Scripts: red_area.py

# Compute the area of an MSMS surface colored more red than blue
# (electrostatic coloring) as a ratio of the total area.
#
# Example use.
#
# menu File / Open..., red_area.py,  Creates the new redarea command.
#
# open 1a0m
# surface
# coulombic -10 red 0 white 10 blue #0
# redarea #0
#
# menu Favorites / Reply Log
#   -> "Surface MSMS main surface of 1a0m, red area 1400, total area 1888, ratio 0.7414"
#

def red_area(surface):

    red_area = tot_area = 0
    for p in surface.surfacePieces:
        va, ta = p.geometry  # Vertices and triangles
        rgba = p.vertexColors
        mask = (rgba[:,0] >= rgba[:,2])  # Red component >= blue
        import _surface
        a = _surface.vertex_areas(va, ta)
        tot_area += a.sum()
        red_area += (mask*a).sum()
    return red_area, tot_area

def red_area_command(cmd_name, args):

    from chimera.specifier import evalSpec
    for s in evalSpec(args).models():
        import _surface
        if isinstance(s, _surface.SurfaceModel):
            r,t = red_area(s)
            from chimera.replyobj import status, info
            msg = 'Surface %s, red area %.4g, total area %.4g, ratio %.4g' % (s.name, r, t, r/t)
            status(msg)
            info(msg + '\n')

from Midas.midas_text import addCommand
addCommand('redarea', red_area_command)