Source Code for Module generic_fns.angles

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2003-2005 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               # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation; either version 2 of the License, or           # 
 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              # 
 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 relax; if not, write to the Free Software                        # 
 19  # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA   # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  from math import acos, pi, sin 
 24  from Numeric import dot 
 25   
 26   
 27 -class Angles: 
 28 -    def __init__(self, relax): 
 29          """Class containing the functions relating to angles.""" 
 30   
 31          self.relax = relax 
 32   
 33   
 34 -    def angles(self, run): 
 35          """Function for calculating the angle defining the XH vector in the diffusion frame.""" 
 36   
 37          # Test if the run exists. 
 38          if not run in self.relax.data.run_names: 
 39              raise RelaxNoRunError, run 
 40   
 41          # Test if the PDB file has been loaded. 
 42          if not self.relax.data.pdb.has_key(run): 
 43              raise RelaxNoPdbError, run 
 44   
 45          # Test if sequence data is loaded. 
 46          if not self.relax.data.res.has_key(run): 
 47              raise RelaxNoSequenceError, run 
 48   
 49          # Test if the diffusion tensor data is loaded. 
 50          if not self.relax.data.diff.has_key(run): 
 51              raise RelaxNoTensorError, run 
 52   
 53          # Arguments. 
 54          self.run = run 
 55   
 56          # Sphere. 
 57          if self.relax.data.diff[self.run].type == 'sphere': 
 58              return 
 59   
 60          # Spheroid. 
 61          elif self.relax.data.diff[self.run].type == 'spheroid': 
 62              self.spheroid_frame() 
 63   
 64          # Ellipsoid. 
 65          elif self.relax.data.diff[self.run].type == 'ellipsoid': 
 66              raise RelaxError, "No coded yet." 
 67   
 68   
 69 -    def ellipsoid_frame(self, run=None): 
 70          """Function for calculating the spherical angles of the XH vector in the ellipsoid frame.""" 
 71   
 72          # Arguments. 
 73          self.run = run 
 74   
 75          # Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes. 
 76          Dx, Dy, Dz = self.relax.generic.diffusion_tensor.unit_axes() 
 77   
 78          # Loop over the sequence. 
 79          for i in xrange(len(self.relax.data.res[self.run])): 
 80              # Test if the vector exists. 
 81              if not hasattr(self.relax.data.res[self.run][i], 'xh_vect'): 
 82                  print "No angles could be calculated for residue '" + `self.relax.data.res[self.run][i].num` + " " + self.relax.data.res[self.run][i].name + "'." 
 83                  continue 
 84   
 85              # dz and dx direction cosines. 
 86              dz = dot(Dz, self.relax.data.res[self.run][i].xh_vect) 
 87              dx = dot(Dx, self.relax.data.res[self.run][i].xh_vect) 
 88   
 89              # Calculate the polar angle theta. 
 90              self.relax.data.res[self.run][i].theta = acos(dz) 
 91   
 92              # Calculate the azimuthal angle phi. 
 93              self.relax.data.res[self.run][i].phi = acos(dx / sin(self.relax.data.res[self.run][i].theta)) 
 94   
 95   
 96 -    def spheroid_frame(self, run=None): 
 97          """Function for calculating the angle alpha of the XH vector within the spheroid frame.""" 
 98   
 99          # Arguments. 
100          self.run = run 
101   
102          # Get the unit vector Dpar of the diffusion tensor axis. 
103          Dpar = self.relax.generic.diffusion_tensor.unit_axes() 
104   
105          # Loop over the sequence. 
106          for i in xrange(len(self.relax.data.res[self.run])): 
107              # Test if the vector exists. 
108              if not hasattr(self.relax.data.res[self.run][i], 'xh_vect'): 
109                  print "No angles could be calculated for residue '" + `self.relax.data.res[self.run][i].num` + " " + self.relax.data.res[self.run][i].name + "'." 
110                  continue 
111   
112              # Calculate alpha. 
113              self.relax.data.res[self.run][i].alpha = acos(dot(Dpar, self.relax.data.res[self.run][i].xh_vect)) 
114   
115   
116 -    def wrap_angles(self, angle, lower, upper): 
117          """Convert the given angle to be between the lower and upper values.""" 
118   
119          while 1: 
120              if angle > upper: 
121                  angle = angle - upper 
122              elif angle < lower: 
123                  angle = angle + upper 
124              else: 
125                  break 
126   
127          return angle 
128