def test_init_projection(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/2X1F.pdb')
proj = fpp.Projection2D(cg, [1., 1., 1.])
self.assertTrue(
ftuv.is_almost_colinear(proj.proj_direction, np.array([1., 1.,
1.])),
msg=
"The projection direction was not stored correctly. Should be coliniar"
" with {}, got {}".format(np.array([1., 1., 1.]),
proj.proj_direction))
def test_create_orthonormal_basis(self):
#Note: If the input vectors are not orthogonal, the result are 3 vectors that might not form a basis.
basis1 = ftuv.create_orthonormal_basis(np.array([0.0, 0.0, 2.0]))
self.assertTrue(
ftuv.is_almost_colinear(basis1[0], np.array([0., 0., 2.])))
basis2 = ftuv.create_orthonormal_basis(np.array([0.0, 0.0, 2.0]),
np.array([0.0, 3.6, 0.]))
self.assertTrue(
ftuv.is_almost_colinear(basis2[0], np.array([0., 0., 2.])))
self.assertTrue(
ftuv.is_almost_colinear(basis2[1], np.array([0., 3.6, 0])))
basis3 = ftuv.create_orthonormal_basis(np.array([0.0, 0.0, 2.0]),
np.array([0.0, 3.6, 0.]),
np.array([1., 0, 0]))
self.assertTrue(
ftuv.is_almost_colinear(basis3[0], np.array([0., 0., 2.])))
self.assertTrue(
ftuv.is_almost_colinear(basis3[1], np.array([0., 3.6, 0])))
self.assertTrue(
ftuv.is_almost_colinear(basis3[2], np.array([1., 0, 0])))
for basis in [basis1, basis2, basis3]:
self.assertAlmostEqual(np.dot(basis[0], basis[1]), 0)
self.assertAlmostEqual(np.dot(basis[0], basis[2]), 0)
self.assertAlmostEqual(np.dot(basis[2], basis[1]), 0)
for b in basis:
self.assertAlmostEqual(ftuv.magnitude(b), 1)
def test_create_orthonormal_basis(self):
#Note: If the input vectors are not orthogonal, the result are 3 vectors that might not form a basis.
basis1=ftuv.create_orthonormal_basis(np.array([0.0,0.0,2.0]))
self.assertTrue( ftuv.is_almost_colinear(basis1[0], np.array([0.,0.,2.])) )
basis2=ftuv.create_orthonormal_basis(np.array([0.0,0.0,2.0]), np.array([0.0, 3.6, 0.]))
self.assertTrue( ftuv.is_almost_colinear(basis2[0], np.array([0.,0.,2.])) )
self.assertTrue( ftuv.is_almost_colinear(basis2[1], np.array([0.,3.6,0])) )
basis3=ftuv.create_orthonormal_basis(np.array([0.0,0.0,2.0]), np.array([0.0, 3.6, 0.]), np.array([1,0,0]))
self.assertTrue( ftuv.is_almost_colinear(basis3[0], np.array([0.,0.,2.])) )
self.assertTrue( ftuv.is_almost_colinear(basis3[1], np.array([0.,3.6,0])) )
self.assertTrue( ftuv.is_almost_colinear(basis3[2], np.array([1.,0,0])) )
for basis in [basis1, basis2, basis3]:
self.assertAlmostEqual(np.dot(basis[0],basis[1]),0)
self.assertAlmostEqual(np.dot(basis[0],basis[2]),0)
self.assertAlmostEqual(np.dot(basis[2],basis[1]),0)
for b in basis:
self.assertAlmostEqual(ftuv.magnitude(b),1)
def test_get_alignment_matrix(self):
vec1 = np.array([0.5, 0.7, 0.9])
vec2 = np.array([0.345, 3.4347, 0.55])
rotMat = ftuv.get_alignment_matrix(vec1, vec2)
self.assertTrue(ftuv.is_almost_colinear(vec2, np.dot(vec1, rotMat)))
self.assertTrue(ftuv.is_almost_colinear(np.dot(rotMat, vec2), vec1))
def test_is_almost_colinear(self):
self.assertTrue(
ftuv.is_almost_colinear(np.array([0, 0, 0]), np.array([0., 0.,
0.])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([0, 0, 2]), np.array([0., 0.,
3.])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([3, 6, 7]),
np.array([9., 18., 21.])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([3, 6, 0]),
np.array([9., 18., 0.])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([3, 0, 8]),
np.array([9., 0., 24.])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([0, 0, 0]), np.array([0, 20, 0])))
self.assertTrue(
ftuv.is_almost_colinear(np.array([0.0004, 0, 0]),
np.array([0., 0., 0.])))
self.assertFalse(
ftuv.is_almost_colinear(np.array([0, 0, 3]), np.array([2., 0, 0])))
self.assertFalse(
ftuv.is_almost_colinear(np.array([1, 2, 3]),
np.array([2., 4., -6.])))
self.assertFalse(
ftuv.is_almost_colinear(np.array([1, 2, 3]), np.array([3., 4.,
6.])))
self.assertFalse(
ftuv.is_almost_colinear(np.array([1, 2, 3]), np.array([2., 5.,
6.])))
def test_get_alignment_matrix(self):
vec1=np.array([0.5,0.7,0.9])
vec2=np.array([0.345,3.4347,0.55])
rotMat=ftuv.get_alignment_matrix(vec1,vec2)
self.assertTrue( ftuv.is_almost_colinear(vec2, np.dot(vec1, rotMat)) )
self.assertTrue( ftuv.is_almost_colinear(np.dot(rotMat, vec2), vec1) )
def test_is_almost_colinear(self):
self.assertTrue(ftuv.is_almost_colinear(np.array([0,0,0]),np.array([0.,0.,0.])))
self.assertTrue(ftuv.is_almost_colinear(np.array([0,0,2]),np.array([0.,0.,3.])))
self.assertTrue(ftuv.is_almost_colinear(np.array([3,6,7]),np.array([9.,18.,21.])))
self.assertTrue(ftuv.is_almost_colinear(np.array([3,6,0]),np.array([9.,18.,0.])))
self.assertTrue(ftuv.is_almost_colinear(np.array([3,0,8]),np.array([9.,0.,24.])))
self.assertTrue(ftuv.is_almost_colinear(np.array([0,0,0]),np.array([0,20,0])))
self.assertTrue(ftuv.is_almost_colinear(np.array([0.0004,0,0]),np.array([0.,0.,0.])))
self.assertFalse(ftuv.is_almost_colinear(np.array([0,0,3]),np.array([2.,0,0])))
self.assertFalse(ftuv.is_almost_colinear(np.array([1,2,3]),np.array([2.,4.,-6.])))
self.assertFalse(ftuv.is_almost_colinear(np.array([1,2,3]),np.array([3.,4.,6.])))
self.assertFalse(ftuv.is_almost_colinear(np.array([1,2,3]),np.array([2.,5.,6.])))