Source Code for Module target_functions.jw_mapping

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2004-2013 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        # 
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 10  # (at your option) any later version.                                         # 
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 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from math import pi 
 24  from numpy import float64, zeros 
 25   
 26  # relax module imports. 
 27  from lib.auto_relaxation.ri_comps import calc_fixed_csa, calc_fixed_dip, comp_csa_const_func, comp_dip_const_func 
 28   
 29   
 30 -class Mapping: 
 31 -    def __init__(self, frq=None, gx=None, gh=None, mu0=None, h_bar=None): 
 32          """Reduced spectral density mapping.""" 
 33   
 34          # Initialise the data container. 
 35          self.data = Data() 
 36   
 37          # Add the initial data to self.data 
 38          self.data.gx = gx 
 39          self.data.gh = gh 
 40          self.data.mu0 = mu0 
 41          self.data.h_bar = h_bar 
 42   
 43          # The number of frequencies. 
 44          self.data.num_frq = 1 
 45   
 46          # Dipolar and CSA data structures. 
 47          self.data.dip_const_fixed = 0.0 
 48          self.data.csa_const_fixed = [0.0] 
 49          self.data.dip_const_func = 0.0 
 50          self.data.csa_const_func = zeros(1, float64) 
 51   
 52          # Nuclear frequencies. 
 53          frq = frq * 2 * pi 
 54          frqX = frq * self.data.gx / self.data.gh 
 55   
 56          # Calculate the five frequencies which cause R1, R2, and NOE relaxation. 
 57          self.data.frq_list = zeros((1, 5), float64) 
 58          self.data.frq_list[0, 1] = frqX 
 59          self.data.frq_list[0, 2] = frq - frqX 
 60          self.data.frq_list[0, 3] = frq 
 61          self.data.frq_list[0, 4] = frq + frqX 
 62          self.data.frq_sqrd_list = self.data.frq_list ** 2 
 63   
 64   
 65 -    def calc_sigma_noe(self, noe, r1): 
 66          """Function for calculating the sigma NOE value.""" 
 67   
 68          return (noe - 1.0) * r1 * self.data.gx / self.data.gh 
 69   
 70   
 71 -    def func(self, r=None, csa=None, r1=None, r2=None, noe=None): 
 72          """Function for calculating the three spectal density values. 
 73   
 74          Three values are returned, J(0), J(wX), and J(wH) (or J(0.87wH)). 
 75          """ 
 76   
 77          # Calculate the fixed component of the dipolar and CSA constants. 
 78          calc_fixed_dip(self.data) 
 79          calc_fixed_csa(self.data) 
 80   
 81          # Calculate the dipolar and CSA constants. 
 82          comp_dip_const_func(self.data, r) 
 83          comp_csa_const_func(self.data, csa) 
 84   
 85          # Rename the dipolar and CSA constants. 
 86          d = self.data.dip_const_func 
 87          c = self.data.csa_const_func[0] 
 88   
 89          # Calculate the sigma NOE value. 
 90          sigma_noe = self.calc_sigma_noe(noe, r1) 
 91   
 92          # Calculate J(0). 
 93          j0 = -1.5 / (3.0*d + c) * (0.5*r1 - r2 + 0.6*sigma_noe) 
 94   
 95          # Calculate J(wX). 
 96          jwx = 1.0 / (3.0*d + c) * (r1 - 1.4*sigma_noe) 
 97   
 98          # Calculate J(wH). 
 99          jwh = sigma_noe / (5.0*d) 
100   
101          # Return the three values. 
102          return j0, jwx, jwh 
103   
104   
105 -class Data: 
106 -    def __init__(self): 
107          """Empty container for storing data.""" 
108