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

#include "IMP/Model.h"

Inheritance diagram for IMP::kernel::Model:

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

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

void	add_undecorator (ParticleIndex pi, Undecorator *d)

void	clear_particle_caches (ParticleIndex pi)

ScoringFunction *	create_model_scoring_function ()
	Create a scoring function object from the model restraints. More...

ModelObjectsTemp	get_model_objects () const

void	remove_particle (ParticleIndex pi)

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 ()

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. 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)

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < Model > >	ModelsTemp

Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

States
The Model stores a list of ScoreStates which are given an opportunity to update the stored Particles and their internal state before and after the restraints are evaluated. Use the methods below to manipulate the list of ScoreState objects. The value type for the iterators is a ScoreState*. Note The order of addition of ScoreState objects does not matter. 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)

Statistics
The Model can gather various statistics about the restraints and score states used. To use this feature, first turn on statistics gather and then run your optimization (or just call evaluate). Note Telling the model not to gather statistics does not clear existing statistics.
void	clear_all_statistics ()

void	set_gather_statistics (bool tf)

bool	get_gather_statistics () const

void	show_all_statistics (std::ostream &out=std::cout) const

void	show_restraint_time_statistics (std::ostream &out=std::cout) const

void	show_restraint_score_statistics (std::ostream &out=std::cout) const

RestraintStatistics	get_restraint_statistics (Restraint *r) const

void	show_score_state_time_statistics (std::ostream &out=std::cout) const

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...

Model Data
Arbitrary non-particle data can be associated with the Model. This can be used for Model-level caches and such.
void	add_data (ModelKey mk, base::Object *o)

base::Object *	get_data (ModelKey mk) const

void	remove_data (ModelKey mk)

bool	get_has_data (ModelKey mk) const

Methods to debug particles
It is sometimes useful to inspect the list of all particles when debugging. These methods allow you to do that. Note Only use this if you really know what you are doing as Particles can be added to the object from many different places. The value type for the iterators is a Particle*.
unsigned int	get_number_of_particles () const

ParticlesTemp	get_particles () const

Particle *	get_particle (ParticleIndex p) const

ParticleIterator	particles_begin () const

ParticleIterator	particles_end () const

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

Detailed Description

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.

Definition at line 80 of file kernel/declare_Model.h.

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_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.

Definition at line 114 of file kernel/declare_Model.h.

ScoringFunction* IMP::kernel::Model::create_model_scoring_function ( )

Create a scoring function from the model restraints, which can be used to evaluate the score over this model particles.

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

Precondition: get_has_attribute(attribute_key, particle) is true

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

Get all the ModelObjects associated with this Model.

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_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::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
	)

They will be modified by the samplers and optimizers.

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

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.

Friends And Related Function Documentation

typedef IMP::base::Vector<IMP::base::WeakPointer< Model > > ModelsTemp

Definition at line 70 of file kernel/base_types.h.

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

Public Member Functions

Related Functions

States

Statistics

Accessing attributes

Model Data

Methods to debug particles

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation