domino/multiscale.py

We are interested in applying domino to problems systematically in a multiscale manner. This script experiments with those approaches.

## \example domino/multiscale.py
# We are interested in applying domino to problems systematically in a
# multiscale manner. This script experiments with those approaches.

import IMP.domino
import IMP.core


# Use faster built-in 'set' type on newer Pythons; fall back to the older
# 'sets' module on older Pythons
try:
    x = set
    del x
except NameError:
    import sets
    set = sets.Set

m = IMP.kernel.Model()
m.set_log_level(IMP.base.SILENT)
ds = [IMP.core.XYZR.setup_particle(IMP.kernel.Particle(m))
      for i in range(0, 3)]
for i, d in enumerate(ds):
    d.set_radius(1)
    IMP.display.Colored.setup_particle(d, IMP.display.get_display_color(i))

k = 1
h = IMP.core.Harmonic(0, k)
r0 = IMP.core.SingletonRestraint(
    IMP.core.DistanceToSingletonScore(h, IMP.algebra.Vector3D(0, 0, 0)),
    ds[0], "0 at origin")

r1 = IMP.core.SingletonRestraint(IMP.core.AttributeSingletonScore(h,
                                                                  IMP.core.XYZ.get_xyz_keys(
                                                                  )[0]),
                                 ds[1], "1 on axis")

rs = [r0, r1]
for pr in [(0, 1), (1, 2), (0, 2)]:
    r = IMP.core.PairRestraint(IMP.core.HarmonicSphereDistancePairScore(0, k),
                               (ds[pr[0]], ds[pr[1]]),
                               "R for " + str(pr))
    rs.append(r)


bb = IMP.algebra.BoundingBox2D(IMP.algebra.Vector2D(0, 0),
                               IMP.algebra.Vector2D(4, 4))

covers = []
for i in range(0, 6):
    cur = IMP.algebra.get_grid_interior_cover_by_spacing(bb, 4.0 / 2 ** i)
    print cur
    covers.append([IMP.algebra.Vector3D(x[0], x[1], 0) for x in cur])


def setup(cover, scale):
    pst = IMP.domino.ParticleStatesTable()
    st = IMP.domino.XYZStates(cover)
    for p in ds:
        pst.set_particle_states(p, st)
    for r in rs:
        r.set_maximum_score(.5 * scale ** 2)
    lf = IMP.domino.ListSubsetFilterTable(pst)
    rc = IMP.domino.RestraintCache(pst)
    rc.add_restraints(rs)
    fs = [IMP.domino.RestraintScoreSubsetFilterTable(rc),
          lf]
    sampler = IMP.domino.DominoSampler(m, pst)
    sampler.set_subset_filter_tables(fs)
    sampler.set_log_level(IMP.base.SILENT)
    return (sampler, lf, pst)

(sampler, lf, pst) = setup(covers[0], 4.0)

subset = IMP.domino.Subset(ds)
ac = sampler.get_sample_assignments(subset)

print ac


def get_mapping(cover0, cover1):
    nn = IMP.algebra.NearestNeighbor3D(cover0)
    ret = [[] for c in cover0]
    for i, p in enumerate(cover1):
        nns = nn.get_nearest_neighbor(p)
        ret[nns].append(i)
    return ret

mw = IMP.display.PymolWriter("mapping.pym")


def display_mapping(index, cover0, cover1, mapping):
    mw.set_frame(index)
    for i, c in enumerate(mapping):
        for p in c:
            g = IMP.display.PointGeometry(cover1[p])
            g.set_color(IMP.display.get_display_color(i))
            g.set_name("fine")
            mw.add_geometry(g)
    for i, c in enumerate(cover0):
        g = IMP.display.PointGeometry(c)
        g.set_color(IMP.display.get_display_color(i))
        g.set_name("coarse")
        mw.add_geometry(g)


for curi in range(1, len(covers)):
    scale = 4.0 / 2 ** curi
    print scale
    mapping = get_mapping(covers[curi - 1], covers[curi])
    print mapping
    display_mapping(curi - 1, covers[curi - 1], covers[curi], mapping)
    (sampler, lf, pst) = setup(covers[curi], scale)
    lac = ac
    cac = []
    for a in lac:
        for i, p in enumerate(subset):
            s = a[i]
            allowed = mapping[s]
            lf.set_allowed_states(p, allowed)
        ccac = sampler.get_sample_assignments(subset)
        print a, ccac
        cac = cac + ccac
    ac = list(set(cac))
    print "for scale", scale, "got", ac
    sw = IMP.display.PymolWriter("solutions." + str(curi) + ".pym")
    for i, a in enumerate(ac):
        IMP.domino.load_particle_states(subset, a, pst)
        sw.set_frame(i)
        for p in ds:
            g = IMP.core.XYZRGeometry(p)
            sw.add_geometry(g)
        for c in covers[curi]:
            g = IMP.display.PointGeometry(c)
            g.set_color(IMP.display.Color(1, 1, 1))
            g.set_name("grid")
            sw.add_geometry(g)