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core::scoring::constraints::Constraint Class Referenceabstract

Actually a restraint, like a virtual rubber band between a pair of atoms. More...

#include <Constraint.hh>

Inheritance diagram for core::scoring::constraints::Constraint:
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Public Types

typedef id::AtomID AtomID
 

Public Member Functions

 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 Size natoms () const =0
 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...
 
virtual AtomID const & atom (Size const index) const =0
 Returns the AtomID referred to by index. 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 void score (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const =0
 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...
 
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 core::Real dist (core::scoring::func::XYZ_Func const &) const =0
 return the raw "distance" before that distance is handed to the FUNC object 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 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 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 Member Functions

void unimplemented_method_error (std::string const &method_name) const
 Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those inside of mini. More...
 

Private Attributes

ScoreType const score_type_
 

Detailed Description

Actually a restraint, like a virtual rubber band between a pair of atoms.

All Constraints are expected to be immutable once created, meaning their internal data (state) should not change over their lifetime. This allows Constraints to be shared between copies of Poses (e.g. in Monte Carlo), and is important for both speed (with thousands of constraints) and correctness.

To "change" a constraint, remove the old one and add a new and different one. The steal() methods have been removed because it is incompatible with the idea of immutable constraints.

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::constraints::Constraint::Constraint ( ScoreType const &  t)

Constructor for Constraint class.

core::scoring::constraints::Constraint::~Constraint ( )
overridedefault

Virtual destructor.

Member Function Documentation

virtual AtomID const& core::scoring::constraints::Constraint::atom ( Size const  index) const
pure virtual

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.

Implemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, protocols::constraints_additional::BindingSiteConstraint, core::scoring::constraints::LocalCoordinateConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::MultiConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::aa_composition_energy::SequenceConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::BackboneStubLinearConstraint, protocols::pockets::PocketConstraint, and core::pack::dunbrack::DunbrackConstraint.

Referenced by protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), core::scoring::constraints::cst_eq(), and residues().

core::Size core::scoring::constraints::Constraint::choose_effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  sp,
numeric::random::RandomGenerator &   
)
virtual
virtual ConstraintOP core::scoring::constraints::Constraint::clone ( ) const
pure virtual

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.

Implemented in core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::CoordinateConstraint, protocols::pockets::PocketConstraint, core::pack::dunbrack::RotamerConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::MultiConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::pack::guidance_scoreterms::sap::SapConstraint, core::pack::guidance_scoreterms::sap::SapMathConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::FabConstraint, core::scoring::aa_composition_energy::AACompositionConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::mhc_epitope_energy::MHCEpitopeConstraint, core::scoring::netcharge_energy::NetChargeConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::DistancePairConstraint, and core::pack::dunbrack::DunbrackConstraint.

ConstraintOP core::scoring::constraints::Constraint::clone ( func::FuncOP  ) const
virtual
virtual core::Real core::scoring::constraints::Constraint::dist ( core::scoring::func::XYZ_Func const &  ) const
pure virtual

return the raw "distance" before that distance is handed to the FUNC object

  • If such a distance doesn't make sense for this constraint, just return 0

Implemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::NonResidueTypeConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::ConstantConstraint, protocols::pockets::PocketConstraint, core::scoring::constraints::BasePairConstraint, core::pack::dunbrack::DunbrackConstraint, core::scoring::aa_composition_energy::SequenceConstraint, and core::scoring::constraints::BigBinConstraint.

Referenced by dist(), and protocols::sic_dock::ConstraintSetScore::score().

Real core::scoring::constraints::Constraint::dist ( core::pose::Pose const &  pose) const
virtual

return the raw "distance" before that distance is handed to the FUNC object

  • If such a distance doesn't make sense for this constraint, just return 0

Reimplemented in core::scoring::constraints::AtomPairConstraint.

References core::pose::Pose::conformation(), and dist().

core::Size core::scoring::constraints::Constraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  ) const
virtual
virtual void core::scoring::constraints::Constraint::fill_f1_f2 ( AtomID const &  atom,
core::scoring::func::XYZ_Func const &  xyz_func,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
pure virtual

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!)

Implemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::ConstantConstraint, core::pack::dunbrack::DunbrackConstraint, core::scoring::aa_composition_energy::SequenceConstraint, and core::scoring::constraints::BigBinConstraint.

core::scoring::func::Func const & core::scoring::constraints::Constraint::get_func ( ) const
virtual
virtual Size core::scoring::constraints::Constraint::natoms ( ) const
pure virtual

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.

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.

Implemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::LocalCoordinateConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::BigBinConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::aa_composition_energy::SequenceConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::ResidueCouplingConstraint, protocols::pockets::PocketConstraint, and core::pack::dunbrack::DunbrackConstraint.

Referenced by protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), core::scoring::constraints::cst_eq(), and residues().

bool core::scoring::constraints::Constraint::operator!= ( Constraint const &  other) const

Inequality operator to test whether two constraints are not functionally identical.

virtual bool core::scoring::constraints::Constraint::operator== ( Constraint const &  ) const
pure virtual

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.

Implemented in core::scoring::constraints::RTConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ResidueTypeConstraint, protocols::pockets::PocketConstraint, core::pack::dunbrack::RotamerConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::FabConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::pack::guidance_scoreterms::sap::SapConstraint, core::pack::guidance_scoreterms::sap::SapMathConstraint, core::scoring::constraints::AmbiguousNMRConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::aa_composition_energy::AACompositionConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, core::scoring::mhc_epitope_energy::MHCEpitopeConstraint, core::scoring::netcharge_energy::NetChargeConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, and core::pack::dunbrack::DunbrackConstraint.

void core::scoring::constraints::Constraint::read_constraint ( std::istream &  ,
core::pose::Pose const &   
)
virtual

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.

References unimplemented_method_error().

void core::scoring::constraints::Constraint::read_data ( std::istream &  )
virtual

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,

void core::scoring::constraints::Constraint::read_def ( std::istream &  ,
pose::Pose const &  ,
core::scoring::func::FuncFactory const &   
)
virtual

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.

Reimplemented in core::scoring::constraints::AtomPairConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::pack::dunbrack::DunbrackConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::KofNConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::FabConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, protocols::pockets::PocketConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, and core::scoring::constraints::DistancePairConstraint.

References unimplemented_method_error().

ConstraintOP core::scoring::constraints::Constraint::remap_resid ( core::id::SequenceMapping const &  ) const
virtual

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.

Reimplemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, protocols::constraints_additional::BindingSiteConstraint, core::scoring::constraints::NamedAtomPairConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::SequenceProfileConstraint, core::pack::guidance_scoreterms::sap::SapMathConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::ResidueTypeConstraint, core::scoring::constraints::KofNConstraint, core::pack::guidance_scoreterms::sap::SapConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, and core::scoring::constraints::BasePairConstraint.

References unimplemented_method_error().

ConstraintOP core::scoring::constraints::Constraint::remapped_clone ( pose::Pose const &  ,
pose::Pose const &  ,
id::SequenceMappingCOP  map = nullptr 
) const
virtual
utility::vector1< core::Size > core::scoring::constraints::Constraint::residues ( ) const
virtual
virtual bool core::scoring::constraints::Constraint::same_type_as_me ( Constraint const &  other) const
pure virtual

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.

Implemented in core::scoring::constraints::RTConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ResidueTypeConstraint, protocols::pockets::PocketConstraint, core::pack::dunbrack::RotamerConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::FabConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::pack::guidance_scoreterms::sap::SapConstraint, core::pack::guidance_scoreterms::sap::SapMathConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::BackboneStubLinearConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::AmbiguousNMRConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::aa_composition_energy::AACompositionConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::SiteConstraint, core::scoring::mhc_epitope_energy::MHCEpitopeConstraint, core::scoring::netcharge_energy::NetChargeConstraint, core::scoring::constraints::SiteConstraintResidues, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::ConstantConstraint, and core::pack::dunbrack::DunbrackConstraint.

Referenced by core::pack::dunbrack::DunbrackConstraint::operator==(), core::scoring::constraints::BigBinConstraint::operator==(), core::scoring::constraints::ConstantConstraint::operator==(), core::scoring::mhc_epitope_energy::MHCEpitopeConstraint::operator==(), core::scoring::constraints::DihedralPairConstraint::operator==(), core::scoring::constraints::DihedralConstraint::operator==(), core::scoring::constraints::AmbiguousNMRConstraint::operator==(), core::scoring::constraints::BackboneStubLinearConstraint::operator==(), core::scoring::constraints::AngleConstraint::operator==(), protocols::constraints_additional::SequenceCouplingConstraint::operator==(), core::scoring::constraints::SequenceProfileConstraint::operator==(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::operator==(), core::scoring::constraints::MembraneSpanConstraint::operator==(), core::scoring::constraints::MembraneSpanTermZConstraint::operator==(), core::scoring::constraints::AtomPairConstraint::operator==(), core::scoring::constraints::BasePairConstraint::operator==(), core::scoring::constraints::ResidueCouplingConstraint::operator==(), core::scoring::constraints::LocalCoordinateConstraint::operator==(), core::scoring::constraints::MultiConstraint::operator==(), protocols::constraints_additional::COMCoordinateConstraint::operator==(), protocols::constraints_additional::BindingSiteConstraint::operator==(), core::pack::dunbrack::RotamerConstraint::operator==(), core::scoring::constraints::ResidueTypeConstraint::operator==(), protocols::pockets::PocketConstraint::operator==(), core::scoring::constraints::BackboneStubConstraint::operator==(), core::scoring::constraints::ResidueTypeLinkingConstraint::operator==(), core::scoring::constraints::CoordinateConstraint::operator==(), core::scoring::constraints::NonResidueTypeConstraint::operator==(), core::scoring::constraints::DistancePairConstraint::operator==(), and core::scoring::constraints::RTConstraint::operator==().

virtual void core::scoring::constraints::Constraint::score ( core::scoring::func::XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
pure virtual

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.

Implemented in core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::SequenceProfileConstraint, core::scoring::constraints::LocalCoordinateConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::ResidueTypeConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::NonResidueTypeConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::BasePairConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::ConstantConstraint, protocols::pockets::PocketConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::aa_composition_energy::SequenceConstraint, core::scoring::constraints::BigBinConstraint, and core::pack::dunbrack::DunbrackConstraint.

Referenced by protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy(), and score().

Real core::scoring::constraints::Constraint::score ( pose::Pose const &  pose) const
virtual

Returns the unweighted score of this constraint computed over the given pose.

Reimplemented in core::scoring::constraints::AtomPairConstraint.

References core::scoring::n_score_types, and score().

Real core::scoring::constraints::Constraint::score ( pose::Pose const &  pose,
EnergyMap const &  weights 
) const
virtual

Returns the weighted score of this constraint computed over the given pose.

References core::pose::Pose::conformation(), and score().

ScoreType const& core::scoring::constraints::Constraint::score_type ( ) const
inline

Returns the ScoreType that this Constraint object will use.

References score_type_.

Referenced by core::scoring::constraints::AtomPairConstraint::clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::clone(), protocols::constraints_additional::BindingSiteConstraint::clone(), core::scoring::constraints::CoordinateConstraint::clone(), core::scoring::constraints::RTConstraint::clone(), protocols::pockets::PocketConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::DistancePairConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::RTConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::map_to_CEN(), core::scoring::constraints::DihedralPairConstraint::operator==(), core::scoring::constraints::DihedralConstraint::operator==(), core::scoring::constraints::AngleConstraint::operator==(), core::scoring::constraints::AtomPairConstraint::operator==(), core::scoring::constraints::MembraneSpanConstraint::operator==(), core::scoring::constraints::MembraneSpanTermZConstraint::operator==(), core::scoring::constraints::LocalCoordinateConstraint::operator==(), core::scoring::constraints::MultiConstraint::operator==(), core::scoring::constraints::ResidueTypeConstraint::operator==(), core::scoring::constraints::ResidueTypeLinkingConstraint::operator==(), core::scoring::constraints::CoordinateConstraint::operator==(), core::scoring::constraints::DistancePairConstraint::operator==(), core::scoring::constraints::RTConstraint::operator==(), core::scoring::constraints::NamedAngleConstraint::remap_resid(), core::scoring::constraints::NamedDihedralConstraint::remap_resid(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::NamedAtomPairConstraint::remap_resid(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::NamedAngleConstraint::remapped_clone(), core::scoring::constraints::NamedDihedralConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::RTConstraint::remapped_clone(), core::pack::dunbrack::DunbrackConstraint::score(), core::scoring::constraints::DistancePairConstraint::score(), protocols::pockets::PocketConstraint::score(), core::scoring::constraints::ConstantConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::AmbiguousNMRConstraint::score(), core::scoring::constraints::BackboneStubLinearConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), core::scoring::constraints::NamedAngleConstraint::score(), core::scoring::constraints::NamedDihedralConstraint::score(), core::scoring::constraints::ResidueCouplingConstraint::score(), core::scoring::constraints::MembraneSpanConstraint::score(), core::scoring::constraints::MembraneSpanTermZConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::NonResidueTypeConstraint::score(), protocols::constraints_additional::BindingSiteConstraint::score(), protocols::constraints_additional::COMCoordinateConstraint::score(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::score(), core::scoring::constraints::AngleConstraint::score(), core::pack::dunbrack::RotamerConstraint::score(), core::scoring::constraints::ResidueTypeConstraint::score(), core::scoring::constraints::BackboneStubConstraint::score(), core::scoring::constraints::ResidueTypeLinkingConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::scoring::constraints::RTConstraint::score(), and core::scoring::constraints::CoordinateConstraint::score().

void core::scoring::constraints::Constraint::setup_for_derivatives ( core::scoring::func::XYZ_Func const &  ,
ScoreFunction const &   
) const
virtual
void core::scoring::constraints::Constraint::setup_for_scoring ( core::scoring::func::XYZ_Func const &  ,
ScoreFunction const &   
) const
virtual
void core::scoring::constraints::Constraint::show ( std::ostream &  ) const
virtual

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 in core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::RTConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::DihedralPairConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::DistancePairConstraint, core::scoring::constraints::BasePairConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::ResidueTypeLinkingConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::pack::dunbrack::DunbrackConstraint, core::scoring::constraints::NonResidueTypeConstraint, core::scoring::constraints::ResidueTypeConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::scoring::constraints::ResidueCouplingConstraint, core::scoring::constraints::MembraneSpanConstraint, core::scoring::constraints::MembraneSpanTermZConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::SiteConstraintResidues, and core::scoring::constraints::FabConstraint.

References unimplemented_method_error().

Referenced by core::scoring::constraints::operator<<(), core::scoring::constraints::Constraints::show(), and to_string().

void core::scoring::constraints::Constraint::show_def ( std::ostream &  ,
pose::Pose const &   
) const
virtual

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 in core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AngleConstraint, core::scoring::constraints::AtomPairConstraint, protocols::constraints_additional::BindingSiteConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::NamedAtomPairConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::mhc_epitope_energy::MHCEpitopeConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::KofNConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::scoring::aa_composition_energy::AACompositionConstraint, core::scoring::netcharge_energy::NetChargeConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::BasePairConstraint, and protocols::pockets::PocketConstraint.

References unimplemented_method_error().

Referenced by core::scoring::constraints::print_atom_pair_constraints(), and core::scoring::constraints::Constraints::show_definition().

Size core::scoring::constraints::Constraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1 
) const
virtual
void core::scoring::constraints::Constraint::steal_def ( pose::Pose const &  )
virtual

take coordinates, distances, angles, etc from given pose

Reimplemented in core::scoring::constraints::CoordinateConstraint, and core::scoring::constraints::LocalCoordinateConstraint.

References unimplemented_method_error().

std::string core::scoring::constraints::Constraint::to_string ( ) const

Convenience function, returns the results of show() as a string. Not to be overriden by derived classes.

References core::conformation::membrane::out, and show().

std::string core::scoring::constraints::Constraint::type ( ) const
virtual

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

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint, protocols::constraints_additional::BindingSiteConstraint, core::scoring::constraints::RTConstraint, protocols::constraints_additional::COMCoordinateConstraint, core::scoring::constraints::AmbiguousNMRDistanceConstraint, core::scoring::constraints::AtomPairConstraint, core::scoring::constraints::CoordinateConstraint, core::scoring::constraints::MultiConstraint, core::scoring::constraints::SequenceProfileConstraint, protocols::constraints_additional::SequenceCouplingConstraint, protocols::constraints_additional::AmbiguousMultiConstraint, core::scoring::constraints::KofNConstraint, protocols::constraints_additional::SequenceCoupling1BDConstraint, core::scoring::constraints::AmbiguousConstraint, core::scoring::constraints::BasePairConstraint, core::scoring::constraints::LocalCoordinateConstraint, core::pack::dunbrack::RotamerConstraint, core::scoring::constraints::AmbiguousNMRConstraint, core::scoring::constraints::SiteConstraint, core::scoring::constraints::FabConstraint, core::scoring::constraints::SiteConstraintResidues, core::scoring::constraints::AngleConstraint, core::scoring::constraints::ConstantConstraint, core::scoring::constraints::NamedDihedralConstraint, core::scoring::constraints::NamedAngleConstraint, core::scoring::constraints::BigBinConstraint, core::scoring::constraints::DihedralConstraint, core::scoring::constraints::DihedralPairConstraint, core::scoring::constraints::BackboneStubConstraint, core::scoring::constraints::BackboneStubLinearConstraint, core::scoring::constraints::DistancePairConstraint, protocols::pockets::PocketConstraint, and core::pack::dunbrack::DunbrackConstraint.

Referenced by core::scoring::constraints::print_atom_pair_constraints(), and unimplemented_method_error().

void core::scoring::constraints::Constraint::unimplemented_method_error ( std::string const &  method_name) const
private

Utility method for producing useful error messages and exiting from program. Declared const which is funny, because exiting the program certainly changes the state of this object! This might be replaced with exception handling if we ever start using those inside of mini.

References type().

Referenced by clone(), get_func(), read_constraint(), read_def(), remap_resid(), remapped_clone(), show(), show_def(), and steal_def().

Member Data Documentation

ScoreType const core::scoring::constraints::Constraint::score_type_
private

Referenced by score_type().


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