Source Code for Module generic_fns.paramag

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2012 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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  7  # relax is free software; you can redistribute it and/or modify               # 
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 12  # relax is distributed in the hope that it will be useful,                    # 
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 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module for the manipulation of paramagnetic data.""" 
 25   
 26  # Python module imports. 
 27  from math import sqrt 
 28  from numpy import array, float64, zeros 
 29  import sys 
 30  from warnings import warn 
 31   
 32  # relax module imports. 
 33  from generic_fns import grace, pipes 
 34  from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin, spin_loop 
 35  from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError, RelaxNoSpinError 
 36  from relax_warnings import RelaxWarning 
 37   
 38   
 39 -def centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=False, force=False): 
 40      """Specify the atom in the loaded structure corresponding to the paramagnetic centre. 
 41   
 42      @keyword pos:       The atomic position.  If set, the atom_id string will be ignored. 
 43      @type pos:          list of float 
 44      @keyword atom_id:   The atom identification string. 
 45      @type atom_id:      str 
 46      @keyword pipe:      An alternative data pipe to extract the paramagnetic centre from. 
 47      @type pipe:         None or str 
 48      @keyword verbosity: The amount of information to print out.  The bigger the number, the more information. 
 49      @type verbosity:    int 
 50      @keyword fix:       A flag which if False causes the paramagnetic centre to be optimised during minimisation. 
 51      @type fix:          bool 
 52      @keyword ave_pos:   A flag which if True causes the atomic positions from multiple models to be averaged. 
 53      @type ave_pos:      bool 
 54      @keyword force:     A flag which if True will cause the current paramagnetic centre to be overwritten. 
 55      @type force:        bool 
 56      """ 
 57   
 58      # The data pipe. 
 59      if pipe == None: 
 60          pipe = pipes.cdp_name() 
 61   
 62      # Test the data pipe. 
 63      pipes.test(pipe) 
 64   
 65      # Get the data pipes. 
 66      source_dp = pipes.get_pipe(pipe) 
 67   
 68      # Test if the structure has been loaded. 
 69      if not hasattr(source_dp, 'structure'): 
 70          raise RelaxNoPdbError 
 71   
 72      # Test the centre has already been set. 
 73      if pos != None and not force and hasattr(cdp, 'paramagnetic_centre'): 
 74          raise RelaxError("The paramagnetic centre has already been set to the coordinates " + repr(cdp.paramagnetic_centre) + ".") 
 75   
 76      # The fixed flag. 
 77      if fix: 
 78          print("The paramagnetic centre will be fixed during optimisation.") 
 79      else: 
 80          print("The paramagnetic centre will be optimised.") 
 81      cdp.paramag_centre_fixed = fix 
 82   
 83      # Position is supplied. 
 84      if pos != None: 
 85          centre = array(pos) 
 86          num_pos = 1 
 87          full_pos_list = [] 
 88   
 89      # Position from a loaded structure. 
 90      elif atom_id: 
 91          # Get the positions. 
 92          centre = zeros(3, float64) 
 93          full_pos_list = [] 
 94          num_pos = 0 
 95          for spin, spin_id in spin_loop(atom_id, pipe=pipe, return_id=True): 
 96              # No atomic positions. 
 97              if not hasattr(spin, 'pos'): 
 98                  continue 
 99       
100              # Spin position list. 
101              if isinstance(spin.pos[0], float) or isinstance(spin.pos[0], float64): 
102                  pos_list = [spin.pos] 
103              else: 
104                  pos_list = spin.pos 
105       
106              # Loop over the model positions. 
107              for pos in pos_list: 
108                  full_pos_list.append(pos) 
109                  centre = centre + array(pos) 
110                  num_pos = num_pos + 1 
111       
112          # No positional information! 
113          if not num_pos: 
114              raise RelaxError("No positional information could be found for the spin '%s'." % atom_id) 
115   
116      # No position - so simply exit the function. 
117      else: 
118          return 
119   
120      # Averaging. 
121      centre = centre / float(num_pos) 
122   
123      # Print out. 
124      if verbosity: 
125          print("Paramagnetic centres located at:") 
126          for pos in full_pos_list: 
127              print(("    [%8.3f, %8.3f, %8.3f]" % (pos[0], pos[1], pos[2]))) 
128          print("\nAverage paramagnetic centre located at:") 
129          print(("    [%8.3f, %8.3f, %8.3f]" % (centre[0], centre[1], centre[2]))) 
130   
131      # Set the centre (place it into the current data pipe). 
132      if ave_pos: 
133          if verbosity: 
134              print("\nUsing the average paramagnetic position.") 
135          cdp.paramagnetic_centre = centre 
136      else: 
137          if verbosity: 
138              print("\nUsing all paramagnetic positions.") 
139          cdp.paramagnetic_centre = full_pos_list 
140