Source code for rpxdock.util.numeric

import numpy as np


def svd(x):
    U, Sigma, Vh = np.linalg.svd(x, full_matrices=False, compute_uv=True)
    X_svd = np.dot(U, np.diag(Sigma))
    return X_svd


def pca_eig(coords):
    n = len(coords)
    x = coords - coords.mean(axis=0)
    cov = np.dot(x.T, x) / (n - 1)
    e, evec = np.linalg.eig(cov)
    idx = np.argsort(-np.abs(e))
    return e[idx], evec[idx]


def pca(coords):
    eigen_vals, eigen_vecs = pca_eig(coords)
    return np.dot(x, eigen_vecs)