Python TrajectoryChanges Examples

Example #1

File: ut.py Project: AmelieChatelain/SIMPLEchangepoint

class TestTrajectoryChangesMethods(unittest.TestCase):
    def setUp(self):
        from analyze_changed_distances import TrajectoryChanges
        self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
        self.lam = 16

    def test_selection_pair(self):
        changes_AB = self.trj_changes.changes(
            self.lam,
            selection_pair=('chain A and resid 1 to 10',
                            'chain A and resid 11 to 20'))
        assertRawChangesDict(changes_AB)

    def test_atom_pairs(self):
        changes_specific_atoms = self.trj_changes.changes(
            self.lam,
            atom_pairs=[('(A)ASP-1:CA', '(A)SER-20:CA'),
                        ('(A)ALA-2:CA', '(A)PRO-19:CA')])
        assertRawChangesDict(changes_specific_atoms)

    def test_residue_pairs(self):
        changes_specific_residues = self.trj_changes.changes(
            self.lam,
            residue_pairs=[('(A)ASP-1', '(A)SER-20'),
                           ('(A)ALA-2', '(A)PRO-19')])
        assertRawChangesDict(changes_specific_residues)

Example #2

File: ut.py Project: DEShawResearch/SIMPLEchangepoint

class TestPlotting(unittest.TestCase):
    def setUp(self):
        from analyze_changed_distances import TrajectoryChanges
        self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
        self.lam = 16

    def test_plotDistance(self):
        self.trj_changes.plotDistance(('(A)ASP-1:CA', '(A)SER-20:CA'), lam=self.lam)

    def test_matrixPlotChange(self):
        changes = self.trj_changes.changes(self.lam)
        v = changes.values()[0]
        self.trj_changes.matrixPlotChange(v, lam=self.lam)

Example #3

File: ut.py Project: AmelieChatelain/SIMPLEchangepoint

class TestPlotting(unittest.TestCase):
    def setUp(self):
        from analyze_changed_distances import TrajectoryChanges
        self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
        self.lam = 16

    def test_plotDistance(self):
        self.trj_changes.plotDistance(('(A)ASP-1:CA', '(A)SER-20:CA'),
                                      lam=self.lam)

    def test_matrixPlotChange(self):
        changes = self.trj_changes.changes(self.lam)
        v = changes.values()[0]
        self.trj_changes.matrixPlotChange(v, lam=self.lam)

Example #4

File: ut.py Project: DEShawResearch/SIMPLEchangepoint

class TestTrajectoryChangesMethods(unittest.TestCase):
    def setUp(self):
        from analyze_changed_distances import TrajectoryChanges
        self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
        self.lam = 16

    def test_selection_pair(self):
        changes_AB = self.trj_changes.changes(self.lam, selection_pair=('chain A and resid 1 to 10',
                                                                        'chain A and resid 11 to 20'))
        assertRawChangesDict(changes_AB)

    def test_atom_pairs(self):
        changes_specific_atoms = self.trj_changes.changes(self.lam, atom_pairs=[('(A)ASP-1:CA', '(A)SER-20:CA'),
                                                                                ('(A)ALA-2:CA', '(A)PRO-19:CA')])
        assertRawChangesDict(changes_specific_atoms)

    def test_residue_pairs(self):
        changes_specific_residues = self.trj_changes.changes(self.lam, residue_pairs=[('(A)ASP-1', '(A)SER-20'),
                                                                                     ('(A)ALA-2', '(A)PRO-19')])
        assertRawChangesDict(changes_specific_residues)

Example #5

File: ut.py Project: DEShawResearch/SIMPLEchangepoint

 def setUp(self):
     from analyze_changed_distances import TrajectoryChanges
     self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
     self.lam = 16

Example #6

File: ut.py Project: DEShawResearch/SIMPLEchangepoint

 def test_changes(self):
     from analyze_changed_distances import TrajectoryChanges
     trj_changes = TrajectoryChanges('all_pairs', 'serial')
     changes_16 = trj_changes.changes(16)
     assertRawChangesDict(changes_16)

Example #7

File: ut.py Project: AmelieChatelain/SIMPLEchangepoint

 def setUp(self):
     from analyze_changed_distances import TrajectoryChanges
     self.trj_changes = TrajectoryChanges('all_pairs', 'serial')
     self.lam = 16

Example #8

File: ut.py Project: AmelieChatelain/SIMPLEchangepoint

 def test_changes(self):
     from analyze_changed_distances import TrajectoryChanges
     trj_changes = TrajectoryChanges('all_pairs', 'serial')
     changes_16 = trj_changes.changes(16)
     assertRawChangesDict(changes_16)

Example #9

File: ut.py Project: AmelieChatelain/SIMPLEchangepoint

 def test_constructor(self):
     from analyze_changed_distances import TrajectoryChanges
     trj_changes = TrajectoryChanges('all_pairs', 'serial')