#include <MHCEpitopeConstraint.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopeConstraint:

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

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

	~MHCEpitopeConstraint () override
	Destructor. More...

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

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

bool	same_type_as_me (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	set_selector (select::residue_selector::ResidueSelectorCOP selector_in)
	Set the selector to be used by this constraint. More...

select::residue_selector::ResidueSelectorCOP	selector () const
	Const access to the selector. More...

void	set_selector_name (std::string const &selector_name)
	Stores the name of the selector used to mask the constraint. More...

std::string	get_selector_name ()
	Returns the name of the selector used to mask the constraint. More...

MHCEpitopeEnergySetupCOP	mhc_epitope_energy_setup () const
	Const access to the MHCEpitopeEnergySetup object. More...

void	initialize_from_file (std::string const &filename)
	Initialize the MHCEpitopeEnergySetup object from a file. More...

void	initialize_from_file_contents (std::string const &filecontents)
	Initialize the MHCEpitopeEnergySetup object from the contents of a file. More...

void	set_cst_weight (core::Real cst_weight)
	Set the cst_weight_. More...

core::Real	get_cst_weight () const
	Get the cst_weight_. More...

void	show_def (std::ostream &TO, pose::Pose const &pose) const override
	Print info on the constraint. 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 ConstraintOP	remap_resid (core::id::SequenceMapping const &) const
	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...

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	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
select::residue_selector::ResidueSelectorOP	selector_
	Owning pointer to a ResidueSelector. More...

MHCEpitopeEnergySetupOP	mhc_epitope_setup_
	MHCEpitopeEnergySetup object stored by this object. More...

core::Real	cst_weight_
	A weight score for a particular constraint. More...

std::string	cst_selector_name_ = "full pose"
	The name of the residue selector used to restrict the constraint to part of the pose. More...

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

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::MHCEpitopeConstraint ( )

Constructor.

core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::MHCEpitopeConstraint ( MHCEpitopeConstraint const & src )

Copy constructor.

References cst_weight_, get_cst_weight(), mhc_epitope_setup_, and selector_.

core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::~MHCEpitopeConstraint ( )

overridedefault

Destructor.

Member Function Documentation

core::scoring::constraints::ConstraintOP core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::clone ( ) const

overridevirtual

Clone operator.

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

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::get_cst_weight ( ) const

Get the cst_weight_.

References cst_weight_.

Referenced by MHCEpitopeConstraint().

std::string core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::get_selector_name ( )

inline

Returns the name of the selector used to mask the constraint.

References cst_selector_name_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::initialize_from_file ( std::string const & filename )

Initialize the MHCEpitopeEnergySetup object from a file.

References mhc_epitope_setup_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::initialize_from_file_contents ( std::string const & filecontents )

Initialize the MHCEpitopeEnergySetup object from the contents of a file.

Allows external code to initialize a constriant object without having the object read directly from disk.

References mhc_epitope_setup_.

MHCEpitopeEnergySetupCOP core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::mhc_epitope_energy_setup ( ) const

Const access to the MHCEpitopeEnergySetup object.

References mhc_epitope_setup_.

bool core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::operator== ( 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 cst_selector_name_, cst_weight_, mhc_epitope_setup_, same_type_as_me(), and selector_.

bool core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::same_type_as_me ( 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==().

select::residue_selector::ResidueSelectorCOP core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::selector ( ) const

Const access to the selector.

Returns a null pointer if no selector has been specified.

References selector_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::set_cst_weight ( core::Real cst_weight )

Set the cst_weight_.

References cst_weight_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::set_selector ( select::residue_selector::ResidueSelectorCOP selector_in )

Set the selector to be used by this constraint.

Clones the input.

References selector_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::set_selector_name ( std::string const & selector_name )

inline

Stores the name of the selector used to mask the constraint.

References cst_selector_name_.

void core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::show_def	(	std::ostream &	TO,
		pose::Pose const &	pose
	)		const

overridevirtual

Print info on the constraint.

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

References mhc_epitope_setup_, protocols::sic_dock::range(), and selector_.

Member Data Documentation

std::string core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::cst_selector_name_ = "full pose"

private

The name of the residue selector used to restrict the constraint to part of the pose.

Intended only for reporting purposes. Defaults to "full pose" to indicate no mask.

Referenced by get_selector_name(), operator==(), and set_selector_name().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::cst_weight_

private

A weight score for a particular constraint.

An additional weighting factor, beyond that set in the scorefunction, to reset the weight of a single constraint without changing the other predictors. Useful for increasing/decreasing the importance of one predictor over another.

Referenced by get_cst_weight(), MHCEpitopeConstraint(), operator==(), and set_cst_weight().