container/filter_close_pairs.py

This example shows how to filter the list of close pairs generated in the IMP.container.ClosePairContainer (or IMP.container.CloseBipartitePairContainer). Eventually the filter should probably be implemented in C++, for speed but implementing the filter in python is good for prototyping.

## \example container/filter_close_pairs.py
# This example shows how to filter the list of close pairs generated in
# the IMP.container.ClosePairContainer (or
# IMP.container.CloseBipartitePairContainer). Eventually the filter should
# probably be implemented in C++, for speed but implementing the filter in
# python is good for prototyping.

from __future__ import print_function
import IMP
import IMP.container
import IMP.core
import IMP.algebra

np = 10
bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
                               IMP.algebra.Vector3D(5, 5, 5))
ik = IMP.IntKey("num")
IMP.base.set_log_level(IMP.base.SILENT)
m = IMP.kernel.Model()
l = []
for i in range(0, np):
    p = IMP.kernel.Particle(m)
    p.add_attribute(ik, i)
    IMP.core.XYZR.setup_particle(
        p, IMP.algebra.Sphere3D(IMP.algebra.get_random_vector_in(bb), 1))
    l.append(p)
lsc = IMP.container.ListSingletonContainer(l)
cpc = IMP.container.ClosePairContainer(lsc, 0.0)

m.update()
print("without", [(x[0].get_name(), x[1].get_name()) for x in cpc.get_particle_pairs()])


class ConsecutiveFilter(IMP.PairPredicate):

    def __init__(self):
        IMP.PairPredicate.__init__(self, "ConsecutiveFilter%1%")

    def get_value(self, pp):
        diff = pp[0].get_value(ik) - pp[1].get_value(ik)
        if diff == -1 or diff == 1:
            return 1
        return 0

    def do_get_inputs(self, m, pis):
        return [m.get_particle(i) for i in pis]

    def do_show(self, out):
        pass
f = ConsecutiveFilter()
cpc.add_pair_filter(f)
m.update()
print("with", [(x[0].get_name(), x[1].get_name()) for x in cpc.get_particle_pairs()])