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 (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module for the manipulation of paramagnetic data.""" 
 24   
 25  # Python module imports. 
 26  from math import sqrt 
 27  from numpy import array, float64, zeros 
 28  import sys 
 29  from warnings import warn 
 30   
 31  # relax module imports. 
 32  from generic_fns import grace, pipes 
 33  from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin, spin_loop 
 34  from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError, RelaxNoSpinError 
 35  from relax_warnings import RelaxWarning 
 36   
 37   
 38 -def centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=False, force=False): 
 39      """Specify the atom in the loaded structure corresponding to the paramagnetic centre. 
 40   
 41      @keyword pos:       The atomic position.  If set, the atom_id string will be ignored. 
 42      @type pos:          list of float 
 43      @keyword atom_id:   The atom identification string. 
 44      @type atom_id:      str 
 45      @keyword pipe:      An alternative data pipe to extract the paramagnetic centre from. 
 46      @type pipe:         None or str 
 47      @keyword verbosity: The amount of information to print out.  The bigger the number, the more information. 
 48      @type verbosity:    int 
 49      @keyword fix:       A flag which if False causes the paramagnetic centre to be optimised during minimisation. 
 50      @type fix:          bool 
 51      @keyword ave_pos:   A flag which if True causes the atomic positions from multiple models to be averaged. 
 52      @type ave_pos:      bool 
 53      @keyword force:     A flag which if True will cause the current paramagnetic centre to be overwritten. 
 54      @type force:        bool 
 55      """ 
 56   
 57      # The data pipe. 
 58      if pipe == None: 
 59          pipe = pipes.cdp_name() 
 60   
 61      # Test the data pipe. 
 62      pipes.test(pipe) 
 63   
 64      # Get the data pipes. 
 65      source_dp = pipes.get_pipe(pipe) 
 66   
 67      # Test if the structure has been loaded. 
 68      if not hasattr(source_dp, 'structure'): 
 69          raise RelaxNoPdbError 
 70   
 71      # Test the centre has already been set. 
 72      if pos != None and not force and hasattr(cdp, 'paramagnetic_centre'): 
 73          raise RelaxError("The paramagnetic centre has already been set to the coordinates " + repr(cdp.paramagnetic_centre) + ".") 
 74   
 75      # The fixed flag. 
 76      if fix: 
 77          print("The paramagnetic centre will be fixed during optimisation.") 
 78      else: 
 79          print("The paramagnetic centre will be optimised.") 
 80      cdp.paramag_centre_fixed = fix 
 81   
 82      # Position is supplied. 
 83      if pos != None: 
 84          centre = array(pos) 
 85          num_pos = 1 
 86          full_pos_list = [] 
 87   
 88      # Position from a loaded structure. 
 89      elif atom_id: 
 90          # Get the positions. 
 91          centre = zeros(3, float64) 
 92          full_pos_list = [] 
 93          num_pos = 0 
 94          for spin, spin_id in spin_loop(atom_id, pipe=pipe, return_id=True): 
 95              # No atomic positions. 
 96              if not hasattr(spin, 'pos'): 
 97                  continue 
 98       
 99              # Spin position list. 
100              if isinstance(spin.pos[0], float) or isinstance(spin.pos[0], float64): 
101                  pos_list = [spin.pos] 
102              else: 
103                  pos_list = spin.pos 
104       
105              # Loop over the model positions. 
106              for pos in pos_list: 
107                  full_pos_list.append(pos) 
108                  centre = centre + array(pos) 
109                  num_pos = num_pos + 1 
110       
111          # No positional information! 
112          if not num_pos: 
113              raise RelaxError("No positional information could be found for the spin '%s'." % atom_id) 
114   
115      # No position - so simply exit the function. 
116      else: 
117          return 
118   
119      # Averaging. 
120      centre = centre / float(num_pos) 
121   
122      # Print out. 
123      if verbosity: 
124          print("Paramagnetic centres located at:") 
125          for pos in full_pos_list: 
126              print("    [%8.3f, %8.3f, %8.3f]" % (pos[0], pos[1], pos[2])) 
127          print("\nAverage paramagnetic centre located at:") 
128          print("    [%8.3f, %8.3f, %8.3f]" % (centre[0], centre[1], centre[2])) 
129   
130      # Set the centre (place it into the current data pipe). 
131      if ave_pos: 
132          if verbosity: 
133              print("\nUsing the average paramagnetic position.") 
134          cdp.paramagnetic_centre = centre 
135      else: 
136          if verbosity: 
137              print("\nUsing all paramagnetic positions.") 
138          cdp.paramagnetic_centre = full_pos_list 
139