7 from __future__
import print_function
19 def create_scoring(m, ps):
20 pairs = [[0, 1], [0, 2], [1, 3], [2, 3], [3, 4], [4, 5], [1, 5]]
26 [(ps[p[0]], ps[p[1]])
for p
in pairs],
29 pr.set_maximum_score(.01)
36 dr.set_maximum_score(.01)
40 def create_representation(m):
44 p = m.add_particle(
"P%d" % i)
50 def create_discrete_states(m, ps):
57 vs = vs + [-v
for v
in vs]
58 print(len(vs),
"states for each particle")
63 pst.set_particle_states(m.get_particle(p), states)
67 def create_sampler(m, r, pst):
85 states.set_log_level(IMP.SILENT)
86 s.set_assignments_table(states)
87 s.set_subset_filter_tables(filters)
95 m.set_log_level(IMP.SILENT)
97 print(
"creating representation")
98 ps = create_representation(m)
99 print(
"creating discrete states")
100 pst = create_discrete_states(m, ps)
101 print(
"creating score function")
102 rs = create_scoring(m, ps)
103 print(
"creating sampler")
104 s = create_sampler(m, rs, pst)
111 cs = s.create_sample()
113 print(
"found ", cs.get_number_of_configurations(),
"solutions")
115 for i
in range(cs.get_number_of_configurations()):
116 cs.load_configuration(i)
117 print(
"solution number:", i,
" is:", sf.evaluate(
False))
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
Upper bound harmonic function (non-zero when feature > mean)
Sample best solutions using Domino.
Filter a configuration of the subset using the Model thresholds.
Create a scoring function on a list of restraints.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Class for storing model, its restraints, constraints, and particles.
Do not allow two particles to be in the same state.
Store a list of ParticleIndexPairs.
Apply a function to the distance to a fixed point.
A decorator for a particle with x,y,z coordinates.
void set_log_level(LogLevel l)
Set the current global log level.
Basic functionality that is expected to be used by a wide variety of IMP users.
Applies a SingletonScore to a Singleton.
Applies a PairScore to each Pair in a list.
Divide-and-conquer inferential optimization in discrete space.