pwem.protocols.protocol_projection_edit module

class pwem.protocols.protocol_projection_edit.ProtProjectionEditor(**kwargs)

Bases: EMProtocol

This protocol edits the projection directions of all the items of a set of particles using a formula. This could be useful for applying geometrical transformation to a set of particles.

Several predefined operation are offered such as * apply the rotation matrix define by an origin vector and a target vector * rotate the projection vector around a given vector by A degrees * convert between icosahedral symmetries * convert between dihedral symmetries * convert between tetrahedral symmetries

CHOICE_DIHEDRAL = 3

CHOICE_ICOSAHEDRAL = 2

CHOICE_LABEL = {0: 'move source vector to target vector', 1: 'rotate around vector', 2: 'convert between icosahedral symmetries', 3: 'convert between dihedral symmetries', 4: 'convert between tetrahedral symmetries', 5: 'move to unit cell'}

CHOICE_MOVE_UC = 5

CHOICE_MOVE_VECTOR = 0

CHOICE_ROTATE_VECTOR = 1

CHOICE_TETRAHEDRAL = 4

DIHEDRAL_SYM_NAME = {1: 'Dxn', 2: 'Dyn'}

ICOSAHEDRAL_SYM_NAME = {7: 'I222', 8: 'I222r', 9: 'In25', 10: 'In25r', 11: 'I2n3', 12: 'I2n3r', 13: 'I2n5', 14: 'I2n5r'}

TETRAHEDRAL_SYM_NAME = {3: 'T222', 4: 'Tz3', 5: 'Tz3r'}

applyMatrix(matrix)

Applies the matrix the to whole input set and creates the output

createOutput(inputSet, modifiedSet)

moveToUCStep()

Moves the particle alignment information to the same unit cell based on the symmetry specified.

rotateDiStep()

Compute rotation matrix from one dihedral symmetry to another and apply it to the projection directions

rotateIcosahedralStep()

Compute rotation matrix from one icosahedral symmetry to another and apply it to projection directions. Reconstructed volume should change symmetry

rotateStep()

Compute rotation matrix between user provided vectors

(x,y,z) and (x’,y’,z’) and apply it

to projection directions. Reconstructed volume should rotate

rotateTetraStep()

Compute rotation matrix between tetrahedral symmetries and apply it to the projection directions

rotateVectorStep()

Compute rotation matrix around user provided vector

(x,y,z) and rotate “angle” degrees the projection directions.

Reconstructed volume should rotate around axis