Source Code for Module pipe_control.paramag

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  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 manipulation of paramagnetic data.""" 
 24   
 25  # Python module imports. 
 26  from numpy import array, float64, zeros 
 27   
 28  # relax module imports. 
 29  from lib.errors import RelaxError 
 30  from pipe_control import pipes 
 31  from pipe_control.mol_res_spin import spin_loop 
 32   
 33   
 34 -def centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=False, force=False): 
 35      """Specify the atom in the loaded structure corresponding to the paramagnetic centre. 
 36   
 37      @keyword pos:       The atomic position.  If set, the atom_id string will be ignored. 
 38      @type pos:          list of float 
 39      @keyword atom_id:   The atom identification string. 
 40      @type atom_id:      str 
 41      @keyword pipe:      An alternative data pipe to extract the paramagnetic centre from. 
 42      @type pipe:         None or str 
 43      @keyword verbosity: The amount of information to print out.  The bigger the number, the more information. 
 44      @type verbosity:    int 
 45      @keyword fix:       A flag which if False causes the paramagnetic centre to be optimised during minimisation. 
 46      @type fix:          bool 
 47      @keyword ave_pos:   A flag which if True causes the atomic positions from multiple models to be averaged. 
 48      @type ave_pos:      bool 
 49      @keyword force:     A flag which if True will cause the current paramagnetic centre to be overwritten. 
 50      @type force:        bool 
 51      """ 
 52   
 53      # The data pipe. 
 54      if pipe == None: 
 55          pipe = pipes.cdp_name() 
 56   
 57      # Test the data pipe. 
 58      pipes.test(pipe) 
 59   
 60      # Get the data pipes. 
 61      source_dp = pipes.get_pipe(pipe) 
 62   
 63      # Test the centre has already been set. 
 64      if pos != None and not force and hasattr(cdp, 'paramagnetic_centre'): 
 65          raise RelaxError("The paramagnetic centre has already been set to the coordinates " + repr(cdp.paramagnetic_centre) + ".") 
 66   
 67      # The fixed flag. 
 68      if fix: 
 69          print("The paramagnetic centre position will be fixed during optimisation.") 
 70      else: 
 71          print("The paramagnetic centre position will be optimised.") 
 72      cdp.paramag_centre_fixed = fix 
 73   
 74      # Position is supplied. 
 75      if pos != None: 
 76          centre = array(pos) 
 77          num_pos = 1 
 78          full_pos_list = [] 
 79   
 80      # Position from a loaded structure. 
 81      elif atom_id: 
 82          # Get the positions. 
 83          centre = zeros(3, float64) 
 84          full_pos_list = [] 
 85          num_pos = 0 
 86          for spin, spin_id in spin_loop(atom_id, pipe=pipe, return_id=True): 
 87              # No atomic positions. 
 88              if not hasattr(spin, 'pos'): 
 89                  continue 
 90       
 91              # Spin position list. 
 92              if isinstance(spin.pos[0], float) or isinstance(spin.pos[0], float64): 
 93                  pos_list = [spin.pos] 
 94              else: 
 95                  pos_list = spin.pos 
 96       
 97              # Loop over the model positions. 
 98              for pos in pos_list: 
 99                  full_pos_list.append(pos) 
100                  centre = centre + array(pos) 
101                  num_pos = num_pos + 1 
102       
103          # No positional information! 
104          if not num_pos: 
105              raise RelaxError("No positional information could be found for the spin '%s'." % atom_id) 
106   
107      # No position - so simply exit the function. 
108      else: 
109          return 
110   
111      # Averaging. 
112      centre = centre / float(num_pos) 
113   
114      # Print out. 
115      if verbosity: 
116          print("Paramagnetic centres located at:") 
117          for pos in full_pos_list: 
118              print("    [%8.3f, %8.3f, %8.3f]" % (pos[0], pos[1], pos[2])) 
119          print("\nAverage paramagnetic centre located at:") 
120          print("    [%8.3f, %8.3f, %8.3f]" % (centre[0], centre[1], centre[2])) 
121   
122      # Set the centre (place it into the current data pipe). 
123      if ave_pos: 
124          if verbosity: 
125              print("\nUsing the average paramagnetic position.") 
126          cdp.paramagnetic_centre = centre 
127      else: 
128          if verbosity: 
129              print("\nUsing all paramagnetic positions.") 
130          cdp.paramagnetic_centre = full_pos_list 
131