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

      1  #Details about the tests for DISFG.
      2
      3  #COULD NOT BE TESTED:
      4  #       -weights -> only 'equal' and 'coherent' available now in 5.0.0. Always set to 'coherent' in 2.2.5 because if set to 'none', 2.2.5 switch to 'coherent'.
      5  #       -units_q -> selectable via the GUI in 2.2.5 but does nothing actually. So, always set to '1/nm' in 5.0.0.
      6  #       -atoms_pdb = nMOLDYN/Tests/REFERENCES/ProteinBPTI1.pdb -> NMOLDYN 2.2.5 DOES NOT CONSIDER CA MARKED ATOMS IN A PDB FILE
      7  #       -atoms = {'Protein.0': ['Oxygen', 'SideChain', 'Nitrogen']} -> NMOLDYN 2.2.5 FINDS 46 ATOMS WHEREAS THE ACTUAL NUMBER IS 662
      8  #       -atoms = {'Protein.0': ['BackBone', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 58 ATOMS WHEREAS THE ACTUAL NUMBER IS 347
      9  #       -atoms = {'Protein.0': ['Methyl', 'SideChain', 'Carbon', 'C_alpha']} -> NMOLDYN 2.2.5 FINDS 286 WHEREAS THE ACTUAL NUMBER IS 661
     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'] = 'Incoherent Scattering Function (Gaussian approx.)'
     18  template['REF']['log_file'] = 'logfile.log'
     19  template['REF']['output_files'] = {'fft' : 'DISFG_Sqw_test.nc', 'isf' : 'DISFG_Fqt_test.nc'}
     20  template['REF']['units_frequency'] = 1/Units.ps
     21  template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
     22  template['REF']['weights'] = 'incoherent'
     23  template['REF']['units_q'] = 1/Units.nm
     24  template['REF']['frequency_points'] = 1000000
     25
     26
     27  template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
     28  template['NEW']['weights'] = 'incoherent'
     29  template['NEW']['disfg'] = mktemp(suffix = '_ISFG.nc', prefix = 'nMOLDYN_')
     30  template['NEW']['pyroserver'] = 'monoprocessor'
     31  template['NEW']['analysis'] = 'DynamicIncoherentStructureFactorGaussian_serial(self.testParameters)'
     32
     33  test = []
     34
     35  # Test1
     36  test.append({'REF' : {}, 'NEW' : {}})
     37  # PARAMETERS FOR REFERENCE VERSION.
     38  test[-1]['REF']['time_info'] = (0, 49, 1)
     39  test[-1]['REF']['atoms_pdb'] = '../TrajectoryTest1_1.pdb'
     40  test[-1]['REF']['deuter'] = None
     41  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0], 1.000000, 500, None)
     42  test[-1]['REF']['ft_window'] = 80.0
     43
     44  # PARAMETERS FOR NEW VERSION.
     45  test[-1]['NEW']['timeinfo'] = '1:49:1'
     46  test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_1.nms')
     47  test[-1]['NEW']['deuteration'] = None
     48  test[-1]['NEW']['qShellValues'] = "3.:10.:1."
     49  test[-1]['NEW']['fftWindow'] = 100./80.0
     50
     51
     52  # Test2
     53  test.append({'REF' : {}, 'NEW' : {}})
     54  # PARAMETERS FOR REFERENCE VERSION.
     55  test[-1]['REF']['time_info'] = (0, 19, 1)
     56  test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
     57  test[-1]['REF']['deuter'] = None
     58  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0], 0.800000, 500, None)
     59  test[-1]['REF']['ft_window'] = 10.0
     60
     61  # PARAMETERS FOR NEW VERSION.
     62  test[-1]['NEW']['timeinfo'] = '1:19:1'
     63  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
     64  test[-1]['NEW']['deuteration'] = None
     65  test[-1]['NEW']['qShellValues'] = "3.:10.:1.0"
     66  test[-1]['NEW']['fftWindow'] = 100./10.0
     67
     68
     69  # Test3
     70  test.append({'REF' : {}, 'NEW' : {}})
     71  # PARAMETERS FOR REFERENCE VERSION.
     72  test[-1]['REF']['time_info'] = (0, 19, 2)
     73  test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
     74  test[-1]['REF']['deuter'] = None
     75  test[-1]['REF']['q_vector_set'] = ([3.0, 5.0, 7.0, 9.0], 0.800000, 500, None)
     76  test[-1]['REF']['ft_window'] = 20.0
     77
     78  # PARAMETERS FOR NEW VERSION.
     79  test[-1]['NEW']['timeinfo'] = '1:19:2'
     80  test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
     81  test[-1]['NEW']['deuteration'] = None
     82  test[-1]['NEW']['qShellValues'] = "3.:9.:2.0"
     83  test[-1]['NEW']['fftWindow'] = 100./20.0
     84
     85
     86  # Test4
     87  test.append({'REF' : {}, 'NEW' : {}})
     88  # PARAMETERS FOR REFERENCE VERSION.
     89  test[-1]['REF']['time_info'] = (0, 9, 1)
     90  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
     91  test[-1]['REF']['deuter'] = None
     92  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 1.200000, 500, None)
     93  test[-1]['REF']['ft_window'] = 50.0
     94
     95  # PARAMETERS FOR NEW VERSION.
     96  test[-1]['NEW']['timeinfo'] = '1:9:1'
     97  test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen,oxygen'
     98  test[-1]['NEW']['deuteration'] = None
     99  test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
    100  test[-1]['NEW']['fftWindow'] = 100./50.0
    101
    102
    103  # Test5
    104  test.append({'REF' : {}, 'NEW' : {}})
    105  # PARAMETERS FOR REFERENCE VERSION.
    106  test[-1]['REF']['time_info'] = (5, 29, 3)
    107  test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
    108  test[-1]['REF']['deuter'] = None
    109  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0, 9.0], 0.900000, 500, None)
    110  test[-1]['REF']['ft_window'] = 10.0
    111
    112  # PARAMETERS FOR NEW VERSION.
    113  test[-1]['NEW']['timeinfo'] = '6:29:3'
    114  test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
    115  test[-1]['NEW']['deuteration'] = None
    116  test[-1]['NEW']['qShellValues'] = "4.:9.:1.0"
    117  test[-1]['NEW']['fftWindow'] = 100./10.0
    118
    119
    120  # Test6
    121  test.append({'REF' : {}, 'NEW' : {}})
    122  # PARAMETERS FOR REFERENCE VERSION.
    123  test[-1]['REF']['time_info'] = (4, 23, 2)
    124  test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
    125  test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
    126  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 6.0, 7.0, 9.0], 1.00000, 500, None)
    127  test[-1]['REF']['ft_window'] = 40.0
    128
    129  # PARAMETERS FOR NEW VERSION.
    130  test[-1]['NEW']['timeinfo'] = '5:23:2'
    131  test[-1]['NEW']['subset'] = None
    132  test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
    133  test[-1]['NEW']['qShellValues'] = [3.0, 4.0, 6.0, 7.0, 9.0]
    134  test[-1]['NEW']['fftWindow'] = 100./40.0
    135
    136
    137  # Test7
    138  test.append({'REF' : {}, 'NEW' : {}})
    139  # PARAMETERS FOR REFERENCE VERSION.
    140  test[-1]['REF']['time_info'] = (0, 19, 1)
    141  test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
    142  test[-1]['REF']['deuter'] = None
    143  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 0.500000, 500, None)
    144  test[-1]['REF']['ft_window'] = 80.0
    145
    146  # PARAMETERS FOR NEW VERSION.
    147  test[-1]['NEW']['timeinfo'] = '1:19:1'
    148  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
    149  test[-1]['NEW']['deuteration'] = None
    150  test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
    151  test[-1]['NEW']['fftWindow'] = 100./80.0
    152
    153
    154  # Test8
    155  test.append({'REF' : {}, 'NEW' : {}})
    156  # PARAMETERS FOR REFERENCE VERSION.
    157  test[-1]['REF']['time_info'] = (3, 39, 4)
    158  test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
    159  test[-1]['REF']['deuter'] = None
    160  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0], 1.800000, 500, None)
    161  test[-1]['REF']['ft_window'] = 10.0
    162
    163  # PARAMETERS FOR NEW VERSION.
    164  test[-1]['NEW']['timeinfo'] = '4:39:4'
    165  test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
    166  test[-1]['NEW']['deuteration'] = None
    167  test[-1]['NEW']['qShellValues'] = "3.:6.:1.0"
    168  test[-1]['NEW']['fftWindow'] = 100./10.0
    169
    170
    171  # Test9
    172  test.append({'REF' : {}, 'NEW' : {}})
    173  # PARAMETERS FOR REFERENCE VERSION.
    174  test[-1]['REF']['time_info'] = (0, 19, 1)
    175  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
    176  test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
    177  test[-1]['REF']['q_vector_set'] = ([7.5, 8.5, 9.5], 0.800000, 500, None)
    178  test[-1]['REF']['ft_window'] = 20.0
    179
    180  # PARAMETERS FOR NEW VERSION.
    181  test[-1]['NEW']['timeinfo'] = '1:19:1'
    182  test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
    183  test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
    184  test[-1]['NEW']['qShellValues'] = "7.5:9.5:1.0"
    185  test[-1]['NEW']['fftWindow'] = 100./20.0
    186
    187
    188  # Test10
    189  test.append({'REF' : {}, 'NEW' : {}})
    190  # PARAMETERS FOR REFERENCE VERSION.
    191  test[-1]['REF']['time_info'] = (3, 30, 3)
    192  test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
    193  test[-1]['REF']['deuter'] = None
    194  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0], 1.500000, 500, None)
    195  test[-1]['REF']['ft_window'] = 25.0
    196
    197  # PARAMETERS FOR NEW VERSION.
    198  test[-1]['NEW']['timeinfo'] = '4:30:3'
    199  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
    200  test[-1]['NEW']['deuteration'] = None
    201  test[-1]['NEW']['qShellValues'] = "3.:7.:1.0"
    202  test[-1]['NEW']['fftWindow'] = 100./25.0
    203
    204
    205  # Test11
    206  test.append({'REF' : {}, 'NEW' : {}})
    207  # PARAMETERS FOR REFERENCE VERSION.
    208  test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc']
    209  test[-1]['REF']['time_info'] = (5, 19, 2)
    210  test[-1]['REF']['atoms'] = {'Water': ['Hydrogen']}
    211  test[-1]['REF']['deuter'] = None
    212  test[-1]['REF']['q_vector_set'] = ([5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0], 1.000000, 500, None)
    213  test[-1]['REF']['ft_window'] = 10.0
    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'] = '6:19:2'
    218  test[-1]['NEW']['subset'] = 'objectname AC3 atomelement hydrogen'
    219  test[-1]['NEW']['deuteration'] = None
    220  test[-1]['NEW']['qShellValues'] = "5.:12.:1.0"
    221  test[-1]['NEW']['fftWindow'] = 100./10.0
    222
    223
    224  # Test12
    225  test.append({'REF' : {}, 'NEW' : {}})
    226  # PARAMETERS FOR REFERENCE VERSION.
    227  test[-1]['REF']['trajectory'] = ['../TrajectoryTest3.nc']
    228  test[-1]['REF']['time_info'] = (0, 19, 1)
    229  test[-1]['REF']['atoms'] = {'Water': ['Oxygen', 'Hydrogen']}
    230  test[-1]['REF']['deuter'] = {'Water': ['Hydrogen']}
    231  test[-1]['REF']['q_vector_set'] = ([5.6, 6.4, 7.3, 10.5, 20.4], 0.600000, 500, None)
    232  test[-1]['REF']['ft_window'] = 8.0
    233
    234  # PARAMETERS FOR NEW VERSION.
    235  test[-1]['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest3.nc')
    236  test[-1]['NEW']['timeinfo'] = '1:19:1'
    237  test[-1]['NEW']['subset'] = 'objectname AC3 atomelement hydrogen,oxygen'
    238  test[-1]['NEW']['deuteration'] = 'objectname AC3 atomelement hydrogen'
    239  test[-1]['NEW']['qShellValues'] = (5.6, 6.4, 7.3, 10.5, 20.4)
    240  test[-1]['NEW']['fftWindow'] = 100./8.0
    241