motif_util.py

# -*- mode:python;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
import sys
import os
newpath = os.path.dirname(inspect.getfile(
    inspect.currentframe()))  # script directory
if not newpath in sys.path:
    sys.path.append(newpath)
from pymol_util import *
from xyzMath import *


def showmotifs(sel=None):
    sels = [sel]
    if not sel:
        sels = ['(' + x + ')' for x in cmd.get_object_list()]
    for sel in sels:
        cmd.hide("ev", sel)
        cmd.remove(sel + " and hydro")
        cmd.unbond(sel + " and resn BPY", sel + " and not resn BPY")
        # util.cbc(          sel + ' and (elem C)',first_color=0)
        cmd.show("lines", sel + " and (not name n+c+o) and (chain ~)")
        cmd.show("car", sel + " and not (chain ~)")
        cmd.zoom(sel + " and (chain ~)")
        # cmd.color("blue" , sel + " and name n")
        # cmd.color("red"  , sel + " and name o" )
        # cmd.show( "sti"  , sel + " and resn BPY")
        # cmd.show( "sti"  , "(("+sel+") and (name CA+CB) and (not chain ~)) within 4 of ((" +sel+") and (resn BPY))" )
        # cmd.show("lines" , sel + " and chain Z" )
        # cmd.dss(           sel + " and chain A+B+C+D+E+F")
        # cmd.color("red"  , sel + " and chain Z")
        # cmd.show( "sph"  , sel + " and chain Z and name C22+C25+C30")
        # cmd.set("sphere_scale","0.3")
        cmd.color("white", sel + " and (chain ~) and (elem C)")


def icosmotifs(sel=None):
    showmotifs(sel)
    cmd.color("green", "(chain A+C+E+G+I) and elem C")
    cmd.color("cyan", "(chain B+N+L    ) and elem C")


cmd.extend("motifs", showmotifs)
cmd.extend("icosmotifs", icosmotifs)