Hierarchical clash/collision detection

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 (first use Rmax, not Rg), re-add elliptical benchmarks

ConvexHull in python

http://pymolwiki.org/index.php/PLoS

def convexHull(P):
    # Get a local list copy of the points and sort them lexically.
    # Build the upper and then lower half of the hull, remove duplicates,
    # and return a concatenation of both halfs.
    points = map(None, P)
    points.sort()
    upper = [points[0], points[1]]
    for p in points[2:]:
        upper.append(p)
        while len(upper) > 2 and not _isRightTurn(upper[-3:]):
            del upper[-2]
    points.reverse()
    lower = [points[0], points[1]]
    for p in points[2:]:
        lower.append(p)
        while len(lower) > 2 and not _isRightTurn(lower[-3:]):
            del lower[-2]
    del lower[0]
    del lower[-1]
    return tuple(upper + lower)

Original issue reported on code.google.com by chad.a.davis@gmail.com on 19 Feb 2011 at 4:04

• Blocking: #198

[GoogleCodeExporter]

Will also provide an approach for testing exclusivity of interactions.
I.e. if two dimers cannot be merged due to clash, those interactions are 
exclusive.

Original comment by chad.a.davis@gmail.com on 19 Feb 2011 at 4:04

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[deleted comment]

[GoogleCodeExporter]

Note this is the convex hull of the points projected onto a plane, i.e. it's 2D.

Original comment by chad.a.davis@gmail.com on 24 Feb 2011 at 11:25

[GoogleCodeExporter]

Surface accessible (e.g. accessibility >= 5.0) points can be identified by 
naccess.

Original comment by chad.a.davis@gmail.com on 24 Feb 2011 at 11:29

[GoogleCodeExporter]

Use SBG::Run::check_ints if Spheres (using Rmax) are not rejected

Original comment by chad.a.davis@gmail.com on 19 Oct 2011 at 3:59