Source Code for Module usr_param

  1  # usr_param.py          v0.1                  10 November 2001        Edward d'Auvergne 
  2  # 
  3  # Class containing all the user specified parameters.  Used by the program Modelfree. 
  4  # Make sure the version numbers between the program and this class are identical. 
  5   
  6   
  7 -class usr_param: 
  8 -        def __init__(self): 
  9                  "Class containing parameters specified by the user" 
 10   
 11                  self.init_method_param() 
 12                  self.init_run_param() 
 13                  self.init_mfin_param() 
 14                  self.init_mfpar_param() 
 15                  self.init_mfmodel_param() 
 16   
 17   
 18 -        def init_method_param(self): 
 19                  """Model-free analysis method info. 
 20                   
 21                  self.method can be set to the following strings: 
 22                          Palmer - The method given by Mandel et al., 1995. 
 23                          AIC - method of model-free analysis based on model selection using the 
 24                                  Akaike Information Criteria. 
 25                          BIC - method of model-free analysis based on model selection using the 
 26                                  Schwartz Information Criteria. 
 27                  """ 
 28                  self.method = 'Bootstrap' 
 29   
 30                  # The following three values are only used in Palmer's method and won't affect the others. 
 31                  self.sse_lim = '0.90'       # Set the SSE limit (1 - alpha critical value). 
 32                  self.ftest_lim = '0.80'     # Set the F-test limit (1 - alpha critical value). 
 33                  self.large_sse = '20'        # Set the SSE limit for when much greater than the SSE limit. 
 34   
 35                   
 36 -        def init_run_param(self): 
 37                  "Run file parameters" 
 38                   
 39                  self.pdb_file = 'Ap4Aase_new_3.pdb' 
 40                  self.pdb_path = './' 
 41                  self.pdb_full = self.pdb_path + self.pdb_file 
 42   
 43   
 44 -        def init_mfin_param(self): 
 45                  "mfin file parameters" 
 46   
 47                  self.diff = 'isotropic' 
 48                  #self.diff = 'axial' 
 49                  self.no_sim = '200' 
 50                  self.trim = '0'               # Trim unconverged simulations. 
 51   
 52                  # tm 
 53                  self.tm = {} 
 54                  self.tm['val']   = '11.09' 
 55                  self.tm['flag']  = '1' 
 56                  self.tm['bound'] = '2' 
 57                  self.tm['lower'] = '9.0' 
 58                  self.tm['upper'] = '13.0' 
 59                  self.tm['steps'] = '100' 
 60   
 61                  # dratio 
 62                  self.dratio = {} 
 63                  self.dratio['val']   = '1.123' 
 64                  self.dratio['flag']  = '1' 
 65                  self.dratio['bound'] = '0' 
 66                  self.dratio['lower'] = '0.6' 
 67                  self.dratio['upper'] = '1.5' 
 68                  self.dratio['steps'] = '5' 
 69   
 70                  # theta 
 71                  self.theta = {} 
 72                  self.theta['val']   = '87.493' 
 73                  self.theta['flag']  = '1' 
 74                  self.theta['bound'] = '0' 
 75                  self.theta['lower'] = '-90' 
 76                  self.theta['upper'] = '90' 
 77                  self.theta['steps'] = '10' 
 78   
 79                  # phi 
 80                  self.phi = {} 
 81                  self.phi['val']   = '-52.470' 
 82                  self.phi['flag']  = '1' 
 83                  self.phi['bound'] = '0' 
 84                  self.phi['lower'] = '-90' 
 85                  self.phi['upper'] = '90' 
 86                  self.phi['steps'] = '10' 
 87   
 88   
 89 -        def init_mfpar_param(self): 
 90                  "mfpar file parameters" 
 91   
 92                  self.const = {} 
 93                  self.const['nucleus'] = 'N15' 
 94                  self.const['gamma']   = '-2.710' 
 95                  self.const['rxh']     = '1.020' 
 96                  self.const['csa']     = '-170.00' 
 97   
 98                  self.vector = {} 
 99                  self.vector['atom1'] = 'N' 
100                  self.vector['atom2'] = 'H' 
101   
102   
103 -        def init_mfmodel_param(self): 
104                  "mfmodel file parameters" 
105   
106                  self.md1 = {} 
107                  self.md1['tloc'] = {} 
108                  self.md1['tloc']['start'] = '0.0' 
109                  self.md1['tloc']['flag']  = '0' 
110                  self.md1['tloc']['bound'] = '2' 
111                  self.md1['tloc']['lower'] = '0.000' 
112                  self.md1['tloc']['upper'] = '20.000' 
113                  self.md1['tloc']['steps'] = '20' 
114   
115                  self.md1['theta'] = {} 
116                  self.md1['theta']['start'] = '0.0' 
117                  self.md1['theta']['flag']  = '0' 
118                  self.md1['theta']['bound'] = '2' 
119                  self.md1['theta']['lower'] = '0.000' 
120                  self.md1['theta']['upper'] = '90.000' 
121                  self.md1['theta']['steps'] = '20' 
122   
123                  self.md1['sf2'] = {} 
124                  self.md1['sf2']['start'] = '1.0' 
125                  self.md1['sf2']['flag']  = '0' 
126                  self.md1['sf2']['bound'] = '2' 
127                  self.md1['sf2']['lower'] = '0.000' 
128                  self.md1['sf2']['upper'] = '1.000' 
129                  self.md1['sf2']['steps'] = '20' 
130   
131                  self.md1['ss2'] = {} 
132                  self.md1['ss2']['start'] = '1.0' 
133                  self.md1['ss2']['flag']  = '0' 
134                  self.md1['ss2']['bound'] = '2' 
135                  self.md1['ss2']['lower'] = '0.000' 
136                  self.md1['ss2']['upper'] = '1.000' 
137                  self.md1['ss2']['steps'] = '20' 
138                   
139                  self.md1['te'] = {} 
140                  self.md1['te']['start'] = '0.0' 
141                  self.md1['te']['flag']  = '0' 
142                  self.md1['te']['bound'] = '2' 
143                  self.md1['te']['lower'] = '0.000' 
144                  self.md1['te']['upper'] = '10000.000' 
145                  self.md1['te']['steps'] = '20' 
146   
147                  self.md1['rex'] = {} 
148                  self.md1['rex']['start'] = '0.0' 
149                  self.md1['rex']['flag']  = '0' 
150                  self.md1['rex']['bound'] = '-1' 
151                  self.md1['rex']['lower'] = '0.000' 
152                  self.md1['rex']['upper'] = '20.000' 
153                  self.md1['rex']['steps'] = '20' 
154   
155                  self.md2 = {} 
156                  for param in self.md1.keys(): 
157                          self.md2[param] = {} 
158                          for value in self.md1[param].keys(): 
159                                  self.md2[param][value] = self.md1[param][value] 
160