This class favors a particular rotamer at a particular position by reducing its Dunbrack energy. More...

#include <RotamerConstraint.hh>

Inheritance diagram for core::pack::dunbrack::RotamerConstraint:

Collaboration diagram for core::pack::dunbrack::RotamerConstraint:

Public Member Functions
virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

	RotamerConstraint (pose::Pose const &pose, Size seqpos)

virtual	~RotamerConstraint ()

virtual void	add_residue (conformation::Residue const &rsd)

virtual scoring::constraints::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...

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 index) const
	Returns the AtomID referred to by index. More...

virtual void	score (scoring::constraints::XYZ_Func const &xyz_func, scoring::EnergyMap const &weights, scoring::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, scoring::constraints::XYZ_Func const &xyz, Vector &F1, Vector &F2, scoring::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 void	show (std::ostream &out) const
	This gets used to compare one constraint to another, so it should uniquely reflect all the parameters. 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 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. 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 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...

virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison 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	seqpos_

std::string	rsd_type_name_

utility::vector1< AtomID >	atom_ids_

SingleResidueRotamerLibraryCAP	rotlib_

utility::vector1< ChiVector >	favored_rotamers_

utility::vector1< RotVector >	favored_rotamer_numbers_

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

Detailed Description

This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.

Specifically, the given rotamer well(s) receive a bonus equal to the difference between their minimum energy (for the ideal rotamer in this well) and the minimum energy of any rotamer (at the current phi,psi). This class is used to implement the scoring component of the -unboundrot flag; actually adding those rotamers to the library occurs in core/pack/rotamer_set/UnboundRotamersOperation.

Definition at line 54 of file RotamerConstraint.hh.

Constructor & Destructor Documentation

core::pack::dunbrack::RotamerConstraint::RotamerConstraint	(	pose::Pose const &	pose,
		Size	seqpos
	)

Definition at line 103 of file RotamerConstraint.cc.

References add_residue(), atom_ids_, core::pose::Pose::residue(), and seqpos_.

Referenced by clone().

core::pack::dunbrack::RotamerConstraint::~RotamerConstraint ( )

virtual

Definition at line 129 of file RotamerConstraint.cc.

Member Function Documentation

void core::pack::dunbrack::RotamerConstraint::add_residue ( conformation::Residue const & rsd)

virtual

Definition at line 133 of file RotamerConstraint.cc.

References core::conformation::Residue::chi(), favored_rotamer_numbers_, favored_rotamers_, core::chemical::ResidueType::name(), rot(), core::pack::dunbrack::rotamer_from_chi(), rsd_type_name_, and core::conformation::Residue::type().

Referenced by RotamerConstraint().

id::AtomID const & core::pack::dunbrack::RotamerConstraint::atom ( Size const index) const

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.

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

Definition at line 151 of file RotamerConstraint.cc.

References atom_ids_.

virtual scoring::constraints::ConstraintOP core::pack::dunbrack::RotamerConstraint::clone ( ) const

inlinevirtual

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 73 of file RotamerConstraint.hh.

References RotamerConstraint().

void core::pack::dunbrack::RotamerConstraint::fill_f1_f2	(	AtomID const &	atom,
		scoring::constraints::XYZ_Func const &	xyz_func,
		Vector &	F1,
		Vector &	F2,
		scoring::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 191 of file RotamerConstraint.cc.

Size core::pack::dunbrack::RotamerConstraint::natoms ( ) const

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.

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

Definition at line 144 of file RotamerConstraint.cc.

References atom_ids_.

void core::pack::dunbrack::RotamerConstraint::score	(	scoring::constraints::XYZ_Func const &	xyz_func,
		scoring::EnergyMap const &	weights,
		scoring::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 161 of file RotamerConstraint.cc.

References favored_rotamer_numbers_, core::scoring::constraints::XYZ_Func::residue(), rot(), core::pack::dunbrack::rotamer_from_chi(), rotlib_, rsd_type_name_, core::scoring::constraints::Constraint::score_type(), seqpos_, and core::pack::dunbrack::TR().