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

  1  # Details about the tests for AVACF. 
  2  #COULD NOT BE TESTED: 
  3  #       -projection vector -> bad implementation in nMOLDYN 2.2.5. So, always set to None 
  4  #       -differentiation -> bad implementation in nMOLDYN 2.2.5: always the default differentiation order that is considered i.e. 'fast'. So, always set to fast. 
  5  #       -massWeighting -> There is no mass weighting in version 2.2.5. So always set to False in 5.0.0. 
  6  #       -groups = [{'Protein.0 All': ['*']}] VS parameters['group'] = {0: [['Protein', '', ['all']]]}  
  7  #       -> different implementations in nMOLDYN 2.2.5 and 5.0.0. In 2.2.5, this option takes the whole protein as a single unit whereas in version 5.0.0, it  
  8  #       splits the protein into a set of residus. 
  9  #       -groups = [{'Protein.0 SideChain': ['*']}] VS parameters['group'] = {0: [['Protein', '', ['sidechains']]]}  
 10  #       -> different implementations in nMOLDYN 2.2.5 and 5.0.0. In 2.2.5, this option does not take only the residues sidechains but the whole residues whereas in  
 11  #       5.0.0 it actually takes only the sidechains. 
 12  #       -So, groups = [{'Protein.0 SideChain': ['*']}] can be compared with parameters['group'] = {0: [['Protein', '', ['all']]]} -> test 7. 
 13   
 14  from tempfile import mktemp 
 15  import os 
 16  from MMTK import Units 
 17   
 18  # TEMPLATES FOR REFERENCE AND NEW VERSIONS INPUT FILES. 
 19  template = {'REF' : {}, 'NEW' : {}} 
 20   
 21  template['REF']['title'] = 'Angular Velocity Autocorrelation Function' 
 22  template['REF']['trajectory'] = ['../TrajectoryTest1.nc'] 
 23  template['REF']['log_file'] = 'logfile.log' 
 24  template['REF']['output_files'] = {'avacf' : 'test.plot'} 
 25  template['REF']['projection_vector'] = None 
 26  template['REF']['differentiation'] = 'fast' 
 27  template['REF']['time_steps'] = None 
 28   
 29  template['NEW']['projection'] = None 
 30  template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc') 
 31  template['NEW']['avacf'] = mktemp(suffix = '_AVACF.nc', prefix = 'nMOLDYN_') 
 32  template['NEW']['differentiation'] = 1 
 33  template['NEW']['stepwiserbt'] = 'No' 
 34  template['NEW']['pyroserver'] = 'No' 
 35  template['NEW']['analysis'] = 'AngularVelocityAutoCorrelationFunction_serial(self.testParameters)' 
 36   
 37  test = [] 
 38   
 39  # Test1 
 40  test.append({'REF' : {}, 'NEW' : {}}) 
 41  # PARAMETERS FOR REFERENCE VERSION. 
 42  test[-1]['REF']['time_info'] = (0, 19, 1) 
 43  test[-1]['REF']['groups'] = [{'Protein.0 BackBone': ['*']}] 
 44  test[-1]['REF']['reference'] = [{'Protein.0 BackBone': {'*': None}}] 
 45   
 46   
 47  # PARAMETERS FOR NEW VERSION. 
 48  test[-1]['NEW']['timeinfo'] = '1:19:1' 
 49  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 misc backbone' 
 50  test[-1]['NEW']['referenceframe'] = 1 
 51   
 52   
 53  # Test2 
 54  test.append({'REF' : {}, 'NEW' : {}}) 
 55  # PARAMETERS FOR REFERENCE VERSION. 
 56  test[-1]['REF']['time_info'] = (0, 49, 4) 
 57  test[-1]['REF']['groups'] = [{'Protein.0 Methyl': ['*']}] 
 58  test[-1]['REF']['reference'] = [{'Protein.0 Methyl': {'*': None}}] 
 59   
 60  # PARAMETERS FOR NEW VERSION. 
 61  test[-1]['NEW']['timeinfo'] = '1:49:4' 
 62  test[-1]['NEW']['group'] = 'group1 groupinglevel methyl objectname P892 chemfragment methyl' 
 63  test[-1]['NEW']['referenceframe'] = 1 
 64   
 65   
 66  # Test3 
 67  test.append({'REF' : {}, 'NEW' : {}}) 
 68  # PARAMETERS FOR REFERENCE VERSION. 
 69  test[-1]['REF']['time_info'] = (8, 29, 2) 
 70  test[-1]['REF']['groups'] = [{'Protein.0 Methyl': ['*']}] 
 71  test[-1]['REF']['reference'] = [{'Protein.0 Methyl': {'*': None}}] 
 72   
 73  # PARAMETERS FOR NEW VERSION. 
 74  test[-1]['NEW']['timeinfo'] = '9:29:2' 
 75  test[-1]['NEW']['group'] = 'group1 groupinglevel methyl objectname P892 chemfragment methyl' 
 76  test[-1]['NEW']['referenceframe'] = 9 
 77   
 78   
 79  # Test4 
 80  test.append({'REF' : {}, 'NEW' : {}}) 
 81  # PARAMETERS FOR REFERENCE VERSION. 
 82  test[-1]['REF']['time_info'] = (16, 39, 4) 
 83  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['alanine',\ 
 84                                                        'glycine',\ 
 85                                                        'proline',\ 
 86                                                        'glutamine',\ 
 87                                                        'arginine',\ 
 88                                                        'glutamic_acid',\ 
 89                                                        'leucine',\ 
 90                                                        'serine',\ 
 91                                                        'valine',\ 
 92                                                        'methionine',\ 
 93                                                        'isoleucine',\ 
 94                                                        'asparagine',\ 
 95                                                        'phenylalanine',\ 
 96                                                        'threonine',\ 
 97                                                        'tyrosine']}] 
 98  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'alanine': None, 'glycine': None, 'proline': None, 'glutamine': None, 'arginine': None, 'glutamic_acid': None, 'leucine': None, 'serine': None, 'valine': None, 'methionine': None, 'isoleucine': None, 'asparagine': None, 'phenylalanine': None, 'threonine': None, 'tyrosine': None}}] 
 99   
100  # PARAMETERS FOR NEW VERSION. 
101  test[-1]['NEW']['timeinfo'] = '17:39:4' 
102  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Ala,Gly,Pro,Gln,Arg,Glu,Leu,Ser,Val,Met,Ile,Asn,Phe,Thr,Tyr' 
103  test[-1]['NEW']['referenceframe'] = 17 
104   
105  # Test5 
106  test.append({'REF' : {}, 'NEW' : {}}) 
107  # PARAMETERS FOR REFERENCE VERSION. 
108  test[-1]['REF']['time_info'] = (1, 20, 2) 
109  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['aspartic_acid']}] 
110  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'aspartic_acid': None}}] 
111   
112  # PARAMETERS FOR NEW VERSION. 
113  test[-1]['NEW']['timeinfo'] = '2:20:2' 
114  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Asp' 
115  test[-1]['NEW']['referenceframe'] = 2 
116   
117  # Test6 
118  test.append({'REF' : {}, 'NEW' : {}}) 
119  # PARAMETERS FOR REFERENCE VERSION. 
120  test[-1]['REF']['time_info'] = (1, 20, 2) 
121  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['aspartic_acid']}] 
122  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'aspartic_acid': None}}] 
123   
124  # PARAMETERS FOR NEW VERSION. 
125  test[-1]['NEW']['timeinfo'] = "2:20:2" 
126  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Asp' 
127  test[-1]['NEW']['referenceframe'] = 2 
128   
129  # Test7 
130  test.append({'REF' : {}, 'NEW' : {}}) 
131  # PARAMETERS FOR REFERENCE VERSION. 
132  test[-1]['REF']['time_info'] = (1, 20, 2) 
133  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['valine']}] 
134  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'valine': None}}] 
135   
136  # PARAMETERS FOR NEW VERSION. 
137  test[-1]['NEW']['timeinfo'] = "2:20:2" 
138  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Val' 
139  test[-1]['NEW']['referenceframe'] = 2 
140   
141   
142  # Test8 
143  test.append({'REF' : {}, 'NEW' : {}}) 
144  # PARAMETERS FOR REFERENCE VERSION. 
145  test[-1]['REF']['time_info'] = (1, 20, 2) 
146  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['valine']}] 
147  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'valine': None}}] 
148   
149  # PARAMETERS FOR NEW VERSION. 
150  test[-1]['NEW']['timeinfo'] = "2:20:2" 
151  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Val' 
152  test[-1]['NEW']['referenceframe'] = 2 
153   
154   
155  # Test9 
156  test.append({'REF' : {}, 'NEW' : {}}) 
157  # PARAMETERS FOR REFERENCE VERSION. 
158  test[-1]['REF']['time_info'] = (1, 28, 2) 
159  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['alanine']}] 
160  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'alanine': None}}] 
161   
162  # PARAMETERS FOR NEW VERSION. 
163  test[-1]['NEW']['timeinfo'] = "2:28:2" 
164  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Ala' 
165  test[-1]['NEW']['referenceframe'] = 2 
166   
167   
168  # Test10 
169  test.append({'REF' : {}, 'NEW' : {}}) 
170  # PARAMETERS FOR REFERENCE VERSION. 
171  test[-1]['REF']['time_info'] = (1, 33, 2) 
172  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['proline','glutamine','glutamic_acid']}] 
173  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'proline': None,'glutamine': None,'glutamic_acid': None}}] 
174   
175  # PARAMETERS FOR NEW VERSION. 
176  test[-1]['NEW']['timeinfo'] = "2:33:2" 
177  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Pro,Gln,Glu' 
178  test[-1]['NEW']['referenceframe'] = 2 
179   
180   
181  # Test11 
182  test.append({'REF' : {}, 'NEW' : {}}) 
183  # PARAMETERS FOR REFERENCE VERSION. 
184  test[-1]['REF']['time_info'] = (1, 20, 2) 
185  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['lysine','glycine','arginine']}] 
186  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'lysine': None,'glycine': None,'arginine': None}}] 
187   
188  # PARAMETERS FOR NEW VERSION. 
189  test[-1]['NEW']['timeinfo'] = "2:20:2" 
190  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Lys,Gly,Arg' 
191  test[-1]['NEW']['referenceframe'] = 2 
192   
193   
194  # Test12 
195  test.append({'REF' : {}, 'NEW' : {}}) 
196  # PARAMETERS FOR REFERENCE VERSION. 
197  test[-1]['REF']['time_info'] = (1, 40, 2) 
198  test[-1]['REF']['groups'] = [{'Protein.0 SideChain': ['leucine','methionine']}] 
199  test[-1]['REF']['reference'] = [{'Protein.0 SideChain': {'leucine': None,'methionine': None}}] 
200   
201  # PARAMETERS FOR NEW VERSION. 
202  test[-1]['NEW']['timeinfo'] = "2:40:2" 
203  test[-1]['NEW']['group'] = 'group1 groupinglevel residue objectname P892 restype Leu,Met' 
204  test[-1]['NEW']['referenceframe'] = 2 
205   
206   
207  # Test13 
208  test.append({'REF' : {}, 'NEW' : {}}) 
209  # PARAMETERS FOR REFERENCE VERSION. 
210  test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc'] 
211  test[-1]['REF']['time_info'] = (3, 20, 2) 
212  test[-1]['REF']['groups'] = [{'Water': ['*']}]  
213  test[-1]['REF']['reference'] = [{'Water': {'*': None}}] 
214   
215  # PARAMETERS FOR NEW VERSION. 
216  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest3.nc') 
217  test[-1]['NEW']['timeinfo'] = "4:20:2" 
218  test[-1]['NEW']['group'] = 'group1 groupinglevel cluster objectname AC3 atomelement *' 
219  test[-1]['NEW']['referenceframe'] = 4 
220   
221   
222  # Test14 
223  test.append({'REF' : {}, 'NEW' : {}}) 
224  # PARAMETERS FOR REFERENCE VERSION. 
225  test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc'] 
226  test[-1]['REF']['time_info'] = (1, 45, 3) 
227  test[-1]['REF']['groups'] = [{'Water': ['*']}]  
228  test[-1]['REF']['reference'] = [{'Water': {'*': None}}] 
229   
230  # PARAMETERS FOR NEW VERSION. 
231  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest3.nc') 
232  test[-1]['NEW']['timeinfo'] = "2:45:3" 
233  test[-1]['NEW']['group'] = 'group1 groupinglevel cluster objectname AC3 atomelement *' 
234  test[-1]['NEW']['referenceframe'] = 2 
235