Align Matrix

align_matrix.py

'''
    align_matrix
    ------------

    Aligns two sturctures and prints the distance matrix (complete)
    between the two aligned matrices.

    :author: Alex Huszagh
    :license: Unlicense, or MIT
'''

from pymol import cmd


def align_matrix(first, second):
    '''
    Align two structures and get the full alignment distance pair.

    Args:
        first -         object name for first structure
        second -        object name for second structure
    '''

    cmd.super("%s & guide" %first, "%s & guide" %second, object="aln")

    pairs = cmd.get_raw_alignment('aln')
    for pair in pairs:
        print(pair, cmd.get_distance(pair[0], pair[1]))
    cmd.delete("aln")


cmd.extend('align_matrix', align_matrix)