Source Code for Module generic_fns.paramag

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2011 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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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 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_io import open_write_file, read_spin_data, write_spin_data 
 37  from relax_warnings import RelaxWarning 
 38   
 39   
 40 -def centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=False, force=False): 
 41      """Specify the atom in the loaded structure corresponding to the paramagnetic centre. 
 42   
 43      @keyword pos:       The atomic position.  If set, the atom_id string will be ignored. 
 44      @type pos:          list of float 
 45      @keyword atom_id:   The atom identification string. 
 46      @type atom_id:      str 
 47      @keyword pipe:      An alternative data pipe to extract the paramagnetic centre from. 
 48      @type pipe:         None or str 
 49      @keyword verbosity: The amount of information to print out.  The bigger the number, the more information. 
 50      @type verbosity:    int 
 51      @keyword fix:       A flag which if False causes the paramagnetic centre to be optimised during minimisation. 
 52      @type fix:          bool 
 53      @keyword ave_pos:   A flag which if True causes the atomic positions from multiple models to be averaged. 
 54      @type ave_pos:      bool 
 55      @keyword force:     A flag which if True will cause the current paramagnetic centre to be overwritten. 
 56      @type force:        bool 
 57      """ 
 58   
 59      # The data pipe. 
 60      if pipe == None: 
 61          pipe = pipes.cdp_name() 
 62   
 63      # Test the data pipe. 
 64      pipes.test(pipe) 
 65   
 66      # Get the data pipes. 
 67      source_dp = pipes.get_pipe(pipe) 
 68   
 69      # Test if the structure has been loaded. 
 70      if not hasattr(source_dp, 'structure'): 
 71          raise RelaxNoPdbError 
 72   
 73      # Test the centre has already been set. 
 74      if pos != None and not force and hasattr(cdp, 'paramagnetic_centre'): 
 75          raise RelaxError("The paramagnetic centre has already been set to the coordinates " + repr(cdp.paramagnetic_centre) + ".") 
 76   
 77      # The fixed flag. 
 78      if fix: 
 79          print("The paramagnetic centre will be fixed during optimisation.") 
 80      else: 
 81          print("The paramagnetic centre will be optimised.") 
 82      cdp.paramag_centre_fixed = fix 
 83   
 84      # Position is supplied. 
 85      if pos != None: 
 86          centre = array(pos) 
 87          num_pos = 1 
 88          full_pos_list = [] 
 89   
 90      # Position from a loaded structure. 
 91      elif atom_id: 
 92          # Get the positions. 
 93          centre = zeros(3, float64) 
 94          full_pos_list = [] 
 95          num_pos = 0 
 96          for spin, spin_id in spin_loop(atom_id, pipe=pipe, return_id=True): 
 97              # No atomic positions. 
 98              if not hasattr(spin, 'pos'): 
 99                  continue 
100       
101              # Spin position list. 
102              if isinstance(spin.pos[0], float) or isinstance(spin.pos[0], float64): 
103                  pos_list = [spin.pos] 
104              else: 
105                  pos_list = spin.pos 
106       
107              # Loop over the model positions. 
108              for pos in pos_list: 
109                  full_pos_list.append(pos) 
110                  centre = centre + array(pos) 
111                  num_pos = num_pos + 1 
112       
113          # No positional information! 
114          if not num_pos: 
115              raise RelaxError("No positional information could be found for the spin '%s'." % atom_id) 
116   
117      # No position - so simply exit the function. 
118      else: 
119          return 
120   
121      # Averaging. 
122      centre = centre / float(num_pos) 
123   
124      # Print out. 
125      if verbosity: 
126          print("Paramagnetic centres located at:") 
127          for pos in full_pos_list: 
128              print(("    [%8.3f, %8.3f, %8.3f]" % (pos[0], pos[1], pos[2]))) 
129          print("\nAverage paramagnetic centre located at:") 
130          print(("    [%8.3f, %8.3f, %8.3f]" % (centre[0], centre[1], centre[2]))) 
131   
132      # Set the centre (place it into the current data pipe). 
133      if ave_pos: 
134          if verbosity: 
135              print("\nUsing the average paramagnetic position.") 
136          cdp.paramagnetic_centre = centre 
137      else: 
138          if verbosity: 
139              print("\nUsing all paramagnetic positions.") 
140          cdp.paramagnetic_centre = full_pos_list 
141