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.
 #
 
 from __future__ import print_function
 import IMP.example
 import IMP.statistics
 
 (m, c) = IMP.example.create_model_and_particles()
 ps = IMP.core.DistancePairScore(IMP.core.HarmonicLowerBound(1, 1))
 r = IMP.container.PairsRestraint(ps, IMP.container.ClosePairContainer(c, 2.0))
 m.add_restraint(r)
 # we don't want to see lots of log messages about restraint evaluation
 m.set_log_level(IMP.WARNING)
 
 # the container (c) stores a list of particles, which are alse XYZR particles
 # we can construct a list of all the decorated particles
 xyzrs = c.get_particles()
 
 s = IMP.core.MCCGSampler(m)
 s.set_number_of_attempts(10)
 # but we do want something to watch
 s.set_log_level(IMP.base.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(xyzrs)
     print(sphere)
 
 # cluster the solutions based on their coordinates
 e = IMP.statistics.ConfigurationSetXYZEmbedding(configs, c)
 
 # 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(xyzrs)
     print(sphere)

Definition at line 28 of file kernel/ConfigurationSet.h.

Public Member Functions
	ConfigurationSet (kernel::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

virtual ::IMP::base::VersionInfo	get_version_info () const
	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::base::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::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Member Function Documentation

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 43 of file kernel/ConfigurationSet.h.

void IMP::kernel::ConfigurationSet::load_configuration ( int i ) const

Load the ith configuration into the Model.

Passing -1 returns it to the base configuration.

void IMP::kernel::ConfigurationSet::save_configuration ( )

Save the current configuration of the Model.

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

kernel/ConfigurationSet.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation