Package nMOLDYN :: Package Tests :: Package MSD :: Module TestsContents |
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# Source Code for Module nMOLDYN.Tests.MSD.TestsContents

      1  # Details about the tests for MSD.
      2  # COULD NOT BE TESTED:
      3  #       -projection vector -> bad implementation in nMOLDYN 2.2.5
      4  #       -units_length always set to Units.nm because this is the only length unit available in new version
      5  #       -atoms_pdb = nMOLDYN/Tests/REFERENCES/ProteinBPTI1.pdb -> NMOLDYN 2.2.5 DOES NOT CONSIDER CA MARKED ATOMS IN A PDB FILE
      6  #       -atoms = {'Protein.0': ['Oxygen', 'SideChain', 'Nitrogen']} -> NMOLDYN 2.2.5 FINDS 46 ATOMS WHEREAS THE ACTUAL NUMBER IS 662
      7  #       -atoms = {'Protein.0': ['BackBone', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 58 ATOMS WHEREAS THE ACTUAL NUMBER IS 347
      8  #       -atoms = {'Protein.0': ['Methyl', 'SideChain', 'Carbon', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 286 WHEREAS THE ACTUAL NUMBER IS 661
      9  #       -weights: when some deuteration is done the mass weighting scheme of nMOLDYN2.2.5 do not take into account the mass of the deuterium.
     10  from tempfile import mktemp
     11  import os
     12  from MMTK import Units
     13
     14  # TEMPLATES FOR REFERENCE AND NEW VERSIONS INPUT FILES.
     15  template = {'REF' : {}, 'NEW' : {}}
     16
     17  template['REF']['title'] = 'Mean-Square Displacement'
     18  template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
     19  template['REF']['log_file'] = 'logfile.log'
     20  template['REF']['output_files'] = {'msd': 'test.plot'}
     21  template['REF']['projection_vector'] = None
     22  template['REF']['units_length'] = Units.nm
     23
     24  template['NEW']['pyroserver'] = 'monoprocessor'
     25  template['NEW']['projection'] = None
     26  template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
     27  template['NEW']['msd'] = mktemp(suffix = '_MSD.nc', prefix = 'nMOLDYN_')
     28  template['NEW']['analysis'] = 'MeanSquareDisplacement_serial(self.testParameters)'
     29
     30  test = []
     31
     32  # Test1
     33  test.append({'REF' : {}, 'NEW' : {}})
     34
     35  # PARAMETERS FOR REFERENCE VERSION.
     36  test[-1]['REF']['time_info'] = (0, 49, 1)
     37  test[-1]['REF']['weights'] = "mass"
     38  test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_1.pdb'
     39  test[-1]['REF']['deuter'] = None
     40
     41  # PARAMETERS FOR NEW VERSION.
     42  test[-1]['NEW']['timeinfo'] = '1:49:1'
     43  test[-1]['NEW']['weights'] = 'mass'
     44  test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_1.nms')
     45  test[-1]['NEW']['deuteration'] = None
     46
     47
     48  # Test2
     49  test.append({'REF' : {}, 'NEW' : {}})
     50
     51  # PARAMETERS FOR REFERENCE VERSION.
     52  test[-1]['REF']['time_info'] = (0, 49, 4)
     53  test[-1]['REF']['weights'] = "none"
     54  test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
     55  test[-1]['REF']['deuter'] = None
     56
     57  # PARAMETERS FOR NEW VERSION.
     58  test[-1]['NEW']['timeinfo'] = '1:49:4'
     59  test[-1]['NEW']['weights'] = 'equal'
     60  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
     61  test[-1]['NEW']['deuteration'] = None
     62
     63
     64  # Test3
     65  test.append({'REF' : {}, 'NEW' : {}})
     66
     67  # PARAMETERS FOR REFERENCE VERSION.
     68  test[-1]['REF']['time_info'] = (8, 29, 2)
     69  test[-1]['REF']['weights'] = 'none'
     70  test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
     71  test[-1]['REF']['deuter'] = None
     72
     73  # PARAMETERS FOR NEW VERSION.
     74  test[-1]['NEW']['timeinfo'] = '9:29:2'
     75  test[-1]['NEW']['weights'] = 'equal'
     76  test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
     77  test[-1]['NEW']['deuteration'] = None
     78
     79
     80  # Test4
     81  test.append({'REF' : {}, 'NEW' : {}})
     82
     83  # PARAMETERS FOR REFERENCE VERSION.
     84  test[-1]['REF']['time_info'] = (16, 39, 4)
     85  test[-1]['REF']['weights'] = 'none'
     86  test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
     87  test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
     88
     89  # PARAMETERS FOR NEW VERSION.
     90  test[-1]['NEW']['timeinfo'] = '17:39:4'
     91  test[-1]['NEW']['weights'] = 'equal'
     92  test[-1]['NEW']['subset'] = 'objectname P892 chainname *'
     93  test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
     94
     95
     96  # Test5
     97  test.append({'REF' : {}, 'NEW' : {}})
     98
     99  # PARAMETERS FOR REFERENCE VERSION.
    100  test[-1]['REF']['time_info'] = (1, 20, 2)
    101  test[-1]['REF']['weights'] = 'none'
    102  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
    103  test[-1]['REF']['deuter'] = None
    104
    105  # PARAMETERS FOR NEW VERSION.
    106  test[-1]['NEW']['timeinfo'] = '2:20:2'
    107  test[-1]['NEW']['weights'] = 'equal'
    108  test[-1]['NEW']['subset'] = 'objectname P892 atomelement oxygen,nitrogen'
    109  test[-1]['NEW']['deuteration'] = None
    110
    111
    112  # Test6
    113  test.append({'REF' : {}, 'NEW' : {}})
    114  # PARAMETERS FOR REFERENCE VERSION.
    115  test[-1]['REF']['time_info'] = (1, 20, 2)
    116  test[-1]['REF']['weights'] = 'mass'
    117  test[-1]['REF']['atoms'] = {'Protein.0': ['Nitrogen']}
    118  test[-1]['REF']['deuter'] = None
    119
    120  # PARAMETERS FOR NEW VERSION.
    121  test[-1]['NEW']['timeinfo'] = "2:20:2"
    122  test[-1]['NEW']['weights'] = 'mass'
    123  test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen'
    124  test[-1]['NEW']['deuteration'] = None
    125
    126
    127  # Test7
    128  test.append({'REF' : {}, 'NEW' : {}})
    129  # PARAMETERS FOR REFERENCE VERSION.
    130  test[-1]['REF']['time_info'] = (1, 20, 2)
    131  test[-1]['REF']['weights'] = 'none'
    132  test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
    133  test[-1]['REF']['deuter'] = None
    134
    135  # PARAMETERS FOR NEW VERSION.
    136  test[-1]['NEW']['timeinfo'] = "2:20:2"
    137  test[-1]['NEW']['weights'] = 'equal'
    138  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
    139  test[-1]['NEW']['deuteration'] = None
    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']['weights'] = 'mass'
    147  test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
    148  test[-1]['REF']['deuter'] = None
    149
    150  # PARAMETERS FOR NEW VERSION.
    151  test[-1]['NEW']['timeinfo'] = "2:20:2"
    152  test[-1]['NEW']['weights'] = 'mass'
    153  test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
    154  test[-1]['NEW']['deuteration'] = None
    155
    156
    157  # Test9
    158  test.append({'REF' : {}, 'NEW' : {}})
    159  # PARAMETERS FOR REFERENCE VERSION.
    160  test[-1]['REF']['time_info'] = (1, 20, 2)
    161  test[-1]['REF']['weights'] = 'none'
    162  test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
    163  test[-1]['REF']['deuter'] = None
    164
    165  # PARAMETERS FOR NEW VERSION.
    166  test[-1]['NEW']['timeinfo'] = "2:20:2"
    167  test[-1]['NEW']['weights'] = 'equal'
    168  test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
    169  test[-1]['NEW']['deuteration'] = None
    170
    171
    172  # Test10
    173  test.append({'REF' : {}, 'NEW' : {}})
    174  # PARAMETERS FOR REFERENCE VERSION.
    175  test[-1]['REF']['time_info'] = (1, 20, 2)
    176  test[-1]['REF']['weights'] = 'incoherent'
    177  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
    178  test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
    179
    180  # PARAMETERS FOR NEW VERSION.
    181  test[-1]['NEW']['timeinfo'] = "2:20:2"
    182  test[-1]['NEW']['weights'] = 'incoherent'
    183  test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
    184  test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
    185
    186
    187  # Test11
    188  test.append({'REF' : {}, 'NEW' : {}})
    189  # PARAMETERS FOR REFERENCE VERSION.
    190  test[-1]['REF']['time_info'] = (1, 20, 2)
    191  test[-1]['REF']['weights'] = 'none'
    192  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
    193  test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
    194
    195  # PARAMETERS FOR NEW VERSION.
    196  test[-1]['NEW']['timeinfo'] = "2:20:2"
    197  test[-1]['NEW']['weights'] = 'equal'
    198  test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
    199  test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
    200
    201
    202  # Test12
    203  test.append({'REF' : {}, 'NEW' : {}})
    204  # PARAMETERS FOR REFERENCE VERSION.
    205  test[-1]['REF']['time_info'] = (1, 20, 2)
    206  test[-1]['REF']['weights'] = 'none'
    207  test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
    208  test[-1]['REF']['deuter'] = {'Protein.0': ['SideChain']}
    209
    210  # PARAMETERS FOR NEW VERSION.
    211  test[-1]['NEW']['timeinfo'] = "2:20:2"
    212  test[-1]['NEW']['weights'] = 'equal'
    213  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
    214  test[-1]['NEW']['deuteration'] = 'objectname P892 misc sidechains'
    215
    216
    217  # Test13
    218  test.append({'REF' : {}, 'NEW' : {}})
    219  # PARAMETERS FOR REFERENCE VERSION.
    220  test[-1]['REF']['time_info'] = (1, 20, 2)
    221  test[-1]['REF']['weights'] = 'incoherent'
    222  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Sulfur', 'Hydrogen']}
    223  test[-1]['REF']['deuter'] = {'Protein.0': ['BackBone']}
    224
    225  # PARAMETERS FOR NEW VERSION.
    226  test[-1]['NEW']['timeinfo'] = "2:20:2"
    227  test[-1]['NEW']['weights'] = 'incoherent'
    228  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon,nitrogen,oxygen,sulfur,hydrogen'
    229  test[-1]['NEW']['deuteration'] = 'objectname P892 misc backbone'
    230
    231
    232  # Test14
    233  test.append({'REF' : {}, 'NEW' : {}})
    234  # PARAMETERS FOR REFERENCE VERSION.
    235  test[-1]['REF']['time_info'] = (1, 40, 2)
    236  test[-1]['REF']['weights'] = 'none'
    237  test[-1]['REF']['atoms'] = {'Protein.0': ['C_alpha']}
    238  test[-1]['REF']['deuter'] = None
    239
    240  # PARAMETERS FOR NEW VERSION.
    241  test[-1]['NEW']['timeinfo'] = "2:40:2"
    242  test[-1]['NEW']['weights'] = 'equal'
    243  test[-1]['NEW']['subset'] = 'objectname P892 chemfragment c_alphas'
    244  test[-1]['NEW']['deuteration'] = None
    245