Scoring associated with a SimulationData object. More...

#include <IMP/npctransport/Scoring.h>

Inheritance diagram for IMP::npctransport::Scoring:

Detailed Description

Scoring associated with a SimulationData object.

Definition at line 47 of file Scoring.h.

Public Member Functions
	Scoring (SimulationData *owner_sd, const ::npctransport_proto::Assignment &data)

void	add_chain_restraints (FGChain *chain)

void	add_custom_restraint (IMP::Restraint *r)

void	add_custom_restraints (IMP::Restraints R)

void	add_interaction (const ::npctransport_proto::Assignment_InteractionAssignment &idata)

void	add_restrained_anchor_bead (IMP::Particle *p)

void	add_z_bias_restraint (SingletonContainerAdaptor ps, double k)

void	add_z_bias_restraint (Particle *p, double k)

void	clear_custom_restraints ()

boost::tuple< Restraint , Object >	create_backbone_restraint (double rest_length_factor, double backbone_k, ParticlesTemp beads, std::string name) const
	Create a backbone bond restraint over beads according to class flags. More...

Restraint *	create_bounding_volume_restraint (SingletonContainerAdaptor beads) const

IMP::PairContainer *	create_close_beads_container (SingletonContainerAdaptor non_optimiziable_beads, SingletonContainerAdaptor optimizable_beads) const

IMP::PairContainer *	create_close_beads_container (ParticleIndexes non_optimizable_beads, SingletonContainerAdaptor optimizable_beads) const

container::PredicatePairsRestraint *	create_predicates_pair_restraint (PairContainer *bead_pairs, bool is_attr_interactions_on=true) const

Restraint *	create_slab_restraint (SingletonContainerAdaptor beads) const

IMP::Restraint *	create_z_bias_restraint (SingletonContainerAdaptor ps, double k) const

Restraints	get_all_chain_restraints () const

Restraint *	get_bounding_volume_restraint (bool update=false)

Restraints	get_chain_restraints_on (SingletonContainerAdaptor beads) const

IMP::PairContainer *	get_close_beads_container (bool update=false)

IMP::Restraints	get_custom_restraints () const

IMP::ScoringFunction *	get_custom_scoring_function (const RestraintsTemp &extra_restraints, SingletonContainerAdaptor non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const

IMP::ScoringFunction *	get_custom_scoring_function (const RestraintsTemp &extra_restraints, ParticleIndexes non_optimizable_beads, SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=true) const

double	get_default_backbone_k () const

double	get_excluded_volume_k () const

FGChains	get_fg_chains ()

bool	get_has_bounding_box () const
	returns true if simulation has a bounding simulation box More...

bool	get_has_bounding_sphere () const
	returns true if simulation has a bounding simulation sphere ('cell-like') More...

bool	get_has_bounding_volume () const
	returns true if simulation has any bounding volume (box or sphere are supported) More...

double	get_interaction_k () const

double	get_interaction_range_for (core::ParticleType t1, core::ParticleType t2, bool site_specific=true, bool non_specific=false) const

bool	get_is_backbone_harmonic () const

Model *	get_model ()

Model *	get_model () const

core::OrderedTypePairPredicate *	get_ordered_type_pair_predicate ()

core::OrderedTypePairPredicate const *	get_ordered_type_pair_predicate () const

Restraint *	get_pore_radius_restraint () const

IMP::PairScore const *	get_predicate_pair_score (core::ParticleType t1, core::ParticleType t2) const
	returns the pair score for particles of types t1 and t2 */ More...

IMP::PairScore *	get_predicate_pair_score (core::ParticleType t1, core::ParticleType t2)
	returns the pair score for particles of types t1 and t2 */ More...

container::PredicatePairsRestraint *	get_predicates_pair_restraint (bool update=false)

double	get_range () const

IMP::ScoringFunction *	get_scoring_function (bool force_update=false)

IMP::Restraints	get_scoring_function_restraints (bool force_update=false)

SimulationData *	get_sd ()

SimulationData const *	get_sd () const

boost::tuple< unsigned int, std::vector< unsigned int > , std::vector< unsigned int > , bool >	get_site_interactions_statistics (ParticleIndex pi1, ParticleIndex pi2) const

boost::tuple< unsigned int, std::vector< unsigned int > , std::vector< unsigned int > , bool >	get_site_interactions_statistics (Particle const p1, Particle const p2) const

Restraint *	get_slab_restraint (bool update=false)

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...

IMP::Restraints	get_z_bias_restraints ()

void	remove_particle_type (core::ParticleType pt)

void	set_interaction_k_factor (IMP::core::ParticleType type, double value)

void	set_interaction_range_factor (IMP::core::ParticleType type, double value)

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 ()

Constructor & Destructor Documentation

IMP::npctransport::Scoring::Scoring	(	SimulationData *	owner_sd,
		const ::npctransport_proto::Assignment &	data
	)

Parameters

[in]	owner_sd	npc simulation data object that owns this scoring object
[out]	data	protobuf data with parameters for this assignment, used to parameterize the scoring function

Member Function Documentation

void IMP::npctransport::Scoring::add_chain_restraints ( FGChain * chain )

add FG chain to this scoring object, using the chain->get_chain_restraints() method to retrieve the restraints upon a call to get_scoring_function() or create_scoring_function(), etc.

Parameters

chain an FG chain associated with internal scoring

Returns: pointer to the newly created restraint

Note: if the chain->get_backbone_k() is non-positive, it is reset to this->get_default_backbone_k(); this method assumes that all such chains will be disjoint and so it is later possible to use container::ExclusiveConsecutivePairFilter to filter out all pairs of particles connected by such chain restraints.

void IMP::npctransport::Scoring::add_interaction ( const ::npctransport_proto::Assignment_InteractionAssignment & idata )

add a SitesPairScore restraint that applies to particles of types t0 and t1 (specified in idata) to the PredicatePairsRestraint object that is returned by get_predr(). The restraint is symmetric, and applies to both (t0,t1) and (t1,t0).

A SitesPairScore restraint means site-specific attractive forces between surface binding sites on each particle + non-specific attraction and soft repulsion between the entire particles.

Parameters

idata the protobuf data about the interaction (particle types, interaction coefficients, etc.)

See Also: SitesPairScore

void IMP::npctransport::Scoring::add_restrained_anchor_bead ( IMP::Particle * p )

add anchor bead to scoring function, using current position of p as equilibrium position relative to pore

Parameters

p	anchored particle

Note: currently only cylindrical pore case is supported

void IMP::npctransport::Scoring::add_z_bias_restraint	(	SingletonContainerAdaptor	ps,
		double	k
	)

adds a biasing potential for particles ps towards z, to the restraints returned by get_z_bias_restraints(), and for the scoring function generated by get_scoring_function()

Parameters

ps	container for the particles to be biased
k	force constant

See Also: get_z_bias_restraints(); get_scoring_function()

void IMP::npctransport::Scoring::add_z_bias_restraint	(	Particle *	p,
		double	k
	)

adds a biasing potential for particle p towards z, to the restraints returned by get_z_bias_restraints(), and for the scoring function generated by get_scoring_function()

Parameters

p	the particle to be biased
k	force constant

boost::tuple< Restraint, Object> IMP::npctransport::Scoring::create_backbone_restraint	(	double	rest_length_factor,
		double	backbone_k,
		ParticlesTemp	beads,
		std::string	name
	)		const

Create a backbone bond restraint over beads according to class flags.

create a backbone bond restraint with specified rest_length_factor (relative to sum of spheres radii) and backbone k over beads. The restraint score type is according to the class flags - either a linear or harmonic potential, with k in units of kcal/mol/A or kcal/mol/A^2, respectively, with the harmonic potential corresponding to a relaxing spring.

returns both the restraint and the linear well pair score or harmonic singleton score that is used in it (which one depends on the IMP version, assigns nullptr to the other), as a pointer to a generic object (= common ancestor class)

Restraint* IMP::npctransport::Scoring::create_bounding_volume_restraint ( SingletonContainerAdaptor beads ) const

Creates bounding volume (box or sphere) restraint based on the box_size_ class variable and get_has_bounding_sphere() and get_has_bounding_box() variables (typically based on box_is_on_), , and apply it to all beads returned by get_sd()->get_beads()

Parameters

beads beads on which to apply the constraint

Note: this restraint is (supposed to) guarantee to be always updated with the list inside the container

Returns: a newly created box restraint

IMP::PairContainer* IMP::npctransport::Scoring::create_close_beads_container	(	SingletonContainerAdaptor	non_optimiziable_beads,
		SingletonContainerAdaptor	optimizable_beads
	)		const

creates a new pair container that returns all pairs of particles (a,b) such that: 1) a is any particle from 'non_optimizable_beads' or 'optimizable beads', and b is any particle in 'optimizable_beads' 2) a and b are close (sphere surfaces within range get_range()) 3) a and b do not appear consecutively within the model (e.g., fg repeats) 4) a is not b 5) b and a do not appear in the list (effectively, a list of unordered pairs)

Parameters

non_optimizable_beads	a container for particles that are assumed to be non-optimizable and therefore are not paired among themselves
optimizable_beads	A container for particles that are assumed to be optimizable, and may be paired among themselves or with non_optimizable_beads

Note: it is assumed the two sets of beads are disjoint

IMP::PairContainer* IMP::npctransport::Scoring::create_close_beads_container	(	ParticleIndexes	non_optimizable_beads,
		SingletonContainerAdaptor	optimizable_beads
	)		const

same as other create_close_beads_container variant but based on a list of particle indexes and allowing an empty vector of non-optimizable beads as input. The optimizable beads are still treated dynamically (e.g. if they're associated with a dynamic container)

Definition at line 364 of file Scoring.h.

container::PredicatePairsRestraint* IMP::npctransport::Scoring::create_predicates_pair_restraint	(	PairContainer *	bead_pairs,
		bool	is_attr_interactions_on = `true`
	)		const

Creates a new container for restraints over pairs of beads. Different scores are used for beads of different (ordered) particle types based on interaction_pair_scores, or just a default linear repulsive with k=get_excluded_volume_k() force on all other pairs in bead_pairs.

Parameters

bead_pairs	a container for the pairs of beads to be restrained
is_attr_interactions_on	whether to include attractive interactions that were added by add_interaction()

Restraint* IMP::npctransport::Scoring::create_slab_restraint ( SingletonContainerAdaptor beads ) const

Creates slab bounding volume restraint, based on the slab_thickness_ and tunnel_radius_ class variables, and apply it to all beads returned by get_sd()->get_beads()

Parameters

beads beads on which to apply the constraint

Note: this restraint is (supposed to) guarantee to be always updated with the list inside the container

Returns: a newly created slab restraint

IMP::Restraint* IMP::npctransport::Scoring::create_z_bias_restraint	(	SingletonContainerAdaptor	ps,
		double	k
	)		const

create a z bias restraint pulling along z-axis for the particles in ps. If a slab is present, the force acts only within tunnel radius distance from its central axis.

Parameters

ps	the particles container
k	force constant for biasing ps

Restraints IMP::npctransport::Scoring::get_all_chain_restraints ( ) const

Returns: all restraints of fg nup chains that were added by add_chain_restraints() so far

Restraint* IMP::npctransport::Scoring::get_bounding_volume_restraint ( bool update = false )

returns the box/sphere restraint on >get_sd()->get_beads() which will be used in the next call to get_scoring_function(false) (so manipulating it might affect the scoring function). If update is false, then it is guaranteed that these are the same restraints used by the last call to get_scoring_function.

Parameters

update if true, forces recreation of the cached container, o/w cached version that was used in last call to get_scoring_function(), if applicable

Note: if update=false, might fail to include e.g., new particles that were added after the last call

See Also: get_has_bounding_box(), get_has_bounding_sphere(), get_has_bounding_volume()

Restraints IMP::npctransport::Scoring::get_chain_restraints_on ( SingletonContainerAdaptor beads ) const

returns restraints on all fg nup chains that were added by add_chain_restraints() so far and contain any bead in 'beads'. The restraints are updated directly from the original chain objects chain->get_chain_restraints() object.

Parameters

beads a least of chain fine beads over which restraints are collected

Returns: a list of all chain restraints that have been added so far and contain beads in 'beads'

IMP::PairContainer* IMP::npctransport::Scoring::get_close_beads_container ( bool update = false )

a pair container that was used to define interaction particles that will be used in the next call to get_scoring_function(false) (so manipulating it might affect the scoring function)

Parameters

update if true, forces recreation of the cached container, o/w cached version that was used in last call to get_scoring_function() or to this function will be used

Returns: a container with all pairs of particles (a,b) such that: 1) a is an optimizable bead particle and b is any bead particle (static or not). 2) a and b are close (sphere surfaces within range get_range()+some slack) 3) a and b do not appear consecutively within the model (e.g., bonded fg motifs) 4) a and b are not the same particles 5) b and a do not appear on the list (= unordered list)

Note: if update=false, might fail to include e.g., new particles or new interactions that were added after the last call; TODO: right now will not return any consecutive particles - that's erroneous (e.g., last particle of one chain and first particle of next chain) though may be negligible in practice; supposed to be robust to dynamic changes to the beads list, though need to double check (TODO)

IMP::ScoringFunction* IMP::npctransport::Scoring::get_custom_scoring_function	(	const RestraintsTemp &	extra_restraints,
		SingletonContainerAdaptor	non_optimizable_beads,
		SingletonContainerAdaptor	optimizable_beads,
		bool	is_attr_interactions_on = `true`
	)		const

returns a custom scoring function for the NPC simulation, based on: 1) the chain restraints added by add_chain_restraints() that overlap with 'particles' 2) default repulsive interactions between particles in particles and optimizable particles 3) attractive interactions that depend on pair types, as added by add_interaction() 4) the slab or bounding box restraints if relevant on all particles in 'particles'

Parameters

extra_restraints	ad-hoc restraints to be added to scoring function
non_optimizable_beads	particles container on which to apply bounding volume and pair constraints only if they also involve optimizable beads
optimizable_beads	particles container on which to apply bounding volume and pair constraints, either with other optimizable beads or with non-optimizable ones.
is_attr_interactions_on	if false, only repulsive interactions will be computed between pairs of particles

Note: it is assumed the two sets of beads are disjoint

IMP::ScoringFunction* IMP::npctransport::Scoring::get_custom_scoring_function	(	const RestraintsTemp &	extra_restraints,
		ParticleIndexes	non_optimizable_beads,
		SingletonContainerAdaptor	optimizable_beads,
		bool	is_attr_interactions_on = `true`
	)		const

same as other get_custom_scoring_function variant but based on a list of particle indexes and allowing an empty vector of non-optimizable beads as input

Note: The optimizable beads are still treated dynamically (e.g. if they're associated with a dynamic container)

Definition at line 209 of file Scoring.h.

double IMP::npctransport::Scoring::get_default_backbone_k ( ) const

returns the default spring constant between consecutive beads in a chain of beads - this is used for chains whose k is non-positive

Definition at line 466 of file Scoring.h.

double IMP::npctransport::Scoring::get_excluded_volume_k ( ) const

returns the constant force applied by overlapping spheres on each other

Definition at line 495 of file Scoring.h.

FGChains IMP::npctransport::Scoring::get_fg_chains ( )

returns pointers to the collection of the FG Chains stored in this scoring object (can be used to e.g. scale scoring information up or down during optimization)

Definition at line 691 of file Scoring.h.

bool IMP::npctransport::Scoring::get_has_bounding_box ( ) const

returns true if simulation has a bounding simulation box

Definition at line 448 of file Scoring.h.

bool IMP::npctransport::Scoring::get_has_bounding_sphere ( ) const

returns true if simulation has a bounding simulation sphere ('cell-like')

Definition at line 453 of file Scoring.h.

bool IMP::npctransport::Scoring::get_has_bounding_volume ( ) const

returns true if simulation has any bounding volume (box or sphere are supported)

Definition at line 458 of file Scoring.h.

double IMP::npctransport::Scoring::get_interaction_k ( ) const

returns the default interaction constant, which is used only if interaction_k is not specified for a certain interaction

Definition at line 499 of file Scoring.h.

double IMP::npctransport::Scoring::get_interaction_range_for	(	core::ParticleType	t1,
		core::ParticleType	t2,
		bool	site_specific = `true`,
		bool	non_specific = `false`
	)		const

Returns: maximal actual interaction range (normalized by range factors) for a given interaction type, as set by add_interaction(), over site-site and/or non-specific interactions if applicable. If not applicable, returns -1.0

Parameters

t1,t2	the types of beads in this interaction
site_specific	include site-site ranges
non_specific	include non-specific sphere interaction ranges

Note: if both site_specific and non_specific are true, takes a maximum over both.

Model* IMP::npctransport::Scoring::get_model ( )

returns the model associated with the owned SimulationData

Model* IMP::npctransport::Scoring::get_model ( ) const

returns the model associated with the owned SimulationData

IMP::PairScore const* IMP::npctransport::Scoring::get_predicate_pair_score	(	core::ParticleType	t1,
		core::ParticleType	t2
	)		const

returns the pair score for particles of types t1 and t2 */

IMP::PairScore* IMP::npctransport::Scoring::get_predicate_pair_score	(	core::ParticleType	t1,
		core::ParticleType	t2
	)

returns the pair score for particles of types t1 and t2 */

container::PredicatePairsRestraint* IMP::npctransport::Scoring::get_predicates_pair_restraint ( bool update = false )

Returns the restraints over pairs of particles based on their type, which will be used in the next call to get_scoring_function(false) (so manipulating it might affect the scoring function). Also, if update is false, then it is guaranteed that these are the same restraints used by the last call to get_scoring_function()

Different scores are used for particles of different (ordered) particle types. When called for the first time, returns a new PredicatePairsRestraints over all diffusing particles and sets a default linear repulsion restraint between all pairs returned by get_close_beads_container()

Parameters

update if true, forces recreation of the cached container, o/w cached version that was used in last call to get_scoring_function(), if applicable

Note: if update=false, might fail to include e.g., new particles or new interactions that were added to the simulation after the last call

IMP::ScoringFunction* IMP::npctransport::Scoring::get_scoring_function ( bool force_update = false )

returns a scoring function for the NPC simulation, based on: 1) the chain restraints added by add_chain_restraints() 2) default repulsive interactions on particles in get_beads() 3) attractive interactions that depend on pair types, as added by add_interaction() 4) the slab or bounding box restraints if relevant on all particles in get_beads() 5) z-biasing potential if add_z_bias_restraint() was called for any particles

Parameters

if	force_update is true, forces recreation of the scoring function, o/w cached version may be retrieved if available, which may not be completely up to date.

Note: if force_udpate=false, might fail to include e.g., new particles or new interactions that were added after the last call

IMP::Restraints IMP::npctransport::Scoring::get_scoring_function_restraints ( bool force_update = false )

returns the restrains associated with the scoring function return by get_scoring_function(force_update)

SimulationData* IMP::npctransport::Scoring::get_sd ( )

return the SimulationData object that owns this ScoringFunction

Definition at line 436 of file Scoring.h.

SimulationData const* IMP::npctransport::Scoring::get_sd ( ) const

return the SimulationData object that owns this ScoringFunction

Definition at line 442 of file Scoring.h.

boost::tuple< unsigned int, std::vector<unsigned int>, std::vector<unsigned int>, bool > IMP::npctransport::Scoring::get_site_interactions_statistics	(	ParticleIndex	pi1,
		ParticleIndex	pi2
	)		const

return various statistics about site-site interactions between pi1 and pi2 return a tuple with: a - number of site-site interaction that contribute to the score between pi1 and pi2 in the model, based on their current coordinates and their particle types b - vector of occupied pi1 sites counts (count number of interactions per site) c - vector of occupied pi2 sites counts (count number of interactions per site) d - true if particles are interacting non-specifically (a non-zero contribution of non-specific terms)

boost::tuple< unsigned int, std::vector<unsigned int>, std::vector<unsigned int>, bool > IMP::npctransport::Scoring::get_site_interactions_statistics	(	Particle const *	p1,
		Particle const *	p2
	)		const

return various statistics about site-site interactions between p1 and p2 return a tuple with: a) number of site-site interaction that contribute to the score between p1 and p2 in the model, based on their current coordinates and their particle types b) vector of occupied pi1 sites counts (count number of interactions per site) c) vector of occupied pi2 sites counts (count number of interactions per site)

Definition at line 557 of file Scoring.h.

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Restraint* IMP::npctransport::Scoring::get_slab_restraint ( bool update = false )

returns the slab restraint on >get_sd()->get_beads() which will be used in the next call to get_scoring_function(false) (so manipulating it might affect the scoring function). Also, if update is false, then it is guaranteed that these are the same restraints used by the last call to get_scoring_function()

Parameters

update if true, forces recreation of the cached container, o/w cached version that was used in last call to get_scoring_function(), if applicable

Note: if update=false, might fail to include e.g., new particles that were added after the last call

virtual ::IMP::VersionInfo IMP::npctransport::Scoring::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 727 of file Scoring.h.

IMP::Restraints IMP::npctransport::Scoring::get_z_bias_restraints ( )

return z_bias restraints for all particles that were added using add_z_bias_restraint()

void IMP::npctransport::Scoring::remove_particle_type ( core::ParticleType pt )

remove all scoring function elements related to particle type pt NOTE: a few aspects of the scoring function do not support this function as of 2018-06-19 - namely anchor restraints and z coordinate bias

void IMP::npctransport::Scoring::set_interaction_k_factor	(	IMP::core::ParticleType	type,
		double	value
	)

sets the multiplicative scaling of the interaction k constants for pair interactions involving a particle of this type, for all future calls to add_interaction()

Definition at line 717 of file Scoring.h.

void IMP::npctransport::Scoring::set_interaction_range_factor	(	IMP::core::ParticleType	type,
		double	value
	)

sets the multiplicative scaling of the interaction range for pair interactions involving a particle of this type, for all future calls to add_interaction()

Definition at line 704 of file Scoring.h.

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

Scoring.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation