6 from __future__
import print_function
19 p = m.add_particle(
"p")
23 d.set_coordinates_are_optimized(
True)
29 m.set_log_level(IMP.WARNING)
32 pis = lsc.get_contents()
35 s.set_scoring_function(sf)
36 s.set_number_of_attempts(10)
38 s.set_log_level(IMP.TERSE)
39 s.set_number_of_monte_carlo_steps(10)
41 configs = s.create_sample()
42 for i
in range(0, configs.get_number_of_configurations()):
43 configs.load_configuration(i)
55 for i
in range(0, clustering.get_number_of_clusters()):
57 configs.load_configuration(clustering.get_cluster_representative(i))
PartitionalClusteringWithCenter * create_lloyds_kmeans(Embedding *embedding, unsigned int k, unsigned int iterations)
Embed a configuration using the XYZ coordinates of a set of particles.
Lower bound harmonic function (non-zero when feature < mean)
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
Create a scoring function on a list of restraints.
Return all close unordered pairs of particles taken from the SingletonContainer.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
Code to compute statistical measures.
Class for storing model, its restraints, constraints, and particles.
Store a list of ParticleIndexes.
Score a pair of particles based on the distance between their centers.
algebra::Sphere3D get_enclosing_sphere(const XYZs &v)
Get a sphere enclosing the set of XYZRs.
Applies a PairScore to each Pair in a list.