Source Code for Module lib.nmr

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2013 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  7  #                                                                             # 
  8  # This program is free software: you can redistribute it and/or modify        # 
  9  # it under the terms of the GNU General Public License as published by        # 
 10  # the Free Software Foundation, either version 3 of the License, or           # 
 11  # (at your option) any later version.                                         # 
 12  #                                                                             # 
 13  # This program is distributed in the hope that it will be useful,             # 
 14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 16  # GNU General Public License for more details.                                # 
 17  #                                                                             # 
 18  # You should have received a copy of the GNU General Public License           # 
 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing functions related to basic NMR concepts.""" 
 25   
 26  # Python module imports. 
 27  from math import atan2, pi, sqrt 
 28   
 29  # relax module imports. 
 30  from lib.periodic_table import periodic_table 
 31   
 32   
 33 -def frequency_to_Hz(frq=None, B0=None, isotope=None): 
 34      """Convert the given frequency from ppm to Hertz units. 
 35   
 36      @keyword frq:       The frequency in ppm. 
 37      @type frq:          float 
 38      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 39      @type B0:           float 
 40      @keyword isotope:   The isotope type of the nucleus of interest. 
 41      @type isotope:      str 
 42      @return:            The frequency in Hertz. 
 43      @rtype:             float 
 44      """ 
 45   
 46      # Convert and return. 
 47      return frq * B0 / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio(isotope) * 1e-6 
 48   
 49   
 50 -def frequency_to_ppm(frq=None, B0=None, isotope=None): 
 51      """Convert the given frequency from Hertz to ppm units. 
 52   
 53      @keyword frq:       The frequency in Hertz. 
 54      @type frq:          float 
 55      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 56      @type B0:           float 
 57      @keyword isotope:   The isotope type of the nucleus of interest. 
 58      @type isotope:      str 
 59      @return:            The frequency in ppm. 
 60      @rtype:             float 
 61      """ 
 62   
 63      # Convert and return. 
 64      return frq / B0 * periodic_table.gyromagnetic_ratio('1H') / periodic_table.gyromagnetic_ratio(isotope) / 1e-6 
 65   
 66   
 67 -def frequency_to_ppm_from_rad(frq=None, B0=None, isotope=None): 
 68      """Convert the given frequency from rad/s to ppm units. 
 69   
 70      @keyword frq:       The frequency in rad/s. 
 71      @type frq:          float 
 72      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 73      @type B0:           float 
 74      @keyword isotope:   The isotope type of the nucleus of interest. 
 75      @type isotope:      str 
 76      @return:            The frequency in ppm. 
 77      @rtype:             float 
 78      """ 
 79   
 80      # Convert and return. 
 81      return frq / (2.0 * pi) / B0 * periodic_table.gyromagnetic_ratio('1H') / periodic_table.gyromagnetic_ratio(isotope) / 1e-6 
 82   
 83   
 84 -def frequency_to_rad_per_s(frq=None, B0=None, isotope=None): 
 85      """Convert the given frequency from ppm to rad/s units. 
 86   
 87      @keyword frq:       The frequency in ppm. 
 88      @type frq:          float 
 89      @keyword B0:        The magnetic field strength as the proton frequency in Hertz. 
 90      @type B0:           float 
 91      @keyword isotope:   The isotope type of the nucleus of interest. 
 92      @type isotope:      str 
 93      @return:            The frequency in rad/s. 
 94      @rtype:             float 
 95      """ 
 96   
 97      # Convert and return. 
 98      return frq * 2.0 * pi * B0 / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio(isotope) * 1e-6 
 99   
100   
101 -def rotating_frame_params(chemical_shift=None, spin_lock_offset=None, omega1=None): 
102      """Calculate the rotating frame paramaters. 
103   
104      @keyword chemical_shift:    The chemical shift in rad/s. 
105      @type chemical_shift:       float 
106      @keyword spin_lock_offset:  spin-lock offset in rad/s. 
107      @type spin_lock_offset:     float 
108      @keyword omega1:            Spin-lock field strength in rad/s. 
109      @type omega1:               float 
110      @return:                    The average resonance offset in the rotating frame, angle describing the tilted rotating frame relative to the laboratory, effective field in rotating frame. 
111      @rtype:                     float, float, float 
112      """ 
113   
114      # The average resonance offset in the rotating frame. 
115      Delta_omega = chemical_shift - spin_lock_offset 
116   
117      # Calculate the theta angle describing the tilted rotating frame relative to the laboratory. 
118      # theta = atan(omega1 / Delta_omega). 
119      # If Delta_omega is negative, there follow the symmetry of atan, that atan(-x) = - atan(x). 
120      # Then it should be: theta = pi + atan(-x) = pi - atan(x) = pi - abs(atan( +/- x)). 
121      # 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. 
122      if Delta_omega == 0.0: 
123          theta = pi / 2.0 
124      else: 
125          theta = atan2(omega1, Delta_omega) 
126   
127      # Calculate effective field in rotating frame. 
128      w_eff = sqrt( Delta_omega*Delta_omega + omega1*omega1 ) 
129   
130      return Delta_omega, theta, w_eff 
131