6 from __future__
import print_function
23 m.set_log_level(IMP.SILENT)
39 chainr.set_name(
"The chain restraint")
40 restraints.append(chainr)
45 nbl.add_pair_filter(bpc)
52 (ps[0].get_particle_index(),
53 ps[-1].get_particle_index()))
54 tie.set_name(
"tie ends")
55 restraints.append(tie)
60 r.set_maximum_score(.1)
61 s.set_scoring_function(restraints)
62 s.set_number_of_attempts(10)
64 confs = s.create_sample()
65 print(
"Found", confs.get_number_of_configurations(),
"configurations")
66 fh = RMF.create_rmf_file(
"solutions.rmfz")
68 for i
in range(0, confs.get_number_of_configurations()):
69 confs.load_configuration(i)
RMF::FrameID save_frame(RMF::FileHandle file, std::string name="")
Save the current state of the linked objects as a new RMF frame.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
XYZRs create_xyzr_particles(Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
A container which contains all consecutive particle pairs from an input list.
Return all close unordered pairs of particles taken from the SingletonContainer.
Score distance between two particle centers using a harmonic function.
Class for storing model, its restraints, constraints, and particles.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
void add_hierarchy(RMF::FileHandle fh, atom::Hierarchy hs)
Store a list of ParticleIndexes.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
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 PairScore to a Pair.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Applies a PairScore to each Pair in a list.