Source Code for Module pipe_control.angles

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2005,2007-2008,2010,2012 Edward d'Auvergne               # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  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.                                         # 
 11  #                                                                             # 
 12  # This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Module docstring. 
 23  """Module for the manipulation of angular information.""" 
 24   
 25  # Python module imports. 
 26  from math import acos, sin 
 27  from numpy import dot 
 28  from warnings import warn 
 29   
 30  # relax module imports. 
 31  from lib.errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError, RelaxNoTensorError 
 32  from lib.warnings import RelaxWarning 
 33  from pipe_control.interatomic import interatomic_loop 
 34  from pipe_control.mol_res_spin import exists_mol_res_spin_data, generate_spin_id, spin_loop 
 35  from pipe_control.pipes import check_pipe 
 36   
 37   
 38 -def angle_diff_frame(): 
 39      """Function for calculating the angle defining the XH vector in the diffusion frame.""" 
 40   
 41      # Test if the current data pipe exists. 
 42      check_pipe() 
 43   
 44      # Test if the PDB file has been loaded. 
 45      if not hasattr(cdp, 'structure'): 
 46          raise RelaxNoPdbError 
 47   
 48      # Test if sequence data is loaded. 
 49      if not exists_mol_res_spin_data(): 
 50          raise RelaxNoSequenceError 
 51   
 52      # Test if the diffusion tensor data is loaded. 
 53      if not hasattr(cdp, 'diff_tensor'): 
 54          raise RelaxNoTensorError('diffusion') 
 55   
 56      # Sphere. 
 57      if cdp.diff_tensor.type == 'sphere': 
 58          return 
 59   
 60      # Spheroid. 
 61      elif cdp.diff_tensor.type == 'spheroid': 
 62          spheroid_frame() 
 63   
 64      # Ellipsoid. 
 65      elif cdp.diff_tensor.type == 'ellipsoid': 
 66          raise RelaxError("No coded yet.") 
 67   
 68   
 69 -def ellipsoid_frame(): 
 70      """Calculate the spherical angles of the bond vector in the ellipsoid frame.""" 
 71   
 72      # Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes. 
 73      Dx, Dy, Dz = diffusion_tensor.unit_axes() 
 74   
 75      # Spin loop. 
 76      for spin, mol_name, res_num, res_name in spin_loop(full_info=True): 
 77          # Test if the vector exists. 
 78          if not hasattr(spin, 'xh_vect'): 
 79              # Get the spin id string. 
 80              spin_id = generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin.num, spin_name=spin.name) 
 81   
 82              # Throw a warning. 
 83              warn(RelaxWarning("No angles could be calculated for the spin " + repr(spin_id) + ".")) 
 84   
 85              # Skip the spin. 
 86              continue 
 87   
 88          # dz and dx direction cosines. 
 89          dz = dot(Dz, spin.xh_vect) 
 90          dx = dot(Dx, spin.xh_vect) 
 91   
 92          # Calculate the polar angle theta. 
 93          spin.theta = acos(dz) 
 94   
 95          # Calculate the azimuthal angle phi. 
 96          spin.phi = acos(dx / sin(spin.theta)) 
 97   
 98   
 99 -def spheroid_frame(): 
100      """Function for calculating the angle alpha of the XH vector within the spheroid frame.""" 
101   
102      # Loop over the interatomic info. 
103      for interatom in interatomic_loop(): 
104          # Test if the vector exists. 
105          if not hasattr(interatom, 'vector'): 
106              # Throw a warning. 
107              warn(RelaxWarning("No angles could be calculated for the spin pair '%s' and '%s'." % (interatom.spin_id1, interatom.spin_id2))) 
108   
109              # Skip the container. 
110              continue 
111   
112          # Calculate alpha. 
113          interatom.alpha = acos(dot(cdp.diff_tensor.Dpar_unit, interatom.vector)) 
114