Source Code for Module generic_fns.structure.mass

  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).          # 
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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           # 
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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.                                # 
 16  #                                                                             # 
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 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from numpy import float64, zeros 
 24  from warnings import warn 
 25   
 26  # relax module imports. 
 27  from generic_fns.mol_res_spin import return_molecule, return_residue, return_spin 
 28  from physical_constants import return_atomic_mass 
 29  from relax_errors import RelaxError, RelaxNoPdbError 
 30  from relax_warnings import RelaxWarning 
 31   
 32   
 33   
 34 -def centre_of_mass(atom_id=None, model=None, return_mass=False): 
 35      """Calculate and return the centre of mass of the structure. 
 36   
 37      @keyword atom_id:       The molecule, residue, and atom identifier string.  Only atoms matching this selection will be used. 
 38      @type atom_id:          str or None 
 39      @keyword model:         Only use a specific model. 
 40      @type model:            int or None 
 41      @keyword return_mass:   A flag which if False will cause only the centre of mass to be returned, but if True will cause the centre of mass and the mass itself to be returned as a tuple. 
 42      @type return_mass:      bool 
 43      @return:                The centre of mass vector, and additionally the mass. 
 44      @rtype:                 list of 3 floats (or tuple of a list of 3 floats and one float) 
 45      """ 
 46   
 47      # Test if a structure has been loaded. 
 48      if not hasattr(cdp, 'structure'): 
 49          raise RelaxNoPdbError 
 50   
 51      # Print out. 
 52      print("Calculating the centre of mass.") 
 53   
 54      # Initialise the centre of mass. 
 55      R = zeros(3, float64) 
 56   
 57      # Initialise the total mass. 
 58      M = 0.0 
 59   
 60      # Loop over all atoms. 
 61      for mol_name, res_num, res_name, atom_num, atom_name, element, pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True): 
 62          # Initialise the spin id string. 
 63          id = '' 
 64   
 65          # Get the corresponding molecule container. 
 66          if mol_name == None: 
 67              mol_cont = cdp.mol[0] 
 68          else: 
 69              id = id + '#' + mol_name 
 70              mol_cont = return_molecule(id) 
 71   
 72          # Get the corresponding residue container. 
 73          if res_name == None and res_num == None: 
 74              res_cont = mol_cont.res[0] 
 75          else: 
 76              id = id + ':' + repr(res_num) 
 77              res_cont = return_residue(id) 
 78   
 79          # Get the corresponding spin container. 
 80          if atom_name == None and atom_num == None: 
 81              spin_cont = res_cont.spin[0] 
 82          else: 
 83              id = id + '@' + repr(atom_num) 
 84              spin_cont = return_spin(id) 
 85   
 86          # Deselected spins. 
 87          if spin_cont and not spin_cont.select: 
 88              continue 
 89   
 90          # No element? 
 91          if element == None: 
 92              warn(RelaxWarning("Skipping the atom '%s' as the element type cannot be determined." % id)) 
 93              continue 
 94   
 95          # Atomic mass. 
 96          try: 
 97              mass = return_atomic_mass(element) 
 98          except RelaxError: 
 99              warn(RelaxWarning("Skipping the atom '%s' as the element '%s' is unknown." % (id, element))) 
100   
101          # Total mass. 
102          M = M + mass 
103   
104          # Sum of mass * position. 
105          R = R + mass * pos 
106   
107      # Normalise. 
108      R = R / M 
109   
110      # Final printout. 
111      print("    Total mass:      M = " + repr(M)) 
112      print("    Centre of mass:  R = " + repr(R)) 
113   
114      # Return the centre of mass. 
115      if return_mass: 
116          return R, M 
117      else: 
118          return R 
119