def testTransformTranslation(self):
aSHSource = emconv.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 = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.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 testTransformRotation(self):
aSHSource = emconv.AtomicStructHandler(self.PDBFileName)
structure = aSHSource.getStructure()
structure_copy = deepcopy(structure)
rot = np.deg2rad(10)
theta = np.deg2rad(20.)
psi = np.deg2rad(30.)
rotation_matrix = emconv.euler_matrix(rot, theta, psi, 'szyz')
translation = emconv.translation_matrix([0., 0., 0.])
M = emconv.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 = emconv.euler_matrix(deg2rad(angles[0]),
deg2rad(angles[1]),
deg2rad(angles[2]), 'szyz')
translation = emconv.translation_matrix(shift)
M = emconv.concatenate_matrices(rotation_matrix, translation)
# apply it to the pdb file
# if rotation move to center
aSH = emconv.AtomicStructHandler(pdbFileName)
if angles[0] != 0. or angles[1] != 0. or angles[2] != 0.:
ih = ImageHandler()
x, y, z, n = ih.getDimensions("emd_%s.map" % EMDBID)
x /= 2.
y /= 2.
z /= 2.
localShift = [-x, -y, -z]
rotation_matrix = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.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 = emconv.euler_matrix(0., 0., 0., 'szyz')
translation = emconv.translation_matrix(localShift)
localM = emconv.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 pwem.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)