This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

#include <ResidueTypeLinkingConstraint.hh>

Inheritance diagram for core::scoring::constraints::ResidueTypeLinkingConstraint:

Collaboration diagram for core::scoring::constraints::ResidueTypeLinkingConstraint:

Public Types
typedef core::Real	Real

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

Public Member Functions
	ResidueTypeLinkingConstraint ()

	ResidueTypeLinkingConstraint (pose::Pose const &pose, Size seqpos1, Size seqpos2, Real bonus)

	ResidueTypeLinkingConstraint (pose::Pose const &pose, Size seqpos1, Size seqpos2, std::string AA1name, std::string AA2name, Real bonus)

virtual	~ResidueTypeLinkingConstraint ()

virtual Size	natoms () const
	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 ) const
	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...

void	show (std::ostream &out) 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...

bool	operator== (Constraint const &other) const
	possibility to compare constraint according to data and not just pointers More...

virtual void	score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
	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 void	fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
	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 ConstraintOP	clone () const
	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. More...

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

virtual	~Constraint ()
	Virtual destructor. More...

virtual ConstraintOP	clone (FuncOP) const

virtual ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=NULL) 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 void	read_constraint (std::istream &, core::pose::Pose const &)
	This method is totally redundant with read_def YAY. 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 core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object More...

virtual core::Real	dist (XYZ_Func const &) const

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 (XYZ_Func const &, ScoreFunction const &) const

virtual void	setup_for_derivatives (XYZ_Func const &, ScoreFunction const &) const

virtual Real	score (conformation::Conformation const &) const
	Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. 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 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 &, FuncFactory const &)

virtual void	steal_def (pose::Pose const &)

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 Func const &	get_func () const
	Returns the Func object associated with this Constraint object. More...

bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison 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
Size	seqpos1_

Size	seqpos2_

std::string	AA1name

std::string	AA2name

std::string	rsd1_type_name3_

std::string	rsd2_type_name3_

core::Real	bonus_

Detailed Description

This class favors a particular residue identity at a particular position by reducing its res_type energy.

Definition at line 34 of file ResidueTypeLinkingConstraint.hh.

Member Typedef Documentation

typedef core::Real core::scoring::constraints::ResidueTypeLinkingConstraint::Real

Definition at line 37 of file ResidueTypeLinkingConstraint.hh.

Constructor & Destructor Documentation

core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint ( )

Definition at line 36 of file ResidueTypeLinkingConstraint.cc.

Referenced by clone().

core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint	(	pose::Pose const &	pose,
		Size	seqpos1,
		Size	seqpos2,
		core::Real	bonus
	)

Definition at line 41 of file ResidueTypeLinkingConstraint.cc.

core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint	(	pose::Pose const &	pose,
		Size	seqpos1,
		Size	seqpos2,
		std::string	AA1name,
		std::string	AA2name,
		core::Real	bonus
	)

Definition at line 57 of file ResidueTypeLinkingConstraint.cc.

core::scoring::constraints::ResidueTypeLinkingConstraint::~ResidueTypeLinkingConstraint ( )

virtual

Definition at line 74 of file ResidueTypeLinkingConstraint.cc.

Member Function Documentation

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

inlinevirtual

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.

Definition at line 75 of file ResidueTypeLinkingConstraint.hh.

References core::id::BOGUS_ATOM_ID.

ConstraintOP core::scoring::constraints::ResidueTypeLinkingConstraint::clone ( ) const

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.

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

Definition at line 77 of file ResidueTypeLinkingConstraint.cc.

References ResidueTypeLinkingConstraint().

void core::scoring::constraints::ResidueTypeLinkingConstraint::fill_f1_f2	(	AtomID const &	atom,
		XYZ_Func const &	xyz_func,
		Vector &	F1,
		Vector &	F2,
		EnergyMap const &	weights
	)		const

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!)

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

Definition at line 168 of file ResidueTypeLinkingConstraint.cc.

virtual Size core::scoring::constraints::ResidueTypeLinkingConstraint::natoms ( ) const

inlinevirtual

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.

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

Definition at line 71 of file ResidueTypeLinkingConstraint.hh.

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

virtual

possibility to compare constraint according to data and not just pointers

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

Definition at line 116 of file ResidueTypeLinkingConstraint.cc.

References AA1name, AA2name, bonus_, rsd1_type_name3_, rsd2_type_name3_, core::scoring::constraints::Constraint::score_type(), seqpos1_, and seqpos2_.

utility::vector1< core::Size > core::scoring::constraints::ResidueTypeLinkingConstraint::residues ( ) const

virtual

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

Definition at line 83 of file ResidueTypeLinkingConstraint.cc.

References seqpos1_, and seqpos2_.

void core::scoring::constraints::ResidueTypeLinkingConstraint::score	(	XYZ_Func const &	xyz_func,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

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.

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

Definition at line 151 of file ResidueTypeLinkingConstraint.cc.

References bonus_, core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos1_, and seqpos2_.

void core::scoring::constraints::ResidueTypeLinkingConstraint::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 from core::scoring::constraints::Constraint.

Definition at line 91 of file ResidueTypeLinkingConstraint.cc.

References AA1name, AA2name, bonus_, rsd1_type_name3_, rsd2_type_name3_, seqpos1_, and seqpos2_.