Source Code for Module maths_fns.ri

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003, 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               # 
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 12  # relax is distributed in the hope that it will be useful,                    # 
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 15  # GNU General Public License for more details.                                # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23   
 24  from ri_comps import r1_comps, dr1_comps, d2r1_comps 
 25  from ri_prime import func_ri_prime 
 26   
 27   
 28  # Calculate the NOE value. 
 29  ########################## 
 30   
 31 -def calc_noe(data, i, frq_num, get_r1, params): 
 32      """Calculate the NOE value. 
 33   
 34      Half this code needs to be shifted into the function initialisation code. 
 35      """ 
 36   
 37      # Get the r1 value either from data.ri_prime or by calculation if the value is not in data.ri_prime 
 38      data.r1[i] = get_r1[i](data, i, frq_num, params) 
 39   
 40      # Calculate the NOE. 
 41      if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0: 
 42          data.ri[i] = 1.0 
 43      elif data.r1[i] == 0.0: 
 44          data.ri[i] = 1e99 
 45      else: 
 46          data.ri[i] = 1.0 + data.g_ratio*(data.ri_prime[i] / data.r1[i]) 
 47   
 48   
 49 -def calc_dnoe(data, i, frq_num, get_dr1, params, j): 
 50      """Calculate the derivative of the NOE value. 
 51   
 52      Half this code needs to be shifted into the function initialisation code. 
 53      """ 
 54   
 55      # Calculate the NOE derivative. 
 56      data.dr1[j, i] = get_dr1[i](data, i, frq_num, params, j) 
 57      if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0: 
 58          data.dri[j, i] = 0.0 
 59      elif data.r1[i] == 0.0: 
 60          data.dri[j, i] = 1e99 
 61      else: 
 62          data.dri[j, i] = data.g_ratio * (1.0 / data.r1[i]**2) * (data.r1[i] * data.dri_prime[j, i] - data.ri_prime[i] * data.dr1[j, i]) 
 63   
 64   
 65 -def calc_d2noe(data, i, frq_num, get_d2r1, params, j, k): 
 66      """Calculate the second partial derivative of the NOE value. 
 67   
 68      Half this code needs to be shifted into the function initialisation code. 
 69      """ 
 70   
 71      # Calculate the NOE second derivative. 
 72      data.d2r1[j, k, i] = get_d2r1[i](data, i, frq_num, params, j, k) 
 73      if data.r1[i] == 0.0 and data.ri_prime[i] == 0.0: 
 74          data.d2ri[j, k, i] = 0.0 
 75      elif data.r1[i] == 0.0: 
 76          data.d2ri[j, k, i] = 1e99 
 77      else: 
 78          a = data.ri_prime[i] * (2.0 * data.dr1[j, i] * data.dr1[k, i] - data.r1[i] * data.d2r1[j, k, i]) 
 79          b = data.r1[i] * (data.dri_prime[j, i] * data.dr1[k, i] + data.dr1[j, i] * data.dri_prime[k, i] - data.r1[i] * data.d2ri_prime[j, k, i]) 
 80          data.d2ri[j, k, i] = data.g_ratio * (1.0 / data.r1[i]**3) * (a - b) 
 81   
 82   
 83   
 84  # Calculate the R1 value. 
 85  ######################### 
 86   
 87 -def calc_r1(data, i, frq_num, params): 
 88      """Calculate the R1 value if there is no R1 data corresponding to the NOE data. 
 89   
 90      R1()  =  dip_const_func . dip_Jw_R1_func  +  csa_const_func . csa_Jw_R1_func 
 91      """ 
 92   
 93      # Place data in the R1 data class. 
 94      data.r1_data.remap_table = data.remap_table 
 95      data.r1_data.jw = data.jw 
 96      data.r1_data.dip_const_func = data.dip_const_func 
 97      data.r1_data.csa_const_func = data.csa_const_func 
 98   
 99      # Calculate the r1 components. 
100      r1_comps(data.r1_data, i, params) 
101   
102      # Calculate the r1 value. 
103      ri = func_ri_prime(data.r1_data) 
104      return ri[i] 
105   
106   
107 -def calc_dr1(data, i, frq_num, params, j): 
108      """Calculate the R1 value if there is no R1 data corresponding to the NOE data. 
109   
110      dR1() 
111      -----  =  dip_const_func . dip_Jw_R1_grad  +  csa_const_func . csa_Jw_R1_grad 
112       dJw 
113   
114      dR1() 
115      -----  =  0 
116      dRex 
117   
118      dR1() 
119      -----  =  dip_const_grad . dip_Jw_R1_func 
120       dr 
121   
122      dR1() 
123      -----  =  csa_const_grad . csa_Jw_R1_func 
124      dcsa 
125      """ 
126   
127      # Place data in the R1 data class. 
128      data.r1_data.remap_table = data.remap_table 
129      data.r1_data.djw = data.djw 
130      data.r1_data.dip_const_grad = data.dip_const_grad 
131      data.r1_data.csa_const_grad = data.csa_const_grad 
132   
133      # Calculate the dr1 components. 
134      dr1_comps(data.r1_data, i, params) 
135   
136      # Calculate the dr1 value. 
137      dri = data.r1_data.create_dri_prime[j](data.r1_data) 
138   
139      return dri[i] 
140   
141   
142 -def calc_d2r1(data, i, frq_num, params, j, k): 
143      """Calculate the R1 value if there is no R1 data corresponding to the NOE data.""" 
144   
145      # Place data in the R1 data class. 
146      data.r1_data.remap_table = data.remap_table 
147      data.r1_data.d2jw = data.d2jw 
148      data.r1_data.dip_const_hess = data.dip_const_hess 
149      data.r1_data.csa_const_hess = data.csa_const_hess 
150   
151      # Calculate the dr1 components. 
152      d2r1_comps(data.r1_data, i, params) 
153   
154      # Calculate the dr1 value. 
155      if data.r1_data.create_d2ri_prime[j][k]: 
156          d2ri = data.r1_data.create_d2ri_prime[j][k](data.r1_data) 
157          return d2ri[i] 
158      else: 
159          return 0.0 
160   
161   
162   
163  # Extract the R1 value. 
164  ####################### 
165   
166 -def extract_r1(data, i, frq_num, params): 
167      """Get the R1 value from data.ri_prime""" 
168   
169      return data.ri_prime[data.noe_r1_table[i]] 
170   
171   
172 -def extract_dr1(data, i, frq_num, params, j): 
173      """Get the dR1 value from data.dri_prime""" 
174   
175      return data.dri_prime[j, data.noe_r1_table[i]] 
176   
177   
178 -def extract_d2r1(data, i, frq_num, params, j, k): 
179      """Get the d2R1 value from data.d2ri_prime""" 
180   
181      return data.d2ri_prime[j, k, data.noe_r1_table[i]] 
182