def get_disk_norm(vaxis, haxis, offset=0.):
norm = as_unit(vaxis)
rot1 = make_rotation_matrix(norm, np.array([0., 0., 1.]))
haxis2 = np.dot(rot1, haxis.reshape(3, 1)).T
rot2 = make_rotation_matrix(haxis2, np.array([1., 0., 0.]))
inv_rot = np.dot(rot2, rot1).T
ref_norm = as_unit(np.array([np.cos(offset), np.sin(offset), 0.]))
disk_norm = np.dot(inv_rot, ref_norm.reshape(3, 1)).T
return disk_norm
def test_rot_matrix_vector_rotation_correct(self):
from e3fp.fingerprint.array_ops import make_rotation_matrix, \
as_unit
for i in range(2, 5):
u0 = as_unit(np.random.uniform(size=3))
u1 = as_unit(np.random.uniform(size=3))
rot = make_rotation_matrix(u0, u1)
np.testing.assert_array_almost_equal(u1, np.dot(rot, u0))
def test_rot_matrix_array_rotation_correct(self):
from e3fp.fingerprint.array_ops import make_rotation_matrix, \
as_unit
for i in range(1, 5):
u0 = as_unit(np.random.uniform(size=3))
arr = np.random.uniform(size=(i, 3))
v = arr[0, :]
rot = make_rotation_matrix(v, u0)
rot_arr = np.dot(rot, arr.T).T
u1 = as_unit(rot_arr[0, :])
np.testing.assert_array_almost_equal(u0.flatten(), u1.flatten())
def get_cgo_arc_obj(center,
norm,
start,
radians,
linespacing=0.,
color=[0., 0., 0.],
alpha=1.,
res=.5 * np.pi / 180):
"""Get CGO parameters to create arc in PyMOL"""
logging.debug(("Creating CGO arc with start {}, center {}, norm {}, "
"covering {} deg").format(start, center, norm,
radians * 180 / np.pi))
obj = []
obj = [COLOR] + color
start_ref = start - center
rad = np.linalg.norm(start_ref)
if rad < 1e-7:
return []
rot1 = make_rotation_matrix(norm, np.array([0., 0., 1.]))
start2 = np.dot(rot1, start_ref.reshape(3, 1)).T
rot2 = make_rotation_matrix(start2, np.array([1., 0., 0.]))
inv_rot = np.dot(rot2, rot1).T
angles = np.linspace(0., radians, float(radians) / res)
ref_xyz = np.empty((angles.shape[0], 3), dtype=np.double)
ref_xyz[:, 0] = rad * np.cos(angles)
ref_xyz[:, 1] = rad * np.sin(angles)
ref_xyz[:, 2] = 0
xyz = np.dot(inv_rot, ref_xyz.T).T + center
if linespacing > 0.:
i = 0
skip_num = max(1, int(linespacing / (rad * res)))
while i < (xyz.shape[0] - 1 - skip_num):
for j in range(skip_num):
obj.extend(get_cgo_segment_obj(xyz[i, :], xyz[i + 1, :]))
i += 1
i += skip_num
else:
for i in range(xyz.shape[0] - 1):
obj.extend(get_cgo_segment_obj(xyz[i, :], xyz[i + 1, :]))
return obj
