Module `PDAnalysis.utils`

Expand source code

import numpy as np

### "P" is the set of points to be mapped to "Q"
def rotate_points(P, Q):
    """Rotates a set of of points using the Kabsch algorithm"""
    H = P.T @ Q
    U, S, Vt = np.linalg.svd(H)
    V = Vt.T
    D = np.linalg.det(V @ U.T)
    E = np.array([[1, 0, 0], [0, 1, 0], [0, 0, D]])
    R = V @ E @ U.T
    Pnew = (R @ P.T).T
    return Pnew


### Returns a np.ndarray of positions where two sequences differ
def get_mutation_position(s1, s2):
    """Get the position of mutations between two sequences"""
    return np.where(np.array(list(s1)) != np.array(list(s2)))[0]


def get_shared_indices(idx1, idx2):
    """Get the intersection between two sets of indices"""
    i1 = np.where(np.in1d(idx1, idx2))[0]
    i2 = np.where(np.in1d(idx2, idx1))[0]
    return i1, i2

Functions

def get_mutation_position(s1, s2)

Get the position of mutations between two sequences

Expand source code

def get_mutation_position(s1, s2):
    """Get the position of mutations between two sequences"""
    return np.where(np.array(list(s1)) != np.array(list(s2)))[0]

def get_shared_indices(idx1, idx2)

Get the intersection between two sets of indices

Expand source code

def get_shared_indices(idx1, idx2):
    """Get the intersection between two sets of indices"""
    i1 = np.where(np.in1d(idx1, idx2))[0]
    i2 = np.where(np.in1d(idx2, idx1))[0]
    return i1, i2

def rotate_points(P, Q)

Rotates a set of of points using the Kabsch algorithm

Expand source code

def rotate_points(P, Q):
    """Rotates a set of of points using the Kabsch algorithm"""
    H = P.T @ Q
    U, S, Vt = np.linalg.svd(H)
    V = Vt.T
    D = np.linalg.det(V @ U.T)
    E = np.array([[1, 0, 0], [0, 1, 0], [0, 0, D]])
    R = V @ E @ U.T
    Pnew = (R @ P.T).T
    return Pnew