromagnetic_ratio('1H') / periodic_table.gyromagnetic_ratio(isotope) / 1e-6 
 64   
 65   
 66 -def frequency_to_ppm_from_rad(frq=None, B0=None, isotope=None): 
 67      """Convert the given frequency from rad/s to ppm units. 
 68   
 69      @keyword frq:       The frequency in rad/s. 
 70      @type frq:          float 
 71      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 72      @type B0:           float 
 73      @keyword isotope:   The isotope type of the nucleus of interest. 
 74      @type isotope:      str 
 75      @return:            The frequency in ppm. 
 76      @rtype:             float 
 77      """ 
 78   
 79      # Convert and return. 
 80      return frq / (2.0 * pi) / B0 * periodic_table.gyromagnetic_ratio('1H') / periodic_table.gyromagnetic_ratio(isotope) / 1e-6 
 81   
 82   
 83 -def frequency_to_rad_per_s(frq=None, B0=None, isotope=None): 
 84      """Convert the given frequency from ppm to rad/s units. 
 85   
 86      @keyword frq:       The frequency in ppm. 
 87      @type frq:          float 
 88      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 89      @type B0:           float 
 90      @keyword isotope:   The isotope type of the nucleus of interest. 
 91      @type isotope:      str 
 92      @return:            The frequency in rad/s. 
 93      @rtype:             float 
 94      """ 
 95   
 96      # Convert and return. 
 97      return frq * 2.0 * pi * B0 / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio(isotope) * 1e-6 
 98   
 99   
100 -def rotating_frame_params(chemical_shift=None, spin_lock_offset=None, omega1=None): 
101      """Calculate the rotating frame paramaters. 
102   
103      @keyword chemical_shift:    The chemical shift in rad/s. 
104      @type chemical_shift:       float 
105      @keyword spin_lock_offset:  spin-lock offset in rad/s. 
106      @type spin_lock_offset:     float 
107      @keyword omega1:            Spin-lock field strength in rad/s. 
108      @type omega1:               float 
109      @return:                    The average resonance offset in the rotating frame, angle describing the tilted rotating frame relative to the laboratory, effective field in rotating frame. 
110      @rtype:                     float, float, float 
111      """ 
112   
113      # The average resonance offset in the rotating frame. 
114      Delta_omega = chemical_shift - spin_lock_offset 
115   
116      # Calculate the theta angle describing the tilted rotating frame relative to the laboratory. 
117      # theta = atan(omega1 / Delta_omega). 
118      # If Delta_omega is negative, there follow the symmetry of atan, that atan(-x) = - atan(x). 
119      # Then it should be: theta = pi + atan(-x) = pi - atan(x) = pi - abs(atan( +/- x)). 
120      # This is taken care of with the atan2(y, x) function, which return atan(y / x), in radians, and the result is between -pi and pi. 
121      if Delta_omega == 0.0: 
122          theta = pi / 2.0 
123      else: 
124          theta = atan2(omega1, Delta_omega) 
125   
126      # Calculate effective field in rotating frame. 
127      w_eff = sqrt( Delta_omega*Delta_omega + omega1*omega1 ) 
128   
129      return Delta_omega, theta, w_eff 
130