示例#1
0
 def get_mindist(self, **kwargs):
     from pele.angleaxis import MinPermDistAACluster
     from pele.angleaxis import TransformAngleAxisCluster, MeasureAngleAxisCluster
     transform = TransformAngleAxisCluster(self.aatopology)
     measure = MeasureAngleAxisCluster(self.aatopology, transform=transform,
                                       permlist=[])
     return MinPermDistAACluster(self.aasystem, measure=measure, transform=transform, 
                                 accuracy=0.1, **kwargs)
示例#2
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class TestAATransform(unittest.TestCase):
    def setUp(self):
        self.nrigid = 10
        self.topology = RBTopology()
        self.topology.add_sites([create_water() for _ in range(self.nrigid)])
        self.topology.finalize_setup()
        self.transform = TransformAngleAxisCluster(self.topology)
    
    def test_cpp_rotate(self):
        x0 = np.array([random_aa() for _ in range(2*self.nrigid)]).ravel()
        aa = random_aa()
        mx = aa2mx(aa)
        
        x0_rotated = x0.copy()
        self.transform.rotate(x0_rotated, mx)
        
        x0_rotated_python = x0.copy()
        self.transform._rotate_python(x0_rotated_python, mx)
        
        assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)
        
        mx_reverse = aa2mx(-aa)
        self.transform.rotate(x0_rotated, mx_reverse)
        assert_arrays_almost_equal(self, x0, x0_rotated)
示例#3
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class TestAATransform(unittest.TestCase):
    def setUp(self):
        self.nrigid = 10
        self.topology = RBTopology()
        self.topology.add_sites([create_water() for _ in range(self.nrigid)])
        self.topology.finalize_setup()
        self.transform = TransformAngleAxisCluster(self.topology)

    def test_cpp_rotate(self):
        x0 = np.array([random_aa() for _ in range(2 * self.nrigid)]).ravel()
        aa = random_aa()
        mx = aa2mx(aa)

        x0_rotated = x0.copy()
        self.transform.rotate(x0_rotated, mx)

        x0_rotated_python = x0.copy()
        self.transform._rotate_python(x0_rotated_python, mx)

        assert_arrays_almost_equal(self, x0_rotated, x0_rotated_python)

        mx_reverse = aa2mx(-aa)
        self.transform.rotate(x0_rotated, mx_reverse)
        assert_arrays_almost_equal(self, x0, x0_rotated)
示例#4
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 def setUp(self):
     self.nrigid = 10
     self.topology = RBTopology()
     self.topology.add_sites([create_water() for _ in range(self.nrigid)])
     self.topology.finalize_setup()
     self.transform = TransformAngleAxisCluster(self.topology)
示例#5
0
 def setUp(self):
     self.nrigid = 10
     self.topology = RBTopology()
     self.topology.add_sites([create_water() for _ in range(self.nrigid)])
     self.topology.finalize_setup()
     self.transform = TransformAngleAxisCluster(self.topology)