IMP::ConfigurationSet Class Reference

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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.

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.TERSE)
s.set_number_of_monte_carlo_steps(10)
# find some configurations which move the particles far apart
configs= s.get_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

generate density map of fixed dimension, pdb2density, local fitting, analyze convergence, fit restraint

Examples: six particles optimization, nup84 cg, sample 0, nup84 rb, analyze 0

Inheritance diagram for IMP::ConfigurationSet:

List of all members.

Public Member Functions
	ConfigurationSet (Model *m, std::string name="ConfigurationSet %1%")
Model *	get_model () const
unsigned int	get_number_of_configurations () const
void	load_configuration (int i) const
	Load the ith configuration into the Model.
void	remove_configuration (unsigned int i)
void	save_configuration ()
	Save the current configuration of the Model.
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object.
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)

Static Public Member Functions
static ConfigurationSet *	get_from (IMP::base::Object *o)

Additional Inherited Members
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)

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Member Function Documentation

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