Source Code for Module test_suite.unit_tests._lib._dispersion.test_ns_cpmg_2site_3d

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  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from numpy import array, float64, int16, pi, zeros 
 24  from unittest import TestCase 
 25   
 26  # relax module imports. 
 27  from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D 
 28  from lib.dispersion.ns_matrices import r180x_3d 
 29   
 30   
 31 -class Test_ns_cpmg_2site_3d(TestCase): 
 32      """Unit tests for the lib.dispersion.ns_cpmg_2site_3D relax module.""" 
 33   
 34 -    def setUp(self): 
 35          """Set up for all unit tests.""" 
 36   
 37          # Default parameter values. 
 38          self.r20a = 2.0 
 39          self.r20b = 3.0 
 40          self.pA = 0.95 
 41          self.dw = 2.0 
 42          self.kex = 1000.0 
 43   
 44          # Required data structures. 
 45          # The 3D rotation matrix for an imperfect X-axis pi-pulse. 
 46          self.r180x = r180x_3d() 
 47   
 48          # This is a vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
 49          self.M0 = zeros(7, float64) 
 50          self.M0[0] = 0.5 
 51   
 52          self.num_points = 7 
 53          self.ncyc = array([2, 4, 8, 10, 20, 40, 500]) 
 54          relax_times = 0.04 
 55          cpmg_frqs = self.ncyc / relax_times 
 56          self.inv_relax_times = 1.0 / relax_times 
 57          self.tau_cpmg = 0.25 / cpmg_frqs 
 58          self.R2eff = zeros(self.num_points, float64) 
 59   
 60          # The spin Larmor frequencies. 
 61          self.sfrq = 200. * 1E6 
 62   
 63   
 64 -    def calc_r2eff(self): 
 65          """Calculate and check the R2eff values.""" 
 66   
 67          # Parameter conversions. 
 68          k_AB, k_BA, pB, dw_frq, M0 = self.param_conversion(pA=self.pA, kex=self.kex, dw=self.dw, sfrq=self.sfrq, M0=self.M0) 
 69   
 70          # Calculate the R2eff values. 
 71          r2eff_ns_cpmg_2site_3D(r180x=self.r180x, M0=M0, r20a=self.r20a, r20b=self.r20b, pA=self.pA, pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA, inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff, num_points=self.num_points, power=self.ncyc) 
 72   
 73          if self.kex >= 1.e5: 
 74              for i in range(self.num_points): 
 75                  self.assertAlmostEqual(self.R2eff[i], self.r20a, 5) 
 76          else: 
 77              for i in range(self.num_points): 
 78                  self.assertAlmostEqual(self.R2eff[i], self.r20a) 
 79   
 80   
 81 -    def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None, M0=None): 
 82          """Convert the parameters. 
 83   
 84          @keyword pA:    The population of state A. 
 85          @type pA:       float 
 86          @keyword kex:   The rate of exchange. 
 87          @type kex:      float 
 88          @keyword dw:    The chemical exchange difference between states A and B in ppm. 
 89          @type dw:       float 
 90          @keyword sfrq:  The spin Larmor frequencies in Hz. 
 91          @type sfrq:     float 
 92          @keyword M0:    Vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
 93          @type M0:       numpy float64, rank-1, 7D array 
 94          @return:        The parameters {k_AB, k_BA, pB, dw_frq, M0}. 
 95          @rtype:         tuple of float 
 96          """ 
 97   
 98          # Calculate pB. 
 99          pB = 1.0 - pA 
100   
101          # This is a vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. 
102          M0[1] = pA 
103          M0[4] = pB 
104   
105          # Exchange rates. 
106          k_BA = pA * kex 
107          k_AB = pB * kex 
108   
109          # Calculate spin Larmor frequencies in 2pi. 
110          frqs = sfrq * 2 * pi 
111   
112          # Convert dw from ppm to rad/s. 
113          dw_frq = dw * frqs / 1.e6 
114   
115          # Return all values. 
116          return k_AB, k_BA, pB, dw_frq, M0 
117   
118   
119 -    def test_ns_cpmg_2site_3D_no_rex1(self): 
120          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0.""" 
121   
122          # Parameter reset. 
123          self.dw = 0.0 
124   
125          # Calculate and check the R2eff values. 
126          self.calc_r2eff() 
127   
128   
129 -    def test_ns_cpmg_2site_3D_no_rex2(self): 
130          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0.""" 
131   
132          # Parameter reset. 
133          self.pA = 1.0 
134   
135          # Calculate and check the R2eff values. 
136          self.calc_r2eff() 
137   
138   
139 -    def test_ns_cpmg_2site_3D_no_rex3(self): 
140          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when kex = 0.0.""" 
141   
142          # Parameter reset. 
143          self.kex = 0.0 
144   
145          # Calculate and check the R2eff values. 
146          self.calc_r2eff() 
147   
148   
149 -    def test_ns_cpmg_2site_3D_no_rex4(self): 
150          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and pA = 1.0.""" 
151   
152          # Parameter reset. 
153          self.pA = 1.0 
154          self.dw = 0.0 
155   
156          # Calculate and check the R2eff values. 
157          self.calc_r2eff() 
158   
159   
160 -    def test_ns_cpmg_2site_3D_no_rex5(self): 
161          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0 and kex = 0.0.""" 
162   
163          # Parameter reset. 
164          self.dw = 0.0 
165          self.kex = 0.0 
166   
167          # Calculate and check the R2eff values. 
168          self.calc_r2eff() 
169   
170   
171 -    def test_ns_cpmg_2site_3D_no_rex6(self): 
172          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when pA = 1.0 and kex = 0.0.""" 
173   
174          # Parameter reset. 
175          self.pA = 1.0 
176          self.kex = 0.0 
177   
178          # Calculate and check the R2eff values. 
179          self.calc_r2eff() 
180   
181   
182 -    def test_ns_cpmg_2site_3D_no_rex7(self): 
183          """Test the r2eff_ns_cpmg_2site_3D() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
184   
185          # Parameter reset. 
186          self.dw = 0.0 
187          self.kex = 0.0 
188   
189          # Calculate and check the R2eff values. 
190          self.calc_r2eff() 
191