#include <SapMathConstraint.hh>

Inheritance diagram for core::pack::guidance_scoreterms::sap::SapMathConstraint:

Public Member Functions
	SapMathConstraint ()
	Constructor. More...

	SapMathConstraint (SapMathConstraint const &src)
	Copy constructor. More...

	~SapMathConstraint () override
	Destructor. More...

scoring::constraints::ConstraintOP	clone () const override
	Clone operator. More...

SapMathConstraint &	operator= (SapMathConstraint const &other)

bool	operator== (scoring::constraints::Constraint const &) const override
	Equality operator to test whether two constraints are functionally identical. More...

bool	same_type_as_me (scoring::constraints::Constraint const &other) const override
	Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. More...

void	add_constraint (Real weight, std::string const &name)

void	upper_bound (Real upper)

void	lower_bound (Real lower)

void	penalty_per_unit (Real penalty)

utility::vector1< std::pair < Real, SapConstraintHelperCOP > >	parse_helpers (utility::vector1< SapConstraintHelperCOP > const &helpers) const

Real	get_math_result (utility::vector1< std::pair< Real, SapConstraintHelperCOP > > const &parsed_helpers) const

Real	get_score (utility::vector1< std::pair< Real, SapConstraintHelperCOP > > const &parsed_helpers) const

scoring::constraints::ConstraintOP	remap_resid (core::id::SequenceMapping const &) const override
	apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice. More...

Public Member Functions inherited from core::scoring::aa_composition_energy::SequenceConstraint
	SequenceConstraint (core::scoring::ScoreType const &t)
	Constructor. More...

	SequenceConstraint (SequenceConstraint const &src)
	Copy constructor. More...

	~SequenceConstraint () override
	Destructor. More...

void	score (core::scoring::func::XYZ_Func const &, EnergyMap const &, EnergyMap &) const override
	Implemented because the base class requires it; not used by a sequence constraint. More...

core::Real	dist (core::scoring::func::XYZ_Func const &) const override
	Implemented because the base class requires it; not used by a sequence constraint. More...

void	fill_f1_f2 (core::id::AtomID const &, core::scoring::func::XYZ_Func const &, Vector &, Vector &, EnergyMap const &) const override
	Implemented because the base class requires it; not used by a sequence constraint. More...

core::Size	natoms () const override
	Implemented because the base class requires it; not used by a sequence constraint. More...

core::id::AtomID const &	atom (core::Size const ) const override
	Implemented because the base class requires it; not used by a sequence constraint. More...

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

	~Constraint () override
	Virtual destructor. More...

virtual ConstraintOP	clone (func::FuncOP) const
	Clone the constraint, but where a new Func object is to be used instead. More...

virtual ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map) const
	Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More...

virtual utility::vector1 < core::Size >	residues () const
	Returns the pose numbers of the residues involved in this constraint, in no particular order. More...

virtual void	read_constraint (std::istream &, core::pose::Pose const &)
	This method is totally redundant with read_def YAY DON'T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL. More...

ScoreType const &	score_type () const
	Returns the ScoreType that this Constraint object will use. More...

virtual void	read_data (std::istream &)
	initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More...

virtual Real	score (pose::Pose const &pose) const
	Returns the unweighted score of this constraint computed over the given pose. More...

virtual Real	score (pose::Pose const &pose, EnergyMap const &weights) const
	Returns the weighted score of this constraint computed over the given pose. More...

virtual Real	dist (core::pose::Pose const &) const
	return the raw "distance" before that distance is handed to the FUNC object More...

virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

virtual void	setup_for_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const

virtual void	setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const

virtual void	show (std::ostream &) const
	This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms. More...

virtual void	show_def (std::ostream &, pose::Pose const &) const
	Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def. More...

virtual void	read_def (std::istream &, pose::Pose const &, core::scoring::func::FuncFactory const &)
	Reads the definition of a Constraint from the given std::istream, using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. More...

virtual void	steal_def (pose::Pose const &)
	take coordinates, distances, angles, etc from given pose More...

std::string	to_string () const
	Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...

virtual Size	show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) const
	Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ... More...

virtual core::scoring::func::Func const &	get_func () const
	Returns the func::Func object associated with this Constraint object. More...

bool	operator!= (Constraint const &other) const
	Inequality operator to test whether two constraints are not functionally identical. More...

virtual core::Size	choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)

virtual core::Size	effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const

Private Attributes
utility::vector1< std::pair < Real, std::string > >	helper_weights_

Real	upper_bound_

Real	lower_bound_

Real	penalty_per_unit_

Additional Inherited Members
Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID	AtomID

Constructor & Destructor Documentation

core::pack::guidance_scoreterms::sap::SapMathConstraint::SapMathConstraint ( )

Constructor.

core::pack::guidance_scoreterms::sap::SapMathConstraint::SapMathConstraint ( SapMathConstraint const & src )

Copy constructor.

core::pack::guidance_scoreterms::sap::SapMathConstraint::~SapMathConstraint ( )

overridedefault

Destructor.

Member Function Documentation

void core::pack::guidance_scoreterms::sap::SapMathConstraint::add_constraint	(	Real	weight,
		std::string const &	name
	)

References helper_weights_.

Referenced by protocols::simple_moves::AddSapMathConstraintMover::add_constraint().

core::scoring::constraints::ConstraintOP core::pack::guidance_scoreterms::sap::SapMathConstraint::clone ( ) const

overridevirtual

Clone operator.

Implements core::scoring::constraints::Constraint.

Referenced by protocols::simple_moves::AddSapMathConstraintMover::apply().

Real core::pack::guidance_scoreterms::sap::SapMathConstraint::get_math_result ( utility::vector1< std::pair< Real, SapConstraintHelperCOP > > const & parsed_helpers ) const

Referenced by get_score().

Real core::pack::guidance_scoreterms::sap::SapMathConstraint::get_score ( utility::vector1< std::pair< Real, SapConstraintHelperCOP > > const & parsed_helpers ) const

References get_math_result(), lower_bound_, penalty_per_unit_, and upper_bound_.

void core::pack::guidance_scoreterms::sap::SapMathConstraint::lower_bound ( Real lower )

References lower_bound_.

Referenced by protocols::simple_moves::AddSapMathConstraintMover::set_lower_bound().

SapMathConstraint & core::pack::guidance_scoreterms::sap::SapMathConstraint::operator= ( SapMathConstraint const & other )

References helper_weights_, lower_bound_, penalty_per_unit_, and upper_bound_.

bool core::pack::guidance_scoreterms::sap::SapMathConstraint::operator== ( scoring::constraints::Constraint const & ) const

overridevirtual

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

Implements core::scoring::constraints::Constraint.

References same_type_as_me().

utility::vector1< std::pair< Real, SapConstraintHelperCOP > > core::pack::guidance_scoreterms::sap::SapMathConstraint::parse_helpers ( utility::vector1< SapConstraintHelperCOP > const & helpers ) const

References helper_weights_.

void core::pack::guidance_scoreterms::sap::SapMathConstraint::penalty_per_unit ( Real penalty )

References penalty_per_unit_.

Referenced by protocols::simple_moves::AddSapMathConstraintMover::set_penalty_per_unit().

scoring::constraints::ConstraintOP core::pack::guidance_scoreterms::sap::SapMathConstraint::remap_resid ( core::id::SequenceMapping const & ) const

inlineoverridevirtual

apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

Reimplemented from core::scoring::constraints::Constraint.

bool core::pack::guidance_scoreterms::sap::SapMathConstraint::same_type_as_me ( scoring::constraints::Constraint const & other ) const

overridevirtual

Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

Implements core::scoring::constraints::Constraint.

Referenced by operator==().

void core::pack::guidance_scoreterms::sap::SapMathConstraint::upper_bound ( Real upper )

References upper_bound_.

Referenced by protocols::simple_moves::AddSapMathConstraintMover::set_upper_bound().