Scripts: removecross.py

# When one selected pseudobond crosses another in the current camera view
# remove the longer one.

# Keep every pseudobond that is not crossed by a shorter one
# as viewed along z axis.
def crossing_pbonds(pbonds):
    spbonds = list(pbonds)
    spbonds.sort(key = lambda b: b.length())
    pb_cross = []
    segments = []       # Segments not crossed by shorter one.
    for pb in spbonds:
        a1,a2 = pb.atoms
        xy1 = a1.xformCoord().data()[:2]
        xy2 = a2.xformCoord().data()[:2]
        segment = (xy1,xy2)
        if any_cross(segment, segments):
            pb_cross.append(pb)
        else:
            segments.append(segment)
    return pb_cross

def any_cross(segment, segments):
    for seg2 in segments:
        if crossing(seg2, segment):
            return True
    return False

def crossing(segment1, segment2):
    (p1,p2),(p3,p4) = segment1,segment2
    if p1 == p3 or p1 == p4 or p2 == p3 or p2 == p4:
        return False  # Endpoints match, no crossing
    return opposite_sides(p1, p2, segment2) and opposite_sides(p3, p4, segment1)

# Are two points on opposite sides of a line.
def opposite_sides(p1, p2, segment):
    x1,y1 = p1
    x2,y2 = p2
    (x3,y3),(x4,y4) = segment
    dx,dy = (x4-x3, y4-y3)
    nx,ny = (-dy,dx)  # Normal vector to segment
    side1 = nx*(x1-x3) + ny*(y1-y3)
    side2 = nx*(x2-x3) + ny*(y2-y3)
    return (side1 < 0 and side2 > 0) or (side1 > 0 and side2 < 0)


# Use currently selected pseudobonds
from chimera import selection
pbonds = selection.currentPseudobonds()

# Delete longer crossing pseudobonds
cpbonds = crossing_pbonds(pbonds)
for pb in cpbonds:
    pb.pseudoBondGroup.deletePseudoBond(pb)

print ('%d of %d pseudobonds deleted' % (len(cpbonds), len(pbonds)))