def compute_matrix(self):
""" Compute rotation matrix to align Z axis to this vector. """
if abs(self.vector[0]) < 0.00001 and abs(self.vector[1]) < 0.00001:
rot = math.radians(0.00)
tilt = math.radians(0.00)
else:
rot = math.atan2(self.vector[1], self.vector[0])
tilt = math.acos(self.vector[2])
psi = 0
self.matrix = euler_matrix(-rot, -tilt, -psi)
def matrixFromGeometry(shifts, angles):
""" Create the transformation matrix from a given
2D shifts in X and Y...and the 3 euler angles.
"""
inverseTransform = True
radAngles = -np.deg2rad(angles)
M = transformations.euler_matrix(radAngles[0], radAngles[1], radAngles[2],
'szyz')
if inverseTransform:
M[:3, 3] = -shifts[:3]
M = np.linalg.inv(M)
else:
M[:3, 3] = shifts[:3]
return M
def testTransformTranslation(self):
aSHSource = AtomicStructHandler(self.PDBFileName)
structure = aSHSource.getStructure()
structure_copy = deepcopy(aSHSource.getStructure())
shift = [100., 50., 25.]
# rotation_matrix = euler_matrix(deg2rad(45.), 0., 0., 'szyz')
rotation_matrix = euler_matrix(0., 0., 0., 'szyz')
translation = translation_matrix(shift)
M = concatenate_matrices(rotation_matrix, translation)
aSHSource.transform(M)
for atom1, atom2 in zip(structure.get_atoms(),
structure_copy.get_atoms()):
coord1 = atom1.get_coord()
coord2 = [sum(x) for x in zip(atom2.get_coord(), shift)]
for i in range(3):
self.assertAlmostEqual(coord1[i], coord2[i], 2)
def matrixFromGeometry(shifts, angles, inverseTransform):
""" Create the transformation matrix from a given
2D shifts in X and Y...and the 3 euler angles.
"""
from pyworkflow.em.convert.transformations import euler_matrix
from numpy import deg2rad
radAngles = -deg2rad(angles)
M = euler_matrix(radAngles[0], radAngles[1], radAngles[2], 'szyz')
if inverseTransform:
from numpy.linalg import inv
M[:3, 3] = -shifts[:3]
M = inv(M)
else:
M[:3, 3] = shifts[:3]
return M
def testTransformRotation(self):
aSHSource = AtomicStructHandler(self.PDBFileName)
structure = aSHSource.getStructure()
structure_copy = deepcopy(structure)
rot = numpy.deg2rad(10)
theta = numpy.deg2rad(20.)
psi = numpy.deg2rad(30.)
rotation_matrix = euler_matrix(rot, theta, psi, 'szyz')
translation = translation_matrix([0., 0., 0.])
M = concatenate_matrices(rotation_matrix, translation)
aSHSource.transform(M)
m = M[:3, :3]
for atom1, atom2 in zip(structure.get_atoms(),
structure_copy.get_atoms()):
coord1 = atom1.get_coord()
coord2 = m.dot(atom2.get_coord())
for i in range(3):
self.assertAlmostEqual(coord1[i], coord2[i], 2)
def __applyTransform(suffix, pdbFileName, shift, angles, sampling):
""" auxiliary function, transform PDB and 3dmap files"""
# create a Scipion transformation matrix
from numpy import deg2rad
rotation_matrix = euler_matrix(deg2rad(angles[0]),
deg2rad(angles[1]),
deg2rad(angles[2]), 'szyz')
translation = translation_matrix(shift)
M = concatenate_matrices(rotation_matrix, translation)
# apply it to the pdb file
# if rotation move to center
aSH = AtomicStructHandler(pdbFileName)
if (angles[0] != 0. or angles[1] != 0. or angles[2] != 0.):
from pyworkflow.em.convert import ImageHandler
ih = ImageHandler()
x, y, z, n = ih.getDimensions("emd_%s.map" % EMDBID)
x /= 2.
y /= 2.
z /= 2.
localShift = [-x, -y, -z]
rotation_matrix = euler_matrix(0., 0., 0., 'szyz')
translation = translation_matrix(localShift)
localM = concatenate_matrices(rotation_matrix, translation)
aSH.transform(localM, sampling=sampling)
aSH.transform(M, sampling=sampling)
if (angles[0] != 0. or angles[1] != 0. or angles[2] != 0.):
localShift = [x, y, z]
rotation_matrix = euler_matrix(0., 0., 0., 'szyz')
translation = translation_matrix(localShift)
localM = concatenate_matrices(rotation_matrix, translation)
aSH.transform(localM, sampling=sampling)
aSH.write("%s_%s_transformed.ent" % (suffix, PDBID.lower()))
# get equivalent xmipp transformation
shift, angles = __getXmippEulerAngles(M)
# shift 3map and set sampling
__runXmippProgram("xmipp_transform_geometry",
'-i emd_%s.map '
'-o %s_emd_%s_transform.map '
'--interp linear '
'--shift %f %f %f '
'--rotate_volume euler %f %f %f ' % (
EMDBID,
suffix,
EMDBID,
shift[0], shift[1], shift[2],
angles[0], angles[1], angles[2]
)
)
header = Ccp4Header("%s_emd_%s_transform.map" % (suffix, EMDBID),
readHeader=True)
header.setSampling(sampling)
# put the sampling back, xmipp_transform_geometry erased it
header.writeHeader()
# view the results with chimera
from pyworkflow.em.viewers import Chimera
args = "%s %s %s %s" % (
pdbFileName,
"emd_%s.map" % EMDBID,
"%s_%s_transformed.ent" % (suffix, PDBID.lower()),
"%s_emd_%s_transform.map" % (suffix, EMDBID)
)
Chimera.runProgram(args)