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core::scoring::aa_composition_energy::SequenceConstraint Class Reference

#include <SequenceConstraint.hh>

Inheritance diagram for core::scoring::aa_composition_energy::SequenceConstraint:
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Public Member Functions

 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 () const =0
 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...
 
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 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...
 
virtual bool operator== (Constraint const &) const =0
 Equality operator to test whether two constraints are functionally identical. More...
 
bool operator!= (Constraint const &other) const
 Inequality operator to test whether two constraints are not functionally identical. More...
 
virtual bool same_type_as_me (Constraint const &other) const =0
 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...
 
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

core::id::AtomID dummy_atomid_
 Silly fake atomID necessary for the atom() function that all Constraints have to implement. More...
 

Additional Inherited Members

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

Constructor & Destructor Documentation

core::scoring::aa_composition_energy::SequenceConstraint::SequenceConstraint ( core::scoring::ScoreType const &  t)

Constructor.

core::scoring::aa_composition_energy::SequenceConstraint::SequenceConstraint ( SequenceConstraint const &  src)

Copy constructor.

core::scoring::aa_composition_energy::SequenceConstraint::~SequenceConstraint ( )
overridedefault

Destructor.

Member Function Documentation

core::id::AtomID const& core::scoring::aa_composition_energy::SequenceConstraint::atom ( core::Size  const) const
inlineoverridevirtual

Implemented because the base class requires it; not used by a sequence constraint.

Always returns AtomID(0,0).

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

References dummy_atomid_.

core::Real core::scoring::aa_composition_energy::SequenceConstraint::dist ( core::scoring::func::XYZ_Func const &  ) const
inlineoverridevirtual

Implemented because the base class requires it; not used by a sequence constraint.

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

void core::scoring::aa_composition_energy::SequenceConstraint::fill_f1_f2 ( core::id::AtomID const &  ,
core::scoring::func::XYZ_Func const &  ,
Vector ,
Vector ,
EnergyMap const &   
) const
inlineoverridevirtual

Implemented because the base class requires it; not used by a sequence constraint.

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

core::Size core::scoring::aa_composition_energy::SequenceConstraint::natoms ( ) const
inlineoverridevirtual

Implemented because the base class requires it; not used by a sequence constraint.

Always returns zero.

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

void core::scoring::aa_composition_energy::SequenceConstraint::score ( core::scoring::func::XYZ_Func const &  ,
EnergyMap const &  ,
EnergyMap  
) const
inlineoverridevirtual

Implemented because the base class requires it; not used by a sequence constraint.

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

Member Data Documentation

core::id::AtomID core::scoring::aa_composition_energy::SequenceConstraint::dummy_atomid_
private

Silly fake atomID necessary for the atom() function that all Constraints have to implement.

Not used for anything.

Referenced by atom().


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