IMP::ConfigurationSet Class Reference

A class to store a set of configurations of a model. More...

#include <IMP/ConfigurationSet.h>

Inheritance diagram for IMP::ConfigurationSet:

Detailed Description

A class to store a set of configurations of a model.

The class maintains a set of structures found by a Sampler protocol and allows them to be queried and loaded and saved.

## \example kernel/basic_optimization.py
# This illustrates a basic main loop for optimization and searching for the
# best scoring conformation.
#

import IMP.container
import IMP.statistics
import sys

IMP.setup_from_argv(sys.argv, "Basic optimization")

# Make 100 particles randomly distributed in a cubic box
m = IMP.Model()
lsc = IMP.container.ListSingletonContainer(m)
b = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),
                              IMP.algebra.Vector3D(10,10,10))
for i in range(100):
    p = m.add_particle("p")
    lsc.add(p)
    d = IMP.core.XYZR.setup_particle(m, p,
              IMP.algebra.Sphere3D(IMP.algebra.get_random_vector_in(b), 1))
    d.set_coordinates_are_optimized(True)

ps = IMP.core.DistancePairScore(IMP.core.HarmonicLowerBound(1, 1))
r = IMP.container.PairsRestraint(ps, IMP.container.ClosePairContainer(lsc, 2.0))
sf = IMP.core.RestraintsScoringFunction([r])
# we don't want to see lots of log messages about restraint evaluation
m.set_log_level(IMP.WARNING)

# the container (lsc) stores a list of particle indices
pis = lsc.get_contents()

s = IMP.core.MCCGSampler(m)
s.set_scoring_function(sf)
s.set_number_of_attempts(10)
# but we do want something to watch
s.set_log_level(IMP.TERSE)
s.set_number_of_monte_carlo_steps(10)
# find some configurations which move the particles far apart
configs = s.create_sample()
for i in range(0, configs.get_number_of_configurations()):
    configs.load_configuration(i)
    # print out the sphere containing the point set
    # - Why? - Why not?
    sphere = IMP.core.get_enclosing_sphere(IMP.get_particles(m, pis))
    print(sphere)

# cluster the solutions based on their coordinates
e = IMP.statistics.ConfigurationSetXYZEmbedding(configs, lsc)

# of course, this doesn't return anything of interest since the points are
# randomly distributed, but, again, why not?
clustering = IMP.statistics.create_lloyds_kmeans(e, 3, 1000)
for i in range(0, clustering.get_number_of_clusters()):
    # load the configuration for a central point
    configs.load_configuration(clustering.get_cluster_representative(i))
    sphere = IMP.core.get_enclosing_sphere(IMP.get_particles(m, pis))
    print(sphere)

Definition at line 28 of file ConfigurationSet.h.

Public Member Functions
	ConfigurationSet (Model *m, std::string name="ConfigurationSet %1%")
Model *	get_model () const
unsigned int	get_number_of_configurations () const
virtual std::string	get_type_name () const override
virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...
void	load_configuration (int i) const
	Load the ith configuration into the Model. More...
void	remove_configuration (unsigned int i)
void	save_configuration ()
	Save the current configuration of the Model. More...
Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Additional Inherited Members
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Member Function Documentation

virtual ::IMP::VersionInfo IMP::ConfigurationSet::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 43 of file ConfigurationSet.h.

void IMP::ConfigurationSet::load_configuration

(

int

i

)

const

Load the ith configuration into the Model.

Passing -1 returns it to the base configuration.

void IMP::ConfigurationSet::save_configuration

(

)

Save the current configuration of the Model.

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The documentation for this class was generated from the following file:

• ConfigurationSet.h