Source Code for Module pipe_control.structure.mass

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2014 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 12  # This program is distributed in the hope that it will be useful,             # 
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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  # Python module imports. 
 23  from warnings import warn 
 24   
 25  # relax module imports. 
 26  from lib.errors import RelaxNoPdbError 
 27  from lib.structure.mass import centre_of_mass 
 28  from lib.warnings import RelaxWarning 
 29  from pipe_control.mol_res_spin import return_molecule, return_residue, return_spin 
 30   
 31   
 32   
 33 -def pipe_centre_of_mass(atom_id=None, model=None, return_mass=False, verbosity=1): 
 34      """Calculate and return the centre of mass of the structures in the current data pipe. 
 35   
 36      @keyword atom_id:       The molecule, residue, and atom identifier string.  Only atoms matching this selection will be used. 
 37      @type atom_id:          str or None 
 38      @keyword model:         Only use a specific model. 
 39      @type model:            int or None 
 40      @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. 
 41      @type return_mass:      bool 
 42      @keyword verbosity:     The amount of text to print out.  0 results in no printouts, 1 the full amount. 
 43      @type verbosity:        int 
 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      # Loop over all atoms. 
 53      coord = [] 
 54      element_list = [] 
 55      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, ave=True): 
 56          # Initialise the spin id string. 
 57          id = '' 
 58   
 59          # Get the corresponding molecule container. 
 60          if mol_name == None: 
 61              mol_cont = cdp.mol[0] 
 62          else: 
 63              id = id + '#' + mol_name 
 64              mol_cont = return_molecule(id) 
 65   
 66          # Get the corresponding residue container. 
 67          if res_name == None and res_num == None: 
 68              res_cont = mol_cont.res[0] 
 69          else: 
 70              id = id + ':' + repr(res_num) 
 71              res_cont = return_residue(id) 
 72   
 73          # Get the corresponding spin container. 
 74          if atom_name == None and atom_num == None: 
 75              spin_cont = res_cont.spin[0] 
 76          else: 
 77              id = id + '@' + repr(atom_num) 
 78              spin_cont = return_spin(id) 
 79   
 80          # Deselected spins. 
 81          if spin_cont and not spin_cont.select: 
 82              continue 
 83   
 84          # No element? 
 85          if element == None: 
 86              warn(RelaxWarning("Skipping the atom '%s' as the element type cannot be determined." % id)) 
 87              continue 
 88   
 89          # Store the position and element. 
 90          coord.append(pos) 
 91          element_list.append(element) 
 92   
 93      # Calculate the CoM. 
 94      com, mass = centre_of_mass(pos=coord, elements=element_list, verbosity=verbosity) 
 95   
 96      # Return the centre of mass. 
 97      if return_mass: 
 98          return com, mass 
 99      else: 
100          return com 
101