Package nMOLDYN :: Package Tests :: Package DOS :: Module TestsContents
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Source Code for Module nMOLDYN.Tests.DOS.TestsContents

  1  # Details about the tests for DOS. 
  2  # COULD NOT BE TESTED: 
  3  #       -projection vector -> bad implementation in nMOLDYN 2.2.5 
  4  #       -units_length -> bug in nMOLDYN 2.2.5: No length unit conversion on the DOS. So, always set to nm 
  5  #       -units_length always set to Units.nm because this is the only length unit available in new version  
  6  #       -units_frequency always set to Units.THz because this is the only frequency unit available in new version  
  7  #       -atoms_pdb = nMOLDYN/Tests/REFERENCES/ProteinBPTI1.pdb -> NMOLDYN 2.2.5 DOES NOT CONSIDER CA MARKED ATOMS IN A PDB FILE 
  8  #       -atoms = {'Protein.0': ['Oxygen', 'SideChain', 'Nitrogen']} -> NMOLDYN 2.2.5 FINDS 46 ATOMS WHEREAS THE ACTUAL NUMBER IS 662 
  9  #       -atoms = {'Protein.0': ['BackBone', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 58 ATOMS WHEREAS THE ACTUAL NUMBER IS 347 
 10  #       -atoms = {'Protein.0': ['Methyl', 'SideChain', 'Carbon', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 286 WHEREAS THE ACTUAL NUMBER IS 661 
 11  #       -weights: when some deuteration is done the mass weighting scheme of nMOLDYN2.2.5 do not take into account the mass of the deuterium. 
 12  from tempfile import mktemp 
 13  import os 
 14  from MMTK import Units 
 15   
 16  # TEMPLATES FOR REFERENCE AND NEW VERSIONS INPUT FILES. 
 17  template = {'REF' : {}, 'NEW' : {}} 
 18   
 19  template['REF']['title'] = 'Density Of States' 
 20  template['REF']['log_file'] = 'logfile.log' 
 21  template['REF']['output_files'] = {'dos': 'test.plot'} 
 22  template['REF']['projection_vector'] = None 
 23  template['REF']['units_length'] = Units.nm 
 24  template['REF']['units_frequency'] = 1/Units.ps 
 25  template['REF']['frequency_points'] = 1000000 
 26   
 27  template['NEW']['pyroserver'] = 'NO' 
 28  template['NEW']['projection'] = None 
 29  template['NEW']['dos'] = mktemp(suffix = '_DOS.nc', prefix = 'nMOLDYN_') 
 30  template['NEW']['analysis'] = 'CartesianDensityOfStates_serial(self.testParameters)' 
 31   
 32  test = [] 
 33   
 34  # Test1 
 35  test.append({'REF' : {}, 'NEW' : {}}) 
 36  # PARAMETERS FOR REFERENCE VERSION. 
 37  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
 38  test[-1]['REF']['time_info'] = (0, 49, 1) 
 39  test[-1]['REF']['weights'] = "mass" 
 40  test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_2.pdb' 
 41  test[-1]['REF']['deuter'] = None 
 42  test[-1]['REF']['ft_window'] = 20.0 
 43   
 44  # PARAMETERS FOR NEW VERSION. 
 45  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
 46  test[-1]['NEW']['timeinfo'] = '1:49:1' 
 47  test[-1]['NEW']['weights'] = 'mass' 
 48  test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1_2.nms') 
 49  test[-1]['NEW']['deuteration'] = None 
 50  test[-1]['NEW']['differentiation'] = 0 
 51  test[-1]['NEW']['fftwindow'] = 100./20.0 
 52   
 53   
 54  # Test2 
 55  test.append({'REF' : {}, 'NEW' : {}}) 
 56  # PARAMETERS FOR REFERENCE VERSION. 
 57  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
 58  test[-1]['REF']['time_info'] = (0, 49, 4) 
 59  test[-1]['REF']['weights'] = "none" 
 60  test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]} 
 61  test[-1]['REF']['deuter'] = None 
 62  test[-1]['REF']['ft_window'] = 10.0 
 63   
 64  # PARAMETERS FOR NEW VERSION. 
 65  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
 66  test[-1]['NEW']['timeinfo'] = '1:49:4' 
 67  test[-1]['NEW']['weights'] = 'equal' 
 68  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone' 
 69  test[-1]['NEW']['deuteration'] = None 
 70  test[-1]['NEW']['differentiation'] = 0 
 71  test[-1]['NEW']['fftwindow'] = 100./10.0 
 72   
 73   
 74  # Test3 
 75  test.append({'REF' : {}, 'NEW' : {}}) 
 76  # PARAMETERS FOR REFERENCE VERSION. 
 77  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
 78  test[-1]['REF']['time_info'] = (8, 29, 2) 
 79  test[-1]['REF']['weights'] = 'none'  
 80  test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']} 
 81  test[-1]['REF']['deuter'] = None 
 82  test[-1]['REF']['ft_window'] = 5.0 
 83   
 84  # PARAMETERS FOR NEW VERSION. 
 85  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
 86  test[-1]['NEW']['timeinfo'] = '9:29:2' 
 87  test[-1]['NEW']['weights'] = 'equal' 
 88  test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl' 
 89  test[-1]['NEW']['deuteration'] = None 
 90  test[-1]['NEW']['differentiation'] = 0 
 91  test[-1]['NEW']['fftwindow'] = 100./5.0 
 92   
 93   
 94  # Test4 
 95  test.append({'REF' : {}, 'NEW' : {}}) 
 96  # PARAMETERS FOR REFERENCE VERSION. 
 97  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
 98  test[-1]['REF']['time_info'] = (16, 39, 4) 
 99  test[-1]['REF']['weights'] = 'none'  
100  test[-1]['REF']['atoms'] = {'Protein.0': ['*']} 
101  test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']} 
102  test[-1]['REF']['ft_window'] = 20.0 
103   
104  # PARAMETERS FOR NEW VERSION. 
105  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
106  test[-1]['NEW']['timeinfo'] = '17:39:4' 
107  test[-1]['NEW']['weights'] = 'equal' 
108  test[-1]['NEW']['subset'] = 'objectname P892 chainname *' 
109  test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl' 
110  test[-1]['NEW']['differentiation'] = 0 
111  test[-1]['NEW']['fftwindow'] = 100./20.0 
112   
113   
114  # Test5 
115  test.append({'REF' : {}, 'NEW' : {}}) 
116  # PARAMETERS FOR REFERENCE VERSION. 
117  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
118  test[-1]['REF']['time_info'] = (1, 20, 2) 
119  test[-1]['REF']['weights'] = 'none'  
120  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']} 
121  test[-1]['REF']['deuter'] = None 
122  test[-1]['REF']['ft_window'] = 4.0 
123   
124  # PARAMETERS FOR NEW VERSION. 
125  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
126  test[-1]['NEW']['timeinfo'] = '2:20:2' 
127  test[-1]['NEW']['weights'] = 'equal' 
128  test[-1]['NEW']['subset'] = 'objectname P892 atomelement oxygen,nitrogen' 
129  test[-1]['NEW']['deuteration'] = None 
130  test[-1]['NEW']['differentiation'] = 0 
131  test[-1]['NEW']['fftwindow'] = 100./4.0 
132   
133   
134  # Test6 
135  test.append({'REF' : {}, 'NEW' : {}}) 
136  # PARAMETERS FOR REFERENCE VERSION. 
137  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
138  test[-1]['REF']['time_info'] = (1, 20, 2) 
139  test[-1]['REF']['weights'] = 'mass'  
140  test[-1]['REF']['atoms'] = {'Protein.0': ['Nitrogen']} 
141  test[-1]['REF']['deuter'] = None 
142  test[-1]['REF']['ft_window'] = 40.0 
143   
144  # PARAMETERS FOR NEW VERSION. 
145  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
146  test[-1]['NEW']['timeinfo'] = "2:20:2" 
147  test[-1]['NEW']['weights'] = 'mass' 
148  test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen' 
149  test[-1]['NEW']['deuteration'] = None 
150  test[-1]['NEW']['differentiation'] = 0 
151  test[-1]['NEW']['fftwindow'] = 100./40.0 
152   
153   
154  # Test7 
155  test.append({'REF' : {}, 'NEW' : {}}) 
156  # PARAMETERS FOR REFERENCE VERSION. 
157  test[-1]['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
158  test[-1]['REF']['time_info'] = (1, 20, 2) 
159  test[-1]['REF']['weights'] = 'none'  
160  test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']} 
161  test[-1]['REF']['deuter'] = None 
162  test[-1]['REF']['ft_window'] = 20.0 
163   
164  # PARAMETERS FOR NEW VERSION. 
165  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
166  test[-1]['NEW']['timeinfo'] = "2:20:2" 
167  test[-1]['NEW']['weights'] = 'equal' 
168  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon' 
169  test[-1]['NEW']['deuteration'] = None 
170  test[-1]['NEW']['differentiation'] = 0 
171  test[-1]['NEW']['fftwindow'] = 100./20.0 
172   
173   
174  # Test8 
175  test.append({'REF' : {}, 'NEW' : {}}) 
176  # PARAMETERS FOR REFERENCE VERSION. 
177  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
178  test[-1]['REF']['time_info'] = (1, 20, 2) 
179  test[-1]['REF']['weights'] = 'mass'  
180  test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest2_1.pdb' 
181  test[-1]['REF']['deuter'] = None 
182  test[-1]['REF']['ft_window'] = 80.0 
183   
184  # PARAMETERS FOR NEW VERSION. 
185  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
186  test[-1]['NEW']['timeinfo'] = "2:20:2" 
187  test[-1]['NEW']['weights'] = 'mass' 
188  test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest2_1.nms') 
189  test[-1]['NEW']['deuteration'] = None 
190  test[-1]['NEW']['differentiation'] = 1 
191  test[-1]['NEW']['fftwindow'] = 100./80.0 
192   
193   
194  # Test9 
195  test.append({'REF' : {}, 'NEW' : {}}) 
196  # PARAMETERS FOR REFERENCE VERSION. 
197  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
198  test[-1]['REF']['time_info'] = (1, 20, 1) 
199  test[-1]['REF']['weights'] = 'none'  
200  test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']} 
201  test[-1]['REF']['deuter'] = None 
202  test[-1]['REF']['ft_window'] = 4.0 
203   
204  # PARAMETERS FOR NEW VERSION. 
205  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
206  test[-1]['NEW']['timeinfo'] = "2:20:1" 
207  test[-1]['NEW']['weights'] = 'equal' 
208  test[-1]['NEW']['subset'] = 'objectname P1960 atomelement hydrogen' 
209  test[-1]['NEW']['deuteration'] = None 
210  test[-1]['NEW']['differentiation'] = 1 
211  test[-1]['NEW']['fftwindow'] = 100./4.0 
212   
213   
214  # Test10 
215  test.append({'REF' : {}, 'NEW' : {}}) 
216  # PARAMETERS FOR REFERENCE VERSION. 
217  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
218  test[-1]['REF']['time_info'] = (1, 20, 2) 
219  test[-1]['REF']['weights'] = 'none'  
220  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']} 
221  test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']} 
222  test[-1]['REF']['ft_window'] = 20.0 
223   
224  # PARAMETERS FOR NEW VERSION. 
225  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
226  test[-1]['NEW']['timeinfo'] = "2:20:2" 
227  test[-1]['NEW']['weights'] = 'equal' 
228  test[-1]['NEW']['subset'] = 'objectname P1960 misc sidechains' 
229  test[-1]['NEW']['deuteration'] = 'objectname P1960 atomelement hydrogen' 
230  test[-1]['NEW']['differentiation'] = 1 
231  test[-1]['NEW']['fftwindow'] = 100./20.0 
232   
233   
234  # Test11 
235  test.append({'REF' : {}, 'NEW' : {}}) 
236  # PARAMETERS FOR REFERENCE VERSION. 
237  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
238  test[-1]['REF']['time_info'] = (1, 20, 2) 
239  test[-1]['REF']['weights'] = 'none'  
240  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']} 
241  test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']} 
242  test[-1]['REF']['ft_window'] = 10.0 
243   
244  # PARAMETERS FOR NEW VERSION. 
245  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
246  test[-1]['NEW']['timeinfo'] = "2:20:2" 
247  test[-1]['NEW']['weights'] = 'equal' 
248  test[-1]['NEW']['subset'] = 'objectname P1960 misc sidechains' 
249  test[-1]['NEW']['deuteration'] = 'objectname P1960 misc sidechains' 
250  test[-1]['NEW']['differentiation'] = 1 
251  test[-1]['NEW']['fftwindow'] = 100./10.0 
252   
253   
254  # Test12 
255  test.append({'REF' : {}, 'NEW' : {}}) 
256  # PARAMETERS FOR REFERENCE VERSION. 
257  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
258  test[-1]['REF']['time_info'] = (1, 20, 2) 
259  test[-1]['REF']['weights'] = 'none'  
260  test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']} 
261  test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']} 
262  test[-1]['REF']['ft_window'] = 20.0 
263   
264  # PARAMETERS FOR NEW VERSION. 
265  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
266  test[-1]['NEW']['timeinfo'] = "2:20:2" 
267  test[-1]['NEW']['weights'] = 'equal' 
268  test[-1]['NEW']['subset'] = 'objectname P1960 misc backbone,sidechains' 
269  test[-1]['NEW']['deuteration'] = 'objectname P1960 misc sidechains' 
270  test[-1]['NEW']['differentiation'] = 1 
271  test[-1]['NEW']['fftwindow'] = 100./20.0 
272   
273   
274  # Test13 
275  test.append({'REF' : {}, 'NEW' : {}}) 
276  # PARAMETERS FOR REFERENCE VERSION. 
277  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
278  test[-1]['REF']['time_info'] = (1, 20, 2) 
279  test[-1]['REF']['weights'] = 'none'  
280  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Hydrogen']} 
281  test[-1]['REF']['deuter'] = {'Protein.0': ['BackBone']} 
282  test[-1]['REF']['ft_window'] = 20.0 
283   
284  # PARAMETERS FOR NEW VERSION. 
285  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
286  test[-1]['NEW']['timeinfo'] = "2:20:2" 
287  test[-1]['NEW']['weights'] = 'equal' 
288  test[-1]['NEW']['subset'] = 'objectname P1960 atomelement carbon,nitrogen,oxygen,hydrogen' 
289  test[-1]['NEW']['deuteration'] = 'objectname P1960 misc backbone' 
290  test[-1]['NEW']['differentiation'] = 1 
291  test[-1]['NEW']['fftwindow'] = 100./20.0 
292   
293   
294  # Test14 
295  test.append({'REF' : {}, 'NEW' : {}}) 
296  # PARAMETERS FOR REFERENCE VERSION. 
297  test[-1]['REF']['trajectory'] = ['../TrajectoryTest2.nc'] 
298  test[-1]['REF']['time_info'] = (1, 40, 2) 
299  test[-1]['REF']['weights'] = 'none'  
300  test[-1]['REF']['atoms'] = {'Protein.0': ['C_alpha']} 
301  test[-1]['REF']['deuter'] = None 
302  test[-1]['REF']['ft_window'] = 12.0 
303   
304  # PARAMETERS FOR NEW VERSION. 
305  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest2.nc') 
306  test[-1]['NEW']['timeinfo'] = "2:40:2" 
307  test[-1]['NEW']['weights'] = 'equal' 
308  test[-1]['NEW']['subset'] = 'objectname P1960 chemfragment c_alphas' 
309  test[-1]['NEW']['deuteration'] = None 
310  test[-1]['NEW']['differentiation'] = 1 
311  test[-1]['NEW']['fftwindow'] = 100./12.0 
312