Class for storing model, its restraints, constraints, and particles. More...

#include "IMP/Model.h"

Inheritance diagram for IMP::kernel::Model:

Detailed Description

Class for storing model, its restraints, constraints, and particles.

The Model maintains a standard IMP container for each of Particle, ScoreState and Restraint object types.

Each Float attribute has an associated range which reflects the range of values that it is expected to take on during optimization. The optimizer can use these ranges to make the optimization process more efficient. By default, the range estimates are simply the range of values for that attribute in the various particles, but it can be set to another value. For example, an attribute storing an angle could have the range set to (0,PI).

The ranges are not enforced; they are just guidelines. In order to enforce ranges, see, for example, IMP::example::ExampleSingletonModifier.

Examples:: atom/dope_and_excluded_volume.cpp, and core/simple.cpp.

Definition at line 73 of file kernel/Model.h.

Public Member Functions
	Model (std::string name="Model %1%")

ParticleIndex	add_particle (std::string name)
	Add particle to the model. More...

void	add_undecorator (ParticleIndex pi, Undecorator *d)

void	clear_particle_caches (ParticleIndex pi)

double	evaluate (bool tf, bool warn=true)

bool	get_has_particle (ParticleIndex p) const

double	get_maximum_score (Restraint *r) const

double	get_maximum_score () const

ModelObjectsTemp	get_model_objects () const

unsigned int	get_number_of_particles () const

unsigned int	get_number_of_restraints () const

Particle *	get_particle (ParticleIndex p) const

ParticleIndexes	get_particle_indexes ()

std::string	get_particle_name (ParticleIndex pi)
	Get the name of a particle. More...

ParticlesTemp	get_particles () const

Restraint *	get_restraint (unsigned int i) const

RestraintSet *	get_root_restraint_set ()

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...

	operator Restraint * () const

ParticleIterator	particles_begin () const

ParticleIterator	particles_end () const

void	remove_particle (ParticleIndex pi)

void	remove_particle (Particle *p)

void	set_maximum_score (Restraint *r, double s)

void	set_maximum_score (double s)

void	update ()
	Sometimes it is useful to be able to make sure the model is up to date. 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)

States
ScoreStates can be added to the Model in order to keep them alive as long as the model is alive. Being added does affect their ability to perform their required action. See ScoreState for more information. Note Familiarity with these methods is not required to use imp.
void	remove_score_state (ScoreState *d)

void	remove_score_states (const ScoreStates &d)

void	set_score_states (const ScoreStates &ps)

void	set_score_states_order (const ScoreStates &objs)

unsigned int	add_score_state (ScoreState *obj)

void	add_score_states (const ScoreStates &objs)

void	clear_score_states ()

unsigned int	get_number_of_score_states () const

bool	get_has_score_states ()

ScoreState *	get_score_state (unsigned int i) const

ScoreStates	get_score_states () const

void	reserve_score_states (unsigned int sz)

Accessing attributes
All the attribute data associated with each Particle is stored in the Model. For each type of attribute, there are the methods detailed below (where, eg, TypeKey is FloatKey or StringKey)
void	add_attribute (TypeKey attribute_key, ParticleIndex particle, Type value)

void	remove_attribute (TypeKey attribute_key, ParticleIndex particle)

bool	get_has_attribute (TypeKey attribute_key, ParticleIndex particle) const

void	set_attribute (TypeKey attribute_key, ParticleIndex particle, Type value)

Type	get_attribute (TypeKey attribute_key, ParticleIndex particle)

void	add_cache_attribute (TypeKey attribute_key, ParticleIndex particle, Type value)

void	set_is_optimized (TypeKey attribute_key, ParticleIndex particle, bool true_or_false)
	Optimized attributes are the parameters of the model. More...

Storing data in the model
One can store data associated with the model. This is used, for example, to keep a central ScoreState to normalize rigid body rotational variables.
void	add_data (kernel::ModelKey mk, base::Object *o)

base::Object *	get_data (kernel::ModelKey mk) const

void	remove_data (kernel::ModelKey mk)

bool	get_has_data (kernel::ModelKey mk) const

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 ()

Constructor & Destructor Documentation

IMP::kernel::Model::Model ( std::string name = "Model %1%" )

Construct an empty model

Member Function Documentation

void IMP::kernel::Model::add_attribute	(	TypeKey	attribute_key,
		ParticleIndex	particle,
		Type	value
	)

Precondition: get_has_attribute(attribute_key, particle) is false

void IMP::kernel::Model::add_cache_attribute	(	TypeKey	attribute_key,
		ParticleIndex	particle,
		Type	value
	)

Cache attributes, unklike normal attributes, can be added during evaluation. They are also cleared by the clear_cache_attributes() method. Cache attributes should be used when one is adding data to a particle to aid scoring (eg cache the rigid body collision acceleration structure).

When some pertinent aspect of the particle changes, the clear method should be called (yes, this is a bit vague). Examples where it should be cleared include changing the set of members of a core::RigidBody or their coordinates, changing the members of an atom::Hierarchy.

void IMP::kernel::Model::add_data	(	kernel::ModelKey	mk,
		base::Object *	o
	)

Store a piece of data in the model referenced by the key.

ParticleIndex IMP::kernel::Model::add_particle ( std::string name )

Add particle to the model.

Examples:: atom/dope_and_excluded_volume.cpp.

void IMP::kernel::Model::add_undecorator	(	ParticleIndex	pi,
		Undecorator *	d
	)

Add the passed Undecorator to the particle.

void IMP::kernel::Model::clear_particle_caches ( ParticleIndex pi )

Clear all the cache attributes of a given particle.

double IMP::kernel::Model::evaluate	(	bool	tf,
		bool	warn = `true`
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a ScoringFunction instead.

Type IMP::kernel::Model::get_attribute	(	TypeKey	attribute_key,
		ParticleIndex	particle
	)

Precondition: get_has_attribute(attribute_key, particle) is true

base::Object* IMP::kernel::Model::get_data ( kernel::ModelKey mk ) const

Get back some data stored in the model.

bool IMP::kernel::Model::get_has_data ( kernel::ModelKey mk ) const

Check if the model has a certain piece of data attached.

bool IMP::kernel::Model::get_has_particle ( ParticleIndex p ) const

Get the particle from an index.

double IMP::kernel::Model::get_maximum_score ( Restraint * r ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Get the maximum directly from the restraint.

double IMP::kernel::Model::get_maximum_score ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should use a ScoringFunction or a RestraintSet.

ModelObjectsTemp IMP::kernel::Model::get_model_objects ( ) const

Get all the ModelObjects associated with this Model.

unsigned int IMP::kernel::Model::get_number_of_particles ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().

unsigned int IMP::kernel::Model::get_number_of_restraints ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a RestraintSet instead.

Particle* IMP::kernel::Model::get_particle ( ParticleIndex p ) const

Get the particle from an index.

ParticleIndexes IMP::kernel::Model::get_particle_indexes ( )

Get all particle indexes

std::string IMP::kernel::Model::get_particle_name ( ParticleIndex pi )

Get the name of a particle.

ParticlesTemp IMP::kernel::Model::get_particles ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().

Restraint* IMP::kernel::Model::get_restraint ( unsigned int i ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a RestraintSet instead.

RestraintSet* IMP::kernel::Model::get_root_restraint_set ( )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Using a ScoringFunction instead.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 321 of file kernel/Model.h.

IMP::kernel::Model::operator Restraint * ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use a ScoringFunction instead.

Definition at line 386 of file kernel/Model.h.

ParticleIterator IMP::kernel::Model::particles_begin ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().

ParticleIterator IMP::kernel::Model::particles_end ( ) const

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use get_particle_indexes().

void IMP::kernel::Model::remove_attribute	(	TypeKey	attribute_key,
		ParticleIndex	particle
	)

Precondition: get_has_attribute(attribute_key, particle) is true

void IMP::kernel::Model::remove_data ( kernel::ModelKey mk )

Remove data stored in the model.

void IMP::kernel::Model::remove_particle ( ParticleIndex pi )

Remove a particle from the Model. The particle will then be inactive and cannot be used for anything and all data stored in the particle is lost.

void IMP::kernel::Model::remove_particle ( Particle * p )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the ParticleIndex version.

void IMP::kernel::Model::set_attribute	(	TypeKey	attribute_key,
		ParticleIndex	particle,
		Type	value
	)

Precondition: get_has_attribute(attribute_key, particle) is true

void IMP::kernel::Model::set_is_optimized	(	TypeKey	attribute_key,
		ParticleIndex	particle,
		bool	true_or_false
	)

Optimized attributes are the parameters of the model.

They will be modified by the samplers and optimizers.

void IMP::kernel::Model::set_maximum_score	(	Restraint *	r,
		double	s
	)

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Set get the maximum directly on the restraint.

void IMP::kernel::Model::set_maximum_score ( double s )

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. You should use a ScoringFunction or a RestraintSet.

void IMP::kernel::Model::update ( )

Sometimes it is useful to be able to make sure the model is up to date.

This method updates all the state but does not necessarily compute the score. Use this to make sure that your containers and rigid bodies are up to date.

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

kernel/Model.h

Detailed Description

Public Member Functions

States

Accessing attributes

Storing data in the model

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation