Source Code for Module maths_fns.jw_mapping

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from math import pi 
 25  from numpy import float64, zeros 
 26   
 27  # relax module imports. 
 28  from ri_comps import calc_fixed_csa, calc_fixed_dip, comp_csa_const_func, comp_dip_const_func 
 29   
 30   
 31 -class Mapping: 
 32 -    def __init__(self, frq=None, gx=None, gh=None, mu0=None, h_bar=None): 
 33          """Reduced spectral density mapping.""" 
 34   
 35          # Initialise the data container. 
 36          self.data = Data() 
 37   
 38          # Add the initial data to self.data 
 39          self.data.gx = gx 
 40          self.data.gh = gh 
 41          self.data.mu0 = mu0 
 42          self.data.h_bar = h_bar 
 43   
 44          # The number of frequencies. 
 45          self.data.num_frq = 1 
 46   
 47          # Dipolar and CSA data structures. 
 48          self.data.dip_const_fixed = 0.0 
 49          self.data.csa_const_fixed = [0.0] 
 50          self.data.dip_const_func = 0.0 
 51          self.data.csa_const_func = zeros(1, float64) 
 52   
 53          # Nuclear frequencies. 
 54          frq = frq * 2 * pi 
 55          frqX = frq * self.data.gx / self.data.gh 
 56   
 57          # Calculate the five frequencies which cause R1, R2, and NOE relaxation. 
 58          self.data.frq_list = zeros((1, 5), float64) 
 59          self.data.frq_list[0, 1] = frqX 
 60          self.data.frq_list[0, 2] = frq - frqX 
 61          self.data.frq_list[0, 3] = frq 
 62          self.data.frq_list[0, 4] = frq + frqX 
 63          self.data.frq_sqrd_list = self.data.frq_list ** 2 
 64   
 65   
 66 -    def calc_sigma_noe(self, noe, r1): 
 67          """Function for calculating the sigma NOE value.""" 
 68   
 69          return (noe - 1.0) * r1 * self.data.gx / self.data.gh 
 70   
 71   
 72 -    def func(self, r=None, csa=None, r1=None, r2=None, noe=None): 
 73          """Function for calculating the three spectal density values. 
 74   
 75          Three values are returned, J(0), J(wX), and J(wH) (or J(0.87wH)). 
 76          """ 
 77   
 78          # Calculate the fixed component of the dipolar and CSA constants. 
 79          calc_fixed_dip(self.data) 
 80          calc_fixed_csa(self.data) 
 81   
 82          # Calculate the dipolar and CSA constants. 
 83          comp_dip_const_func(self.data, r) 
 84          comp_csa_const_func(self.data, csa) 
 85   
 86          # Rename the dipolar and CSA constants. 
 87          d = self.data.dip_const_func 
 88          c = self.data.csa_const_func[0] 
 89   
 90          # Calculate the sigma NOE value. 
 91          sigma_noe = self.calc_sigma_noe(noe, r1) 
 92   
 93          # Calculate J(0). 
 94          j0 = -1.5 / (3.0*d + c) * (0.5*r1 - r2 + 0.6*sigma_noe) 
 95   
 96          # Calculate J(wX). 
 97          jwx = 1.0 / (3.0*d + c) * (r1 - 1.4*sigma_noe) 
 98   
 99          # Calculate J(wH). 
100          jwh = sigma_noe / (5.0*d) 
101   
102          # Return the three values. 
103          return j0, jwx, jwh 
104   
105   
106 -class Data: 
107 -    def __init__(self): 
108          """Empty container for storing data.""" 
109