def test_rot(self):
one = geometry.TRTMatrix()
mat = geometry.TRTMatrix()
for (theta, axis) in self.l:
mat.add_rotation(rotmat(theta, axis))
for (theta, axis) in reversed(self.l):
mat.add_rotation(rotmat(-theta, axis))
map(self.assertAlmostEqual,
itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*one.rotation_matrix.tolist()))
def test_transpose(self):
one = geometry.TRTMatrix()
mat = geometry.TRTMatrix()
for (theta, axis) in self.l:
mat.add_rotation(rotmat(theta, axis))
trmat = geometry.TRTMatrix().rotation_matrix
for i in range(3):
for j in range(3):
trmat[i, j] = mat.rotation_matrix[j, i]
mat.add_rotation(trmat)
map(self.assertAlmostEqual,
itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*one.rotation_matrix.tolist()))
def test_transform(self):
for (theta, axis) in self.l:
mat = geometry.TRTMatrix()
mat.add_rotation(rotmat(theta, axis))
vec = [0, 0, 0]
vec[axis] = randomcoord(1)[0]
map(self.assertAlmostEqual, mat.transform(0, 0, 0), (0, 0, 0))
map(self.assertAlmostEqual, mat.transform(*vec), vec)
def test_dotprod(self):
mat = geometry.TRTMatrix()
for (theta, axis) in self.l:
mat.add_rotation(rotmat(theta, axis))
for dummy in range(100):
v1 = randomcoord()
v2 = randomcoord()
self.assertAlmostEqual(dot(mat.transform(*v1), mat.transform(*v2)),
dot(v1, v2))
def test_linearity(self):
mat = geometry.TRTMatrix()
for (theta, axis) in self.l:
mat.add_rotation(rotmat(theta, axis))
scale = lambda vec, f: [x * f for x in vec]
for dummy in range(100):
vec = randomcoord()
for f in randomcoord(100):
map(self.assertAlmostEqual, mat.transform(*scale(vec, f)),
scale(mat.transform(*vec), f))
def to_trtmatrix(self):
""" Returns geometry.TRTMatrix containing the same transformation. """
res = geometry.TRTMatrix()
for i in range(3):
for j in range(3):
res.rotation_matrix[i, j] = self.U[j][i]
res.translation_vector[i] = self.Tr[i]
return res
def multifit(self):
dev_prv = numpy.inf
dev = 999999
mtxs_prv = [geometry.TRTMatrix() for i in self.tokens[0]]
while dev_prv - dev > .1:
dev_prv = dev
rmsds, mtxs = zip(*self.iter_once(mtxs=mtxs_prv))
dev = max([rmsd**2 * len(self.tokens) for rmsd in rmsds])
mtxs_prv = [i.combine(j) for i, j in zip(mtxs_prv, mtxs)]
#~ print "ITER %f" % (dev_prv - dev)
return zip(rmsds, mtxs_prv)
def test_trans(self):
mat1 = geometry.TRTMatrix()
mat2 = geometry.TRTMatrix()
mat = geometry.TRTMatrix()
for (theta, axis) in self.l:
mat.add_rotation(rotmat(theta, axis))
mat1.add_rotation(rotmat(theta, axis))
mat2.add_rotation(rotmat(theta, axis))
for dummy in range(100):
v1 = randomcoord()
v2 = mat.transform(*v1)
if random.choice([True, False]):
mat1.add_prerotational_translation(v1)
mat2.add_translation(v2)
else:
mat2.add_prerotational_translation(v1)
mat1.add_translation(v2)
for dummy in range(100):
vec = randomcoord()
map(self.assertAlmostEqual, mat1.transform(*vec),
mat2.transform(*vec))
def iter_once(self, mtxs=None):
if not mtxs:
mtxs = [geometry.TRTMatrix() for i in self.tokens[0]]
n = len(self.tokens[0])
av_stc = [
reduce(
operator.add,
[mtx.transform(vec=coords)
for coords, mtx in zip(vec, mtxs)]) / n for vec in self.tokens
]
ovfs = [Overfit() for i in self.tokens[0]]
for row, av_atm in zip(self.tokens, av_stc):
for atm, ovf, mtx in zip(row, ovfs, mtxs):
ovf.add_point(av_atm, mtx.transform(vec=atm))
return [ovf.overfit() for ovf in ovfs]
def assertIdent(self, motif, res, msg):
almost_equal = functools.partial(self.assertAlmostEqual, msg=msg)
rmsd, pair_al, mat = res
almost_equal(rmsd, 0, places=3)
one = geometry.TRTMatrix()
map(almost_equal, itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*one.rotation_matrix.tolist()))
map(almost_equal, mat.prerotational_translation_vector.tolist(),
one.prerotational_translation_vector.tolist())
map(almost_equal, mat.translation_vector.tolist(),
one.translation_vector.tolist())
self.assertListEqual(*map(list, zip(*list(pair_al))), msg=msg)
self.assertListEqual(list(motif),
list(zip(*list(pair_al))[0]),
msg=msg)
def test_identity(self):
for dummy in range(10):
point_list = [
self.points1[n]
for n in random.sample(range(100), random.randint(3, 50))
]
overfit_obj = overfit.Overfit()
overfit_obj.add(point_list, point_list)
rmsd, mat = overfit_obj.overfit()
self.assertAlmostEqual(rmsd, 0, places=3)
one = geometry.TRTMatrix()
map(self.assertAlmostEqual,
itertools.chain(*mat.rotation_matrix.tolist()),
itertools.chain(*one.rotation_matrix.tolist()))
map(self.assertAlmostEqual,
mat.prerotational_translation_vector.tolist(),
one.prerotational_translation_vector.tolist())
map(self.assertAlmostEqual, mat.translation_vector.tolist(),
one.translation_vector.tolist())
def test_basicops(self):
mat = geometry.TRTMatrix()
mat.add_translation(randomcoord())
mat.add_prerotational_translation(randomcoord())
mat.add_rotation(
rotmat(random.uniform(-math.pi, math.pi), random.choice(range(3))))
def test_init(self):
geometry.TRTMatrix()
