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protocols::constraints_additional::SequenceCoupling1BDConstraint Class Reference

#include <SequenceCoupling1BDConstraint.hh>

Inheritance diagram for protocols::constraints_additional::SequenceCoupling1BDConstraint:
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Public Types

typedef
core::sequence::SequenceCoupling 
SequenceCoupling
 
typedef
core::sequence::SequenceCouplingCOP 
SequenceCouplingCOP
 
typedef core::id::SequenceMapping SequenceMapping
 
typedef core::pose::Pose Pose
 
typedef
core::conformation::Conformation 
Conformation
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef
core::scoring::func::FuncFactory 
FuncFactory
 
typedef
core::scoring::func::XYZ_Func 
XYZ_Func
 
typedef
core::scoring::constraints::ConstraintOP 
ConstraintOP
 
- Public Types inherited from core::scoring::constraints::SequenceProfileConstraint
typedef
core::sequence::SequenceProfile 
SequenceProfile
 
typedef
core::sequence::SequenceProfileCOP 
SequenceProfileCOP
 
typedef core::id::SequenceMapping SequenceMapping
 
typedef core::pose::Pose Pose
 
typedef
core::conformation::Conformation 
Conformation
 
typedef core::scoring::EnergyMap EnergyMap
 
typedef
core::scoring::func::FuncFactory 
FuncFactory
 
typedef
core::scoring::func::XYZ_Func 
XYZ_Func
 
typedef
core::scoring::constraints::ConstraintOP 
ConstraintOP
 
- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Public Member Functions

 SequenceCoupling1BDConstraint ()
 
 SequenceCoupling1BDConstraint (Pose const &, core::Size, SequenceProfileCOP profile)
 
 SequenceCoupling1BDConstraint (core::Size, SequenceProfileCOP profile)
 
 ~SequenceCoupling1BDConstraint () 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== (core::scoring::constraints::Constraint const &other) const override
 Equality operator to test whether two constraints are functionally identical. More...
 
bool same_type_as_me (core::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...
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
void read_def (std::istream &, Pose const &, FuncFactory const &) override
 used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file) 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 score (XYZ_Func const &, EnergyMap const &, EnergyMap &) const override
 Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself. More...
 
void fill_f1_f2 (AtomID const &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const override
 
- Public Member Functions inherited from core::scoring::constraints::SequenceProfileConstraint
 SequenceProfileConstraint ()
 
 SequenceProfileConstraint (Pose const &, core::Size, SequenceProfileCOP profile=nullptr, core::id::SequenceMappingCOP mapping=nullptr)
 
 SequenceProfileConstraint (core::Size, SequenceProfileCOP profile=nullptr, core::id::SequenceMappingCOP mapping=nullptr)
 
 ~SequenceProfileConstraint () override
 
void show_def (std::ostream &, 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...
 
core::Size seqpos () const
 
void seqpos (core::Size seqpos)
 
void set_sequence_profile (SequenceProfileCOP profile, core::id::SequenceMappingCOP mapping=nullptr)
 
SequenceProfileCOP sequence_profile () const
 
core::id::SequenceMappingCOP profile_mapping () const
 
core::Size natoms () const override
 Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero. More...
 
AtomID const & atom (core::Size const ) const override
 Returns the AtomID referred to by index. More...
 
utility::vector1< core::Sizeresidues () const override
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
ConstraintOP remap_resid (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...
 
ConstraintOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map) const override
 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...
 
core::Real dist (core::chemical::AA aa) const
 
core::Real dist (core::scoring::func::XYZ_Func const &xyz) const override
 return the raw "distance" before that distance is handed to the FUNC object More...
 
void fill_f1_f2 (AtomID const &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const override
 
void weight (core::Real const w)
 
core::Real weight () const
 
- 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 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 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 fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0
 Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!) 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
 

Additional Inherited Members

- Protected Member Functions inherited from core::scoring::constraints::SequenceProfileConstraint
 SequenceProfileConstraint (SequenceProfileConstraint const &src)
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( )
protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( Pose const &  pose,
core::Size  numpos,
SequenceProfileCOP  profile 
)
protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( core::Size  numpos,
SequenceProfileCOP  profile 
)
protocols::constraints_additional::SequenceCoupling1BDConstraint::~SequenceCoupling1BDConstraint ( )
overridedefault

Member Function Documentation

ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::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.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

void protocols::constraints_additional::SequenceCoupling1BDConstraint::fill_f1_f2 ( AtomID const &  ,
XYZ_Func const &  ,
core::Vector ,
core::Vector ,
EnergyMap const &   
) const
override
bool protocols::constraints_additional::SequenceCoupling1BDConstraint::operator== ( core::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.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

References core::chemical::operator==().

void protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def ( std::istream &  is,
Pose const &  pose,
FuncFactory const &   
)
overridevirtual

used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)

one line definition "SequenceProfile resindex profilefilename" (profilefilename can also be set to "none" in the constraints file, and specified by -in::file::pssm)

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

References core::pack::dunbrack::c, core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile(), core::pose::Pose::size(), and protocols::constraints_additional::TR().

bool protocols::constraints_additional::SequenceCoupling1BDConstraint::same_type_as_me ( core::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.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

void protocols::constraints_additional::SequenceCoupling1BDConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
overridevirtual

Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

References protocols::cluster::calibur::aa, core::chemical::ResidueTypeBase::aa(), core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::sequence_profile(), protocols::constraints_additional::TR(), and core::conformation::Residue::type().

void protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.

References core::scoring::constraints::SequenceProfileConstraint::seqpos(), and core::scoring::constraints::SequenceProfileConstraint::sequence_profile().

std::string protocols::constraints_additional::SequenceCoupling1BDConstraint::type ( ) const
inlineoverridevirtual

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

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.


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