Source Code for Module generic_fns.structure.mass

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2011 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               # 
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 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              # 
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 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
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 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from numpy import float64, zeros 
 25  from warnings import warn 
 26   
 27  # relax module imports. 
 28  from generic_fns.mol_res_spin import return_molecule, return_residue, return_spin 
 29  from physical_constants import return_atomic_mass 
 30  from relax_errors import RelaxError, RelaxNoPdbError 
 31  from relax_warnings import RelaxWarning 
 32   
 33   
 34   
 35 -def centre_of_mass(atom_id=None, model=None, return_mass=False): 
 36      """Calculate and return the centre of mass of the structure. 
 37   
 38      @keyword atom_id:       The molecule, residue, and atom identifier string.  Only atoms matching this selection will be used. 
 39      @type atom_id:          str or None 
 40      @keyword model:         Only use a specific model. 
 41      @type model:            int or None 
 42      @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. 
 43      @type return_mass:      bool 
 44      @return:                The centre of mass vector, and additionally the mass. 
 45      @rtype:                 list of 3 floats (or tuple of a list of 3 floats and one float) 
 46      """ 
 47   
 48      # Test if a structure has been loaded. 
 49      if not hasattr(cdp, 'structure'): 
 50          raise RelaxNoPdbError 
 51   
 52      # Print out. 
 53      print("Calculating the centre of mass.") 
 54   
 55      # Initialise the centre of mass. 
 56      R = zeros(3, float64) 
 57   
 58      # Initialise the total mass. 
 59      M = 0.0 
 60   
 61      # Loop over all atoms. 
 62      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): 
 63          # Initialise the spin id string. 
 64          id = '' 
 65   
 66          # Get the corresponding molecule container. 
 67          if mol_name == None: 
 68              mol_cont = cdp.mol[0] 
 69          else: 
 70              id = id + '#' + mol_name 
 71              mol_cont = return_molecule(id) 
 72   
 73          # Get the corresponding residue container. 
 74          if res_name == None and res_num == None: 
 75              res_cont = mol_cont.res[0] 
 76          else: 
 77              id = id + ':' + repr(res_num) 
 78              res_cont = return_residue(id) 
 79   
 80          # Get the corresponding spin container. 
 81          if atom_name == None and atom_num == None: 
 82              spin_cont = res_cont.spin[0] 
 83          else: 
 84              id = id + '@' + repr(atom_num) 
 85              spin_cont = return_spin(id) 
 86   
 87          # Deselected spins. 
 88          if spin_cont and not spin_cont.select: 
 89              continue 
 90   
 91          # No element? 
 92          if element == None: 
 93              warn(RelaxWarning("Skipping the atom '%s' as the element type cannot be determined." % id)) 
 94              continue 
 95   
 96          # Atomic mass. 
 97          try: 
 98              mass = return_atomic_mass(element) 
 99          except RelaxError: 
100              warn(RelaxWarning("Skipping the atom '%s' as the element '%s' is unknown." % (id, element))) 
101   
102          # Total mass. 
103          M = M + mass 
104   
105          # Sum of mass * position. 
106          R = R + mass * pos 
107   
108      # Normalise. 
109      R = R / M 
110   
111      # Final print out. 
112      print(("    Total mass:      M = " + repr(M))) 
113      print(("    Centre of mass:  R = " + repr(R))) 
114   
115      # Return the centre of mass. 
116      if return_mass: 
117          return R, M 
118      else: 
119          return R 
120