PyMOL script to highlight mutated residues between two proteins

diffseq.py

"""
(c) 2016 Joao Rodrigues
"""

from __future__ import print_function
from pymol import cmd


# Autocomplete
def _autocomplete():
    return cmd.Shortcut(cmd.get_names())
cmd.auto_arg[0]['diffseq'] = [_autocomplete, 'object name', '']
cmd.auto_arg[1]['diffseq'] = [_autocomplete, 'object name', '']


def diffseq(objectA, objectB):
    """
DESCRIPTION

    Highlight sequence differences between two proteins.

USAGE

    diffseq protA, protB
    """

    # Color white
    cmd.color('white', '{} or {}'.format(objectA, objectB))

    # Align
    cmd.align(objectA, objectB, object='_aln')

    # Map
    def _id_to_resn(selection):
        obj, at_id = selection
        _s = {'_r': []}
        cmd.iterate('{} and id {}'.format(obj, at_id),
                    '_r.append(resn)', space=_s)

        return _s['_r'][0]

    raw_aln = cmd.get_raw_alignment('_aln')
    for resA, resB in raw_aln:
        resn_A = _id_to_resn(resA)
        resn_B = _id_to_resn(resB)

        if resn_A != resn_B:
            cmd.show('spheres', '{} and id {}'.format(*resA))
            cmd.color('orange', '{} and id {}'.format(*resA))

            cmd.show('spheres', '{} and id {}'.format(*resB))
            cmd.color('orange', '{} and id {}'.format(*resB))

    cmd.delete('_aln')

cmd.extend('diffseq', diffseq)