Source Code for Module functions.dri

 1  from Numeric import copy 
 2   
 3 -class dRi: 
 4 -        def __init__(self): 
 5                  "An additional layer of equations to simplify the relaxation equations, gradients, and hessians." 
 6                   
 7   
 8   
 9 -        def dRi(self): 
10                  """An additional layer of equations to simplify the relaxation equations, gradients, and hessians. 
11   
12                  The R1 and R2 equations are left alone, while the NOE is decomposed into the cross relaxation rate equation and the R1 equation. 
13   
14   
15                  The relaxation gradients 
16                  ~~~~~~~~~~~~~~~~~~~~~~~~ 
17   
18                  Data structure:  self.data.dri 
19                  Dimension:  2D, (parameters, relaxation data) 
20                  Type:  Numeric array, Float64 
21                  Dependencies:  self.data.ri_prime, self.data.dri_prime 
22                  Required by:  self.data.dchi2, self.data.d2chi2 
23   
24   
25                  Formulae 
26                  ~~~~~~~~ 
27   
28                           dR1()       dR1'() 
29                          -------  =  ------- 
30                          dthetaj     dthetaj 
31   
32   
33                           dR2()       dR2'() 
34                          -------  =  ------- 
35                          dthetaj     dthetaj 
36   
37   
38                           dNOE()     gH      1      /        dsigma_noe()                    dR1()  \  
39                          -------  =  -- . ------- . | R1() . ------------  -  sigma_noe() . ------- | 
40                          dthetaj     gN   R1()**2   \          dthetaj                      dthetaj / 
41   
42   
43                  """ 
44   
45                  # Calculate the transformed relaxation gradients (the transformed relaxation values have been previously calculated by the dChi2 function). 
46                  self.dRi_prime() 
47   
48                  # Copy the relaxation gradients from self.data.dri_prime 
49                  self.data.dri = copy.deepcopy(self.data.dri_prime) 
50   
51                  # Loop over the relaxation values and modify the NOE gradients. 
52                  for i in range(self.mf.data.num_ri): 
53                          if self.mf.data.data_types[i] == 'NOE': 
54                                  r1 = self.data.ri_prime[self.mf.data.noe_r1_table[i]] 
55                                  if r1 == None: 
56                                          raise NameError, "Incomplete code, need to somehow calculate the r1 value." 
57                                  for param in range(len(self.data.ri_param_types)): 
58                                          if r1 == 0.0: 
59                                                  self.data.dri[param, i] = 1e99 
60                                          else: 
61                                                  self.data.dri[param, i] = (self.mf.data.gh/self.mf.data.gx) * (1.0 / r1**2) * (r1 * self.data.dri_prime[param, i] - self.data.ri_prime[i] * self.data.dri_prime[param, self.mf.data.noe_r1_table[i]]) 
62