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

      1  #Details about the tests for EISF.
      2
      3  #COULD NOT BE TESTED:
      4  #       -units_q -> selectable via the GUI in 2.2.5 but does nothing actually. So, always set to '1/nm' in 5.0.0.
      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  from tempfile import mktemp
     10  import os
     11  from MMTK import Units
     12
     13  # TEMPLATES FOR REFERENCE AND NEW VERSIONS INPUT FILES.
     14  template = {'REF' : {}, 'NEW' : {}}
     15
     16  template['REF']['title'] = 'Elastic Incoherent Scattering Function'
     17  template['REF']['log_file'] = 'logfile.log'
     18  template['REF']['output_files'] = {'eisf' : 'test.plot'}
     19  template['REF']['trajectory'] = ['../TrajectoryTest1.nc']
     20  template['REF']['weights'] = 'incoherent'
     21  template['REF']['units_q'] = 1/Units.nm
     22
     23
     24  template['NEW']['trajectory'] = os.path.join(nmoldyn_package_path, 'Tests', 'TrajectoryTest1.nc')
     25  template['NEW']['weights'] = 'incoherent'
     26  template['NEW']['eisf'] = mktemp(suffix = '_EISF.nc', prefix = 'nMOLDYN_')
     27  template['NEW']['qVectorsGenerator'] = "3d isotropic"
     28  template['NEW']['qVectorsDirection'] = None
     29  template['NEW']['qVectorsPerShell'] = 500
     30  template['NEW']['pyroserver'] = 'monoprocessor'
     31  template['NEW']['analysis'] = 'ElasticIncoherentStructureFactor_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
     43  # PARAMETERS FOR NEW VERSION.
     44  test[-1]['NEW']['timeinfo'] = '1:49:1'
     45  test[-1]['NEW']['subset'] = 'filename %s' % os.path.join(nmoldyn_package_path,"Tests",'TrajectoryTest1_1.nms')
     46  test[-1]['NEW']['deuteration'] = None
     47  test[-1]['NEW']['qShellValues'] = "3.:10.:1."
     48  test[-1]['NEW']['qShellWidth'] = 1.0
     49
     50
     51  # Test2
     52  test.append({'REF' : {}, 'NEW' : {}})
     53  # PARAMETERS FOR REFERENCE VERSION.
     54  test[-1]['REF']['time_info'] = (0, 19, 1)
     55  test[-1]['REF']['atoms'] = {'Protein.0': ["BackBone"]}
     56  test[-1]['REF']['deuter'] = None
     57  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)
     58
     59  # PARAMETERS FOR NEW VERSION.
     60  test[-1]['NEW']['timeinfo'] = '1:19:1'
     61  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone'
     62  test[-1]['NEW']['deuteration'] = None
     63  test[-1]['NEW']['qShellValues'] = "3.:10.:1.0"
     64  test[-1]['NEW']['qShellWidth'] = 0.8
     65
     66
     67  # Test3
     68  test.append({'REF' : {}, 'NEW' : {}})
     69  # PARAMETERS FOR REFERENCE VERSION.
     70  test[-1]['REF']['time_info'] = (0, 19, 2)
     71  test[-1]['REF']['atoms'] = {'Protein.0': ['Methyl']}
     72  test[-1]['REF']['deuter'] = None
     73  test[-1]['REF']['q_vector_set'] = ([3.0, 5.0, 7.0, 9.0], 0.800000, 500, None)
     74
     75  # PARAMETERS FOR NEW VERSION.
     76  test[-1]['NEW']['timeinfo'] = '1:19:2'
     77  test[-1]['NEW']['subset'] = 'objectname P892 chemfragment methyl'
     78  test[-1]['NEW']['deuteration'] = None
     79  test[-1]['NEW']['qShellValues'] = "3.:9.:2.0"
     80  test[-1]['NEW']['qShellWidth'] = 0.8
     81
     82
     83  # Test4
     84  test.append({'REF' : {}, 'NEW' : {}})
     85  # PARAMETERS FOR REFERENCE VERSION.
     86  test[-1]['REF']['time_info'] = (0, 9, 1)
     87  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen','Nitrogen']}
     88  test[-1]['REF']['deuter'] = None
     89  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 1.200000, 500, None)
     90
     91  # PARAMETERS FOR NEW VERSION.
     92  test[-1]['NEW']['timeinfo'] = '1:9:1'
     93  test[-1]['NEW']['subset'] = 'objectname P892 atomelement nitrogen,oxygen'
     94  test[-1]['NEW']['deuteration'] = None
     95  test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
     96  test[-1]['NEW']['qShellWidth'] = 1.2
     97
     98
     99  # Test5
    100  test.append({'REF' : {}, 'NEW' : {}})
    101  # PARAMETERS FOR REFERENCE VERSION.
    102  test[-1]['REF']['time_info'] = (5, 29, 3)
    103  test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
    104  test[-1]['REF']['deuter'] = None
    105  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0, 9.0], 0.900000, 500, None)
    106
    107  # PARAMETERS FOR NEW VERSION.
    108  test[-1]['NEW']['timeinfo'] = '6:29:3'
    109  test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
    110  test[-1]['NEW']['deuteration'] = None
    111  test[-1]['NEW']['qShellValues'] = "4.:9.:1.0"
    112  test[-1]['NEW']['qShellWidth'] = 0.9
    113
    114
    115  # Test6
    116  test.append({'REF' : {}, 'NEW' : {}})
    117  # PARAMETERS FOR REFERENCE VERSION.
    118  test[-1]['REF']['time_info'] = (4, 23, 2)
    119  test[-1]['REF']['atoms'] = {'Protein.0': ['*']}
    120  test[-1]['REF']['deuter'] = {'Protein.0': ['Methyl']}
    121  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 6.0, 7.0, 9.0], 1.00000, 500, None)
    122
    123  # PARAMETERS FOR NEW VERSION.
    124  test[-1]['NEW']['timeinfo'] = '5:23:2'
    125  test[-1]['NEW']['subset'] = None
    126  test[-1]['NEW']['deuteration'] = 'objectname P892 chemfragment methyl'
    127  test[-1]['NEW']['qShellValues'] = [3.0, 4.0, 6.0, 7.0, 9.0]
    128  test[-1]['NEW']['qShellWidth'] = 1.0
    129
    130
    131  # Test7
    132  test.append({'REF' : {}, 'NEW' : {}})
    133  # PARAMETERS FOR REFERENCE VERSION.
    134  test[-1]['REF']['time_info'] = (0, 19, 1)
    135  test[-1]['REF']['atoms'] = {'Protein.0': ['Carbon']}
    136  test[-1]['REF']['deuter'] = None
    137  test[-1]['REF']['q_vector_set'] = ([4.0, 5.0, 6.0, 7.0, 8.0], 0.500000, 500, None)
    138
    139  # PARAMETERS FOR NEW VERSION.
    140  test[-1]['NEW']['timeinfo'] = '1:19:1'
    141  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon'
    142  test[-1]['NEW']['deuteration'] = None
    143  test[-1]['NEW']['qShellValues'] = "4.:8.:1.0"
    144  test[-1]['NEW']['qShellWidth'] = 0.5
    145
    146
    147  # Test8
    148  test.append({'REF' : {}, 'NEW' : {}})
    149  # PARAMETERS FOR REFERENCE VERSION.
    150  test[-1]['REF']['time_info'] = (3, 39, 4)
    151  test[-1]['REF']['atoms'] = {'Protein.0': ['Sulfur']}
    152  test[-1]['REF']['deuter'] = None
    153  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0], 1.800000, 500, None)
    154
    155  # PARAMETERS FOR NEW VERSION.
    156  test[-1]['NEW']['timeinfo'] = '4:39:4'
    157  test[-1]['NEW']['subset'] = 'objectname P892 atomelement sulfur'
    158  test[-1]['NEW']['deuteration'] = None
    159  test[-1]['NEW']['qShellValues'] = "3.:6.:1.0"
    160  test[-1]['NEW']['qShellWidth'] = 1.8
    161
    162
    163  # Test9
    164  test.append({'REF' : {}, 'NEW' : {}})
    165  # PARAMETERS FOR REFERENCE VERSION.
    166  test[-1]['REF']['time_info'] = (0, 19, 1)
    167  test[-1]['REF']['atoms'] = {'Protein.0': ['SideChain']}
    168  test[-1]['REF']['deuter'] = {'Protein.0': ['Hydrogen']}
    169  test[-1]['REF']['q_vector_set'] = ([7.5, 8.5, 9.5], 0.800000, 500, None)
    170
    171  # PARAMETERS FOR NEW VERSION.
    172  test[-1]['NEW']['timeinfo'] = '1:19:1'
    173  test[-1]['NEW']['subset'] = 'objectname P892 misc sidechains'
    174  test[-1]['NEW']['deuteration'] = 'objectname P892 atomelement hydrogen'
    175  test[-1]['NEW']['qShellValues'] = "7.5:9.5:1.0"
    176  test[-1]['NEW']['qShellWidth'] = 0.8
    177
    178
    179  # Test10
    180  test.append({'REF' : {}, 'NEW' : {}})
    181  # PARAMETERS FOR REFERENCE VERSION.
    182  test[-1]['REF']['time_info'] = (3, 30, 3)
    183  test[-1]['REF']['atoms'] = {'Protein.0': ['BackBone','SideChain']}
    184  test[-1]['REF']['deuter'] = None
    185  test[-1]['REF']['q_vector_set'] = ([3.0, 4.0, 5.0, 6.0, 7.0], 1.500000, 500, None)
    186
    187  # PARAMETERS FOR NEW VERSION.
    188  test[-1]['NEW']['timeinfo'] = '4:30:3'
    189  test[-1]['NEW']['subset'] = 'objectname P892 misc backbone,sidechains'
    190  test[-1]['NEW']['deuteration'] = None
    191  test[-1]['NEW']['qShellValues'] = "3.:7.:1.0"
    192  test[-1]['NEW']['qShellWidth'] = 1.5
    193
    194
    195  # Test11
    196  test.append({'REF' : {}, 'NEW' : {}})
    197  # PARAMETERS FOR REFERENCE VERSION.
    198  test[-1]['REF']['time_info'] = (5, 19, 2)
    199  test[-1]['REF']['atoms'] = {'Protein.0': ['Hydrogen']}
    200  test[-1]['REF']['deuter'] = None
    201  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)
    202
    203  # PARAMETERS FOR NEW VERSION.
    204  test[-1]['NEW']['timeinfo'] = '6:19:2'
    205  test[-1]['NEW']['subset'] = 'objectname P892 atomelement hydrogen'
    206  test[-1]['NEW']['deuteration'] = None
    207  test[-1]['NEW']['qShellValues'] = "3.:10.:1.0"
    208  test[-1]['NEW']['qShellWidth'] = 1.0
    209
    210
    211  # Test12
    212  test.append({'REF' : {}, 'NEW' : {}})
    213  # PARAMETERS FOR REFERENCE VERSION.
    214  test[-1]['REF']['time_info'] = (0, 19, 1)
    215  test[-1]['REF']['atoms'] = {'Protein.0': ['Oxygen', 'Nitrogen', 'Carbon', 'Sulfur', 'Hydrogen']}
    216  test[-1]['REF']['deuter'] = None
    217  test[-1]['REF']['q_vector_set'] = ([3.2, 4.2, 5.6, 6.4, 7.3], 0.600000, 500, None)
    218
    219  # PARAMETERS FOR NEW VERSION.
    220  test[-1]['NEW']['timeinfo'] = '1:19:1'
    221  test[-1]['NEW']['subset'] = 'objectname P892 atomelement carbon,hydrogen,nitrogen,oxygen,sulfur'
    222  test[-1]['NEW']['deuteration'] = None
    223  test[-1]['NEW']['qShellValues'] = (3.2, 4.2, 5.6, 6.4, 7.3)
    224  test[-1]['NEW']['qShellWidth'] = 0.6
    225