Vector Quantization Informations

VQ.VQ(D, n, epochs, alpha0=0.5, lam0=False)[source]

Function to clusters a set of vectors (D) into a number (n) of codebook vectors

Arguments:
n
number of VQ points to generate
epochs
number of iterations to run the algorithm
alpha0
NOTE: Ask Daven regarding this parameter.
lam0
NOTE: Ask Daven regarding this parameter.
VQ.get_VQ_points(emmap, threshold, noOfPoints, epochs, output_file=None, lap_fil=True)[source]

Function to generate VQ point given a density map

Arguments:

emmap
Map (to be clustered) instance.
threshold
voxels with density above this value are used in the VQ run.
noOfPoints
num of VQ points to output.
epochs
num of iterations to run the algorithm
output_file
file to output to. In PDB format
lap_fil
True if you want to Laplacian filter the map first, False otherwise. Note that filtering the map will change the density values of the map, which is relevant for the threshold parameter.
VQ.map_points(emmap, threshold)[source]

Function to return all map grid coordinated whose density value is greater than a given cutoff value.

Arguments:
emmap
Instance of a map object.
threshold
Density value used as a cutoff.
VQ.write_to_pdb(vq, output_file=None)[source]

Function to write the VQ point in PDB ATOM record format.

Arguments:
vq
A list of vector object containing the VQ points.
output_file
Name of the output file.