localrec.utils module

class localrec.utils.Vector3

Bases: object

compute_length()

compute_matrix()

Compute rotation matrix to align Z axis to this vector.

compute_unit_vector()

get_length()

get_matrix()

print_vector()

set_length(d)

set_vector(v)

localrec.utils.create_subparticles(particle, symmetry_matrices, subparticle_vector_list, part_image_size, randomize, subparticles_total, align_subparticles, handness, angpix)

Obtain all subparticles from a given particle and set the properties of each such subparticle.

localrec.utils.filter_distorigin(subparticles, subpart, distorigin)

return True is particle must be kept

localrec.utils.filter_mindist(subparticles, subpart, mindist, keepRedundant)

Return True if subpart is not close to any other subparticle by mindist. That is returns True is particle must ne kept

localrec.utils.filter_side(subpart, side)

localrec.utils.filter_subparticles(subparticles, filters)

localrec.utils.filter_top(subpart, top)

localrec.utils.filter_unique(subparticles, subpart, unique)

Return True if subpart is not close to any other subparticle by unique (angular distance). For this function we assume that subpart is not contained inside.

localrec.utils.geometryFromMatrix(matrix)

localrec.utils.load_vectors(cmm_file, vectors_str, distances_str, angpix)

Load subparticle vectors either from Chimera CMM file or from a vectors string. Distances can also be specified for each vector in the distances_str.

localrec.utils.matrixFromGeometry(shifts, angles, inverseTransform)

Create the transformation matrix from a given 2D shifts in X and Y…and the 3 euler angles.

localrec.utils.vector_from_two_eulers(rot, tilt)

function that obtains a vector from the first two Euler angles

localrec.utils.vectors_from_cmm(input_cmm, angpix)

function that obtains the input vector from a cmm file

localrec.utils.vectors_from_string(input_str)

Function to parse vectors from an string. Our (arbitrary) convention is: x1,y1,z1; x2,y2,z2 … etc

localrec.utils.within_mindist(p1, p2, mindist, keepRedundant)

Returns True if two particles are closer to each other than the given distance in the projection.

localrec.utils.within_unique(p1, p2, unique)

Returns True if two particles are closer to each other than the given angular distance.