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core::scoring::constraints::ConstantConstraint Class Reference

A Constant Constraint. More...

#include <ConstantConstraint.hh>

Inheritance diagram for core::scoring::constraints::ConstantConstraint:
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Public Member Functions

 ConstantConstraint (func::FuncOP func_in, ScoreType scotype=constant_constraint)
 Constructor. More...
 
 ~ConstantConstraint () override
 
ConstraintOP clone () const override
 Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned. More...
 
bool operator== (Constraint const &other) const override
 Equality operator to test whether two constraints are functionally identical. More...
 
bool same_type_as_me (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...
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
Real score () const
 compute score More...
 
void score (func::XYZ_Func const &, EnergyMap const &, EnergyMap &emap) const override
 compute score More...
 
core::Real dist (core::scoring::func::XYZ_Func const &xyz) const override
 
void fill_f1_f2 (AtomID const &, func::XYZ_Func const &, Vector &F1, Vector &F2, EnergyMap const &) const override
 compute atom deriv More...
 
Size natoms () const override
 number of atoms — zero More...
 
AtomID const & atom (Size const n) const override
 Returns the AtomID referred to by index. More...
 
Size show_violations (std::ostream &, pose::Pose const &, Size, core::Real) const override
 output violation of constraint (none!) More...
 
void show (std::ostream &out) const override
 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...
 
void show_def (std::ostream &out, pose::Pose const &) const override
 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...
 
- 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 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 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
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
 

Protected Member Functions

 ConstantConstraint (ConstantConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...
 

Private Attributes

func::FuncOP func_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Detailed Description

A Constant Constraint.

Constructor & Destructor Documentation

core::scoring::constraints::ConstantConstraint::ConstantConstraint ( func::FuncOP  func_in,
ScoreType  scotype = constant_constraint 
)

Constructor.

Referenced by clone().

core::scoring::constraints::ConstantConstraint::~ConstantConstraint ( )
overridedefault
core::scoring::constraints::ConstantConstraint::ConstantConstraint ( ConstantConstraint const &  src)
protected

Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains.

Member Function Documentation

id::AtomID const & core::scoring::constraints::ConstantConstraint::atom ( Size const  index) const
overridevirtual

Returns the AtomID referred to by index.

Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.

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

ConstraintOP core::scoring::constraints::ConstantConstraint::clone ( ) const
overridevirtual

Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned.

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

References ConstantConstraint().

core::Real core::scoring::constraints::ConstantConstraint::dist ( core::scoring::func::XYZ_Func const &  xyz) const
overridevirtual

In this case, 0 is literally what's being passed to the func

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

void core::scoring::constraints::ConstantConstraint::fill_f1_f2 ( AtomID const &  ,
func::XYZ_Func const &  ,
Vector F1,
Vector F2,
EnergyMap const &   
) const
overridevirtual

compute atom deriv

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

Size core::scoring::constraints::ConstantConstraint::natoms ( ) const
overridevirtual

number of atoms — zero

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

bool core::scoring::constraints::ConstantConstraint::operator== ( 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 func_, same_type_as_me(), and core::scoring::constraints::Constraint::same_type_as_me().

bool core::scoring::constraints::ConstantConstraint::same_type_as_me ( 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==().

Real core::scoring::constraints::ConstantConstraint::score ( ) const

compute score

References func_.

Referenced by score().

void core::scoring::constraints::ConstantConstraint::score ( func::XYZ_Func const &  ,
EnergyMap const &  ,
EnergyMap emap 
) const
overridevirtual
void core::scoring::constraints::ConstantConstraint::show ( std::ostream &  ) const
overridevirtual

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.

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

References func_.

Referenced by show_def().

void core::scoring::constraints::ConstantConstraint::show_def ( std::ostream &  ,
pose::Pose const &   
) const
overridevirtual

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.

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

References show().

Size core::scoring::constraints::ConstantConstraint::show_violations ( std::ostream &  ,
pose::Pose const &  ,
Size  ,
core::Real   
) const
overridevirtual

output violation of constraint (none!)

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

std::string core::scoring::constraints::ConstantConstraint::type ( ) const
overridevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

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

Member Data Documentation

func::FuncOP core::scoring::constraints::ConstantConstraint::func_
private

Referenced by operator==(), score(), and show().


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