Source Code for Module test_suite.unit_tests._lib._dispersion.test_it99

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2014 Edward d'Auvergne                                        # 
  4  # Copyright (C) 2014 Troels E. Linnet                                         # 
  5  #                                                                             # 
  6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 16  # GNU General Public License for more details.                                # 
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 19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Python module imports. 
 24  from numpy import array, float64, ones, pi, zeros 
 25  from unittest import TestCase 
 26   
 27  # relax module imports. 
 28  from lib.dispersion.it99 import r2eff_IT99 
 29   
 30   
 31 -class Test_it99(TestCase): 
 32      """Unit tests for the lib.dispersion.it99 relax module.""" 
 33   
 34 -    def setUp(self): 
 35          """Set up for all unit tests.""" 
 36   
 37          # Default parameter values. 
 38          self.r20 = 2.0 
 39          self.pA = 0.95 
 40          self.dw = 2.0 
 41          self.kex = 1000.0 
 42   
 43          # Required data structures. 
 44          self.num_points = 7 
 45          self.ncyc = array([2, 4, 8, 10, 20, 40, 500]) 
 46          relax_times = 0.04 
 47          self.cpmg_frqs = self.ncyc / relax_times 
 48          self.R2eff = zeros(self.num_points, float64) 
 49   
 50          # The spin Larmor frequencies. 
 51          self.sfrq = 200. * 1E6 
 52   
 53   
 54 -    def calc_r2eff(self): 
 55          """Calculate and check the R2eff values.""" 
 56   
 57          # Parameter conversions. 
 58          pB, dw_frq, tex = self.param_conversion(pA=self.pA, kex=self.kex, dw=self.dw, sfrq=self.sfrq) 
 59   
 60          a = ones([self.num_points]) 
 61   
 62          # Calculate the R2eff values. 
 63          r2eff_IT99(r20=self.r20*a, pA=self.pA, dw=dw_frq*a, dw_orig=dw_frq*a, tex=tex, cpmg_frqs=self.cpmg_frqs, back_calc=self.R2eff) 
 64   
 65          # Check all R2eff values. 
 66          if self.kex > 1.e5: 
 67              for i in range(self.num_points): 
 68                  self.assertAlmostEqual(self.R2eff[i], self.r20, 2) 
 69          else: 
 70              for i in range(self.num_points): 
 71                  self.assertAlmostEqual(self.R2eff[i], self.r20) 
 72   
 73   
 74 -    def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None): 
 75          """Convert the parameters. 
 76   
 77          @keyword pA:    The population of state A. 
 78          @type pA:       float 
 79          @keyword kex:   The rate of exchange. 
 80          @type kex:      float 
 81          @keyword dw:    The chemical exchange difference between states A and B in ppm. 
 82          @type dw:       float 
 83          @keyword sfrq:  The spin Larmor frequencies in Hz. 
 84          @type sfrq:     float 
 85          @return:        The parameters {pB, dw_frq, tex}. 
 86          @rtype:         tuple of float 
 87          """ 
 88   
 89          # Calculate pB. 
 90          pB = 1.0 - pA 
 91   
 92          # Calculate spin Larmor frequencies in 2pi. 
 93          frqs = sfrq * 2 * pi 
 94   
 95          # Convert dw from ppm to rad/s. 
 96          dw_frq = dw * frqs / 1.e6 
 97   
 98          # Time of exchange: 1/(2*kex) 
 99          if kex == 0.0: 
100              tex = 0.0 
101          else: 
102              tex = 1 / (2*kex) 
103   
104          # Return all values. 
105          return pB, dw_frq, tex 
106   
107   
108 -    def test_it99_no_rex1(self): 
109          """Test the r2eff_it99() function for no exchange when dw = 0.0.""" 
110   
111          # Parameter reset. 
112          self.dw = 0.0 
113   
114          # Calculate and check the R2eff values. 
115          self.calc_r2eff() 
116   
117   
118 -    def test_it99_no_rex2(self): 
119          """Test the r2eff_it99() function for no exchange when pA = 1.0.""" 
120   
121          # Parameter reset. 
122          self.pA = 1.0 
123   
124          # Calculate and check the R2eff values. 
125          self.calc_r2eff() 
126   
127   
128 -    def test_it99_no_rex3(self): 
129          """Test the r2eff_it99() function for no exchange when kex = 0.0.""" 
130   
131          # Parameter reset. 
132          self.kex = 0.0 
133   
134          # Calculate and check the R2eff values. 
135          self.calc_r2eff() 
136   
137   
138 -    def test_it99_no_rex4(self): 
139          """Test the r2eff_it99() function for no exchange when dw = 0.0 and pA = 1.0.""" 
140   
141          # Parameter reset. 
142          self.pA = 1.0 
143          self.dw = 0.0 
144   
145          # Calculate and check the R2eff values. 
146          self.calc_r2eff() 
147   
148   
149 -    def test_it99_no_rex5(self): 
150          """Test the r2eff_it99() function for no exchange when dw = 0.0 and kex = 0.0.""" 
151   
152          # Parameter reset. 
153          self.dw = 0.0 
154          self.kex = 0.0 
155   
156          # Calculate and check the R2eff values. 
157          self.calc_r2eff() 
158   
159   
160 -    def test_it99_no_rex6(self): 
161          """Test the r2eff_it99() function for no exchange when pA = 1.0 and kex = 0.0.""" 
162   
163          # Parameter reset. 
164          self.pA = 1.0 
165          self.kex = 0.0 
166   
167          # Calculate and check the R2eff values. 
168          self.calc_r2eff() 
169   
170   
171 -    def test_it99_no_rex7(self): 
172          """Test the r2eff_it99() function for no exchange when dw = 0.0, pA = 1.0, and kex = 0.0.""" 
173   
174          # Parameter reset. 
175          self.dw = 0.0 
176          self.kex = 0.0 
177   
178          # Calculate and check the R2eff values. 
179          self.calc_r2eff() 
180   
181   
182 -    def test_it99_no_rex8(self): 
183          """Test the r2eff_cr72() function for no exchange when kex = 1e19.""" 
184   
185          # Parameter reset. 
186          self.kex = 1e19 
187   
188          # Calculate and check the R2eff values. 
189          self.calc_r2eff() 
190