Source Code for Module prompt.paramag

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2005,2007-2010 Edward d'Auvergne                         # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
  6  #                                                                             # 
  7  # relax 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 2 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # relax 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing the user function class for paramagnetic related functions.""" 
 25  __docformat__ = 'plaintext' 
 26   
 27  # relax module imports. 
 28  from base_class import User_fn_class 
 29  import arg_check 
 30  from generic_fns import paramag 
 31  from relax_errors import RelaxError 
 32   
 33   
 34 -class Paramag(User_fn_class): 
 35      """Class for handling paramagnetic information.""" 
 36   
 37 -    def centre(self, pos=None, atom_id=None, pipe=None, verbosity=1, fix=True, ave_pos=True, force=False): 
 38          """Specify which atom is the paramagnetic centre. 
 39   
 40          Keyword Arguments 
 41          ~~~~~~~~~~~~~~~~~ 
 42   
 43          pos:  The atomic position. 
 44   
 45          atom_id:  The atom ID string. 
 46   
 47          pipe:  The data pipe containing the structures to extract the centre from. 
 48   
 49          verbosity:  The amount of information to print out. 
 50   
 51          fix:  A flag specifying if the paramagnetic centre should be fixed during optimisation. 
 52   
 53          ave_pos:  A flag specifying if the position of the atom is to be averaged across all models. 
 54   
 55          force:  A flag which if True will cause the current paramagnetic centre to be overwritten. 
 56   
 57   
 58          Description 
 59          ~~~~~~~~~~~ 
 60   
 61          This function is required for specifying where the paramagnetic centre is located in the 
 62          loaded structure file.  If no structure number is given, then the average atom position will 
 63          be calculated if multiple structures are loaded. 
 64   
 65          A different set of structures than those loaded into the current data pipe can also be used 
 66          to determine the position, or its average.  This can be achieved by loading the alternative 
 67          structures into another data pipe, and then specifying that pipe through the pipe argument. 
 68   
 69          If the ave_pos flag is set to True, the average position from all models will be used as the 
 70          position of the paramagnetic centre.  If False, then the positions from all structures will 
 71          be used.  If multiple positions are used, then a fast paramagnetic centre motion will be 
 72          assumed so that PCSs for a single tensor will be calculated for each position, and the PCS 
 73          values linearly averaged. 
 74   
 75   
 76          Examples 
 77          ~~~~~~~~ 
 78   
 79          If the paramagnetic centre is the lanthanide Dysprosium which is labelled as Dy in a loaded 
 80          PDB file, then type one of: 
 81   
 82          relax> paramag.centre('Dy') 
 83          relax> paramag.centre(atom_id='Dy') 
 84   
 85          If the carbon atom 'C1' of residue '4' in the PDB file is to be used as the paramagnetic 
 86          centre, then type: 
 87   
 88          relax> paramag.centre(':4@C1') 
 89           
 90          To state that the Dy3+ atomic position is [0.136, 12.543, 4.356], type one of: 
 91   
 92          relax> paramag.centre([0.136, 12.543, 4.356]) 
 93          relax> paramag.centre(pos=[0.136, 12.543, 4.356]) 
 94   
 95          To find an unknown paramagnetic centre, type: 
 96   
 97          relax> paramag.centre(fix=False) 
 98          """ 
 99   
100          # Function intro text. 
101          if self._exec_info.intro: 
102              text = self._exec_info.ps3 + "paramag.centre(" 
103              text = text + "pos=" + repr(pos) 
104              text = text + ", atom_id=" + repr(atom_id) 
105              text = text + ", pipe=" + repr(pipe) 
106              text = text + ", verbosity=" + repr(verbosity) 
107              text = text + ", fix=" + repr(fix) 
108              text = text + ", ave_pos=" + repr(ave_pos) 
109              text = text + ", force=" + repr(force) + ")" 
110              print(text) 
111   
112          # The argument checks. 
113          arg_check.is_num_list(pos, 'atomic position', size=3, can_be_none=True) 
114          arg_check.is_str(atom_id, 'atom ID string', can_be_none=True) 
115          arg_check.is_str(pipe, 'data pipe', can_be_none=True) 
116          arg_check.is_int(verbosity, 'verbosity level') 
117          arg_check.is_bool(fix, 'fix flag') 
118          arg_check.is_bool(ave_pos, 'average position flag') 
119          arg_check.is_bool(force, 'force flag') 
120   
121          # Execute the functional code. 
122          paramag.centre(pos=pos, atom_id=atom_id, pipe=pipe, verbosity=verbosity, fix=fix, ave_pos=ave_pos, force=force) 
123