Source Code for Module target_functions.ens_pivot_finder

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 2  #                                                                             # 
 3  # Copyright (C) 2011-2013 Edward d'Auvergne                                   # 
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 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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21   
22  # Module docstring. 
23  """Module for the target function for handling all types of structural superimpositions.""" 
24   
25  # Python module imports. 
26  from copy import deepcopy 
27   
28  # relax module import. 
29  from lib.structure.statistics import atomic_rmsd 
30  from lib.structure.superimpose import fit_to_mean 
31   
32   
33 -class Pivot_finder: 
34      """Class for finding the optimal pivot point for motions between the given models.""" 
35   
36 -    def __init__(self, models, coord): 
37          """Set up the class for pivot point optimisation for an ensemble of structures. 
38   
39          @keyword models:    The list of models to use.  If set to None, then all models will be used. 
40          @type models:       list of int or None 
41          @keyword coord:     The array of molecular coordinates.  The first dimension corresponds to the model, the second the atom, the third the coordinate. 
42          @type coord:        rank-3 numpy array 
43          """ 
44   
45          # Store the args. 
46          self.models = models 
47          self.coord = coord 
48   
49          # Store a copy of the coordinates for restoration. 
50          self.orig_coord = deepcopy(coord) 
51   
52   
53 -    def func(self, params): 
54          """Target function for the optimisation of the motional pivot point from an ensemble of structures. 
55   
56          @param params:  The parameter vector from the optimisation algorithm. 
57          @type params:   list 
58          @return:        The target function value defined as the combined RMSD value. 
59          @rtype:         float 
60          """ 
61   
62          # The fit to mean algorithm. 
63          T, R, pivot = fit_to_mean(models=self.models, coord=self.coord, centroid=params, verbosity=0) 
64   
65          # The RMSD. 
66          val = atomic_rmsd(self.coord) 
67   
68          # Restore the coordinates. 
69          self.coord = deepcopy(self.orig_coord) 
70   
71          # Return the RMSD. 
72          return val 
73