Scripts: helixtube.py

#
# Create command htube that shows helices as tubes by moving each CA that is in a helix to the center
# of CA position over a six residue sliding window.  Example
#
#       htube #0 windowSize 6 radius 1.5
#
def helix_tubes(atoms, guideAtom = 'CA', windowSize = 6, radius = 1.5):

    # Make table of guide atoms in sliding window.
    window_atoms = {}
    for a in atoms:
        if a.name == guideAtom:
            rid = a.residue.id
            rnum = rid.position
            for rn in range(rnum - windowSize/2, rnum + windowSize/2 + 1):
                window_atoms.setdefault((rid.chainId,rn),[]).append(a)

    # Move guide atom coordinates to average in window
    from chimera import numpyArrayFromAtoms as atom_coordinates, Point, RibbonStyleFixed
    round = RibbonStyleFixed((radius, radius))
    for a in atoms:
        r = a.residue
        if r.isHelix and a.name == guideAtom:
            chain_id, res_num = r.id.chainId, r.id.position
            win_atoms = window_atoms[(chain_id,res_num)]
            x,y,z = atom_coordinates(win_atoms).mean(axis=0)
            a.setCoord(Point(x,y,z))
            r.ribbonDisplay = True
            r.ribbonStyle = round

def htube_command(cmd_name, args):

    from Commands import parse_arguments, atoms_arg, string_arg, int_arg, float_arg
    required_args = [('atoms', atoms_arg)]
    optional_args = []
    keyword_args = [('guideAtom', string_arg),
                    ('windowSize', int_arg),
                    ('radius', float_arg)]
    kw = parse_arguments(cmd_name, args, required_args, optional_args, keyword_args)
    helix_tubes(**kw)

    
from Midas.midas_text import addCommand
addCommand('htube', htube_command)