Source Code for Module lib.structure.internal.selection

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014-2015 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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  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.                                         # 
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 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
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 15  # GNU General Public License for more details.                                # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module containing the fast structural selection object.""" 
 24   
 25   
 26 -class Internal_selection: 
 27      """The fast structural selection object.""" 
 28   
 29 -    def __init__(self): 
 30          """Set up the object.""" 
 31   
 32          # The molecule index list. 
 33          self._mol_indices = [] 
 34   
 35          # The atom index list of lists. 
 36          self._atom_indices = [] 
 37   
 38   
 39 -    def add_atom(self, mol_index=None, atom_index=None): 
 40          """Add an atom index to the object. 
 41   
 42          @keyword mol_index:     The index of the molecule. 
 43          @type mol_index:        int 
 44          @keyword atom_index:    The index of the atom. 
 45          @type atom_index:       int 
 46          """ 
 47   
 48          # Find the molecule index. 
 49          index = self._mol_indices.index(mol_index) 
 50   
 51          # Store the index. 
 52          self._atom_indices[index].append(atom_index) 
 53   
 54   
 55 -    def add_mol(self, mol_index=None): 
 56          """Add a molecule index to the object. 
 57   
 58          @keyword mol_index:     The index of the molecule. 
 59          @type mol_index:        int 
 60          """ 
 61   
 62          # Store the index. 
 63          self._mol_indices.append(mol_index) 
 64   
 65          # Add a new atom list. 
 66          self._atom_indices.append([]) 
 67   
 68   
 69 -    def count_atoms(self): 
 70          """Return the number of atoms in the selection.""" 
 71   
 72          # No data. 
 73          if self._atom_indices == []: 
 74              return 0 
 75   
 76          # Sum the atoms of all molecules. 
 77          sum = 0 
 78          for i in range(len(self._atom_indices)): 
 79              sum += len(self._atom_indices[i]) 
 80   
 81          # Return the sum. 
 82          return sum 
 83   
 84   
 85 -    def loop(self): 
 86          """Fast loop over all molecule and atom indices. 
 87   
 88          @return:    The molecule and atom index pairs for all atoms. 
 89          @rtype:     int, int 
 90          """ 
 91   
 92          # Molecule loop. 
 93          for mol_index in self._mol_indices: 
 94              # Find the molecule index. 
 95              index = self._mol_indices.index(mol_index) 
 96   
 97              # Atom loop. 
 98              for atom_index in self._atom_indices[index]: 
 99                  yield mol_index, atom_index 
100   
101   
102 -    def mol_loop(self): 
103          """Fast loop over all molecule indices. 
104   
105          @return:    The molecule index. 
106          @rtype:     int 
107          """ 
108   
109          # Molecule loop. 
110          for mol_index in self._mol_indices: 
111              yield mol_index 
112