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core::scoring::mhc_epitope_energy::MHCEpitopeConstraint Class Reference

#include <MHCEpitopeConstraint.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopeConstraint:
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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(), core::scoring::constraints::Constraint::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().

MHCEpitopeEnergySetupOP core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::mhc_epitope_setup_
private
select::residue_selector::ResidueSelectorOP core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::selector_
private

Owning pointer to a ResidueSelector.

Optional; will serve as a mask for this MHCEpitopeConstraint if provided.

Referenced by MHCEpitopeConstraint(), operator==(), selector(), set_selector(), and show_def().


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