Source Code for Module functions.jw_mf_trans

  1  from Numeric import Float64, zeros 
  2  from re import match 
  3   
  4 -class Jw: 
  5 -        def __init__(self): 
  6                  "Function for creating the model-free spectral density values using parameter transformations." 
  7   
  8   
  9 -        def Jw(self): 
 10                  """Function to create the model-free spectral density values using parameter transformations." 
 11   
 12                  The spectral density equation 
 13                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
 14   
 15                  Data structure:  self.data.jw 
 16                  Dimension:  2D, (number of NMR frequencies, 5 spectral density frequencies) 
 17                  Type:  Numeric matrix, Float64 
 18                  Dependencies:  None 
 19                  Required by:  self.data.ri, self.data.dri, self.data.d2ri 
 20   
 21   
 22                  Formulae 
 23                  ~~~~~~~~ 
 24   
 25                  Parameter transformations 
 26                  ~~~~~~~~~~~~~~~~~~~~~~~~~ 
 27                          ae  =  c.te 
 28   
 29                          af  =  c.tf 
 30   
 31                          as  =  c.ts 
 32   
 33   
 34                          therefore: 
 35   
 36                                            tm.ae 
 37                                  te'  =  --------- 
 38                                          ae + c.tm 
 39   
 40                                            tm.af 
 41                                  tf'  =  --------- 
 42                                          af + c.tm 
 43   
 44                                            tm.as 
 45                                  ts'  =  --------- 
 46                                          as + c.tm 
 47   
 48   
 49                  Original 
 50                  ~~~~~~~~ 
 51   
 52                                   2.tm /      S2             (1 - S2)(ae + c.tm) . ae    \  
 53                          J(w)  =  ---- | -------------  +  ----------------------------- | 
 54                                    5   \ 1 + (w.tm)**2     (ae + c.tm)**2 + (w.tm.ae)**2 / 
 55   
 56   
 57                  Extended 
 58                  ~~~~~~~~ 
 59   
 60                                   2.tm /      S2             (1 - S2f)(af + c.tm) . af        (S2f - S2)(as + c.tm) . as   \  
 61                          J(w)  =  ---- | -------------  +  -----------------------------  +  ----------------------------- | 
 62                                    5   \ 1 + (w.tm)**2     (af + c.tm)**2 + (w.tm.af)**2     (as + c.tm)**2 + (w.tm.as)**2 / 
 63   
 64   
 65                  """ 
 66   
 67                  # The value of the constant. 
 68                  self.data.c = 1e10 
 69   
 70                  # Calculate frequency independent terms (to increase speed) 
 71                  self.initialise_jw_values() 
 72   
 73                  # Initialise the spectral density values. 
 74                  self.data.jw = zeros((self.mf.data.num_frq, 5), Float64) 
 75   
 76                  # Isotropic rotational diffusion. 
 77                  if match(self.data.diff_type, 'iso'): 
 78                          if match('m[13]', self.data.model): 
 79                                  for i in range(self.mf.data.num_frq): 
 80                                          self.data.jw[i, 0] = self.calc_jw_iso_m13(i, 0) 
 81                                          self.data.jw[i, 1] = self.calc_jw_iso_m13(i, 1) 
 82                                          self.data.jw[i, 2] = self.calc_jw_iso_m13(i, 2) 
 83                                          self.data.jw[i, 3] = self.calc_jw_iso_m13(i, 3) 
 84                                          self.data.jw[i, 4] = self.calc_jw_iso_m13(i, 4) 
 85                          elif match('m[24]', self.data.model): 
 86                                  for i in range(self.mf.data.num_frq): 
 87                                          self.data.jw[i, 0] = self.calc_jw_iso_m24(i, 0) 
 88                                          self.data.jw[i, 1] = self.calc_jw_iso_m24(i, 1) 
 89                                          self.data.jw[i, 2] = self.calc_jw_iso_m24(i, 2) 
 90                                          self.data.jw[i, 3] = self.calc_jw_iso_m24(i, 3) 
 91                                          self.data.jw[i, 4] = self.calc_jw_iso_m24(i, 4) 
 92                          elif match('m5', self.data.model): 
 93                                  for i in range(self.mf.data.num_frq): 
 94                                          self.data.jw[i, 0] = self.calc_jw_iso_m5(i, 0) 
 95                                          self.data.jw[i, 1] = self.calc_jw_iso_m5(i, 1) 
 96                                          self.data.jw[i, 2] = self.calc_jw_iso_m5(i, 2) 
 97                                          self.data.jw[i, 3] = self.calc_jw_iso_m5(i, 3) 
 98                                          self.data.jw[i, 4] = self.calc_jw_iso_m5(i, 4) 
 99   
100                  # Axially symmetric rotational diffusion. 
101                  elif match(self.data.diff_type, 'axail'): 
102                          raise NameError, "Axially symetric diffusion not implemented yet, quitting program." 
103   
104                  # Anisotropic rotational diffusion. 
105                  elif match(self.data.diff_type, 'aniso'): 
106                          raise NameError, "Anisotropic diffusion not implemented yet, quitting program." 
107   
108                  else: 
109                          raise NameError, "Diffusion type set incorrectly, quitting program." 
110   
111   
112 -        def calc_jw_iso_m13(self, i, frq_index): 
113                  "Calculate the model 1 and 3 spectral density values for isotropic rotational diffusion." 
114   
115                  temp = 0.4 * self.data.tm * (self.data.s2 / (1.0 + self.data.omega_tm_sqrd[i, frq_index])) 
116                  return temp 
117   
118   
119 -        def calc_jw_iso_m24(self, i, frq_index): 
120                  "Calculate the model 2 and 4 spectral density values for isotropic rotational diffusion." 
121   
122                  a = self.data.s2 / (1.0 + self.data.omega_tm_sqrd[i, frq_index]) 
123                  b = (1.0 - self.data.s2) * self.data.ae_plus_c_tm * self.data.ae / (self.data.ae_plus_c_tm_sqrd + self.data.omega_tm_ae_sqrd[i, frq_index]) 
124                  temp = 0.4 * self.data.tm * (a + b) 
125                  return temp 
126   
127   
128 -        def calc_jw_iso_m5(self, i, frq_index): 
129                  "Calculate the model 5 spectral density values for isotropic rotational diffusion." 
130   
131                  a = self.data.s2s / (1.0 + self.data.omega_tm_sqrd[i, frq_index]) 
132                  b = (1.0 - self.data.s2s) * self.data.as_plus_c_tm * self.data.as / (self.data.as_plus_c_tm_sqrd + self.data.omega_tm_as_sqrd[i, frq_index]) 
133                  temp = 0.4 * self.data.tm * self.data.s2f * (a + b) 
134                  return temp 
135   
136   
137 -        def initialise_jw_values(self): 
138                  "Remap the parameters in self.data.params" 
139   
140                  # Isotropic dependent values. 
141                  if match(self.data.diff_type, 'iso'): 
142                          self.data.tm = self.data.diff_params 
143                          self.data.tm_sqrd = self.data.tm ** 2 
144                          self.data.omega_tm_sqrd = zeros((self.mf.data.num_frq, 5), Float64) 
145   
146                  # Diffusion independent values. 
147                  if match('m[13]', self.data.model): 
148                          self.data.s2 = self.data.params[0] 
149   
150                  elif match('m[24]', self.data.model): 
151                          self.data.s2 = self.data.params[0] 
152                          self.data.ae = self.data.params[1] 
153                          self.data.ae_plus_c_tm = self.data.ae + self.data.c * self.data.tm 
154                          self.data.ae_plus_c_tm_sqrd = self.data.ae_plus_c_tm ** 2 
155                          self.data.omega_tm_ae_sqrd = zeros((self.mf.data.num_frq, 5), Float64) 
156   
157                  elif match('m5', self.data.model): 
158                          self.data.s2f = self.data.params[0] 
159                          self.data.s2s = self.data.params[1] 
160                          self.data.s2 = self.data.s2f * self.data.s2s 
161                          self.data.as = self.data.params[2] 
162                          self.data.as_plus_c_tm = self.data.as + self.data.c * self.data.tm 
163                          self.data.as_plus_c_tm_sqrd = self.data.as_plus_c_tm ** 2 
164                          self.data.omega_tm_as_sqrd = zeros((self.mf.data.num_frq, 5), Float64) 
165   
166                  for i in range(self.mf.data.num_frq): 
167                          for frq_index in range(5): 
168                                  self.data.omega_tm_sqrd[i, frq_index] = self.mf.data.frq_sqrd_list[i][frq_index] * self.data.tm_sqrd 
169                                  if match('m[24]', self.data.model): 
170                                          self.data.omega_tm_ae_sqrd[i, frq_index] = (self.mf.data.frq_list[i][frq_index] * self.data.tm * self.data.ae)**2 
171                                  elif match('m5', self.data.model): 
172                                          self.data.omega_tm_as_sqrd[i, frq_index] = (self.mf.data.frq_list[i][frq_index] * self.data.tm * self.data.as)**2 
173