#include <NamedAngleConstraint.hh>

Inheritance diagram for core::scoring::constraints::NamedAngleConstraint:

Public Member Functions
	NamedAngleConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, id::NamedAtomID const &a3, func::FuncOP func, ScoreType scoretype=angle_constraint)

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

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...

ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=nullptr) 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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes. More...

ConstraintOP	remap_resid (core::id::SequenceMapping const &seqmap) const override
	This overrride updates the sequence numbering but not the atom names. More...

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

bool	same_type_as_me (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...

void	show_def (std::ostream &out, pose::Pose const &pose) 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...

void	show_def_nopose (std::ostream &out) const

void	read_def (std::istream &in, pose::Pose const &pose, func::FuncFactory const &func_factory) override

void	score (func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override
	compute score More...

void	setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override

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...

Public Member Functions inherited from core::scoring::constraints::AngleConstraint
	AngleConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, core::scoring::func::FuncOP func_in, ScoreType scotype=angle_constraint)
	Constructor. More...

	AngleConstraint (core::scoring::func::FuncOP func_in, ScoreType scoretype=angle_constraint)
	Constructor without atom IDs – if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid! More...

Real	score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
	compute score More...

virtual core::Real	score (conformation::Conformation const &) const

Real	angle (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
	compute More...

void	fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
	compute atom deriv More...

Size	natoms () const override
	number of atoms — always 3 for angles More...

AtomID const &	atom (Size const n) const override
	return AtomID for atom 1,2,3 More...

Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1) const override
	output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 ) 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...

core::scoring::func::Func const &	get_func () const override
	Returns the func::Func object associated with this Constraint object. More...

Real	func (Real const theta) const
	evaluate func at theta More...

Real	dfunc (Real const theta) const
	evaluate dfunc at theta More...

void	p1_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const

void	p2_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const

AtomID const &	atom1 () const

AtomID const &	atom2 () const

AtomID const &	atom3 () 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 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 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_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const

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...

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

Protected Member Functions
	NamedAngleConstraint (NamedAngleConstraint const &src)

Protected Member Functions inherited from core::scoring::constraints::AngleConstraint
	AngleConstraint (AngleConstraint const &src)
	Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...

func::FuncCOP	func () const
	const access to func More...

void	set_func (func::FuncOP f)
	set func More...

void	atom1 (AtomID newid) const

void	atom2 (AtomID newid) const

void	atom3 (AtomID newid) const

Private Attributes
id::NamedAtomID	named_atom1_

id::NamedAtomID	named_atom2_

id::NamedAtomID	named_atom3_

core::Size	type1_id_

core::Size	type2_id_

core::Size	type3_id_

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

Static Public Member Functions inherited from core::scoring::constraints::AngleConstraint
static void	p1_theta_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &f1, Vector &f2)

static void	helper (Vector const &M, Vector const &w, Vector &F1, Vector &F2)

Constructor & Destructor Documentation

core::scoring::constraints::NamedAngleConstraint::NamedAngleConstraint	(	id::NamedAtomID const &	a1,
		id::NamedAtomID const &	a2,
		id::NamedAtomID const &	a3,
		func::FuncOP	func,
		ScoreType	scoretype = `angle_constraint`
	)

Referenced by clone(), and remap_resid().

core::scoring::constraints::NamedAngleConstraint::NamedAngleConstraint ( NamedAngleConstraint const & src )

protecteddefault

Member Function Documentation

ConstraintOP core::scoring::constraints::NamedAngleConstraint::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::AngleConstraint.

References NamedAngleConstraint().

Referenced by remap_resid().

core::Real core::scoring::constraints::NamedAngleConstraint::dist ( core::scoring::func::XYZ_Func const & ) const

overridevirtual

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 from core::scoring::constraints::AngleConstraint.

References core::scoring::constraints::AngleConstraint::angle(), core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), and protocols::kinmatch::xyz().

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

overridevirtual

possibility to compare constraint according to data and not just pointers

Reimplemented from core::scoring::constraints::AngleConstraint.

References named_atom1_, named_atom2_, named_atom3_, type1_id_, type2_id_, and type3_id_.

void core::scoring::constraints::NamedAngleConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		func::FuncFactory const &	func_factory
	)

overridevirtual

one line definition "AngleConstraint atom1 res1 atom2 res2 atom3 res3 function_type function_definition"

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::id::AtomID::atomno(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::pose::named_atom_id_to_atom_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::scoring::constraints::AngleConstraint::set_func(), core::pose::Pose::size(), and core::scoring::constraints::TR().

ConstraintOP core::scoring::constraints::NamedAngleConstraint::remap_resid ( core::id::SequenceMapping const & seqmap ) const

overridevirtual

This overrride updates the sequence numbering but not the atom names.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::id::NamedAtomID::atom(), clone(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, NamedAngleConstraint(), core::id::NamedAtomID::rsd(), and core::scoring::constraints::Constraint::score_type().

ConstraintOP core::scoring::constraints::NamedAngleConstraint::remapped_clone	(	pose::Pose const &	src,
		pose::Pose const &	dest,
		id::SequenceMappingCOP	map = `nullptr`
	)		const

overridevirtual

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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes.

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.

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::scoring::constraints::AngleConstraint::atom1(), core::scoring::constraints::AngleConstraint::atom2(), core::scoring::constraints::AngleConstraint::atom3(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::pose::named_atom_id_to_atom_id(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

bool core::scoring::constraints::NamedAngleConstraint::same_type_as_me ( 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::AngleConstraint.

void core::scoring::constraints::NamedAngleConstraint::score	(	func::XYZ_Func const &	xyz,
		EnergyMap const &	,
		EnergyMap &	emap
	)		const

overridevirtual

compute score

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), core::scoring::constraints::AngleConstraint::score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::NamedAngleConstraint::setup_for_scoring	(	func::XYZ_Func const &	xyz,
		ScoreFunction const &
	)		const

overridevirtual

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::id::NamedAtomID::atom(), core::scoring::constraints::AngleConstraint::atom1(), core::scoring::constraints::AngleConstraint::atom2(), core::scoring::constraints::AngleConstraint::atom3(), named_atom1_, named_atom2_, named_atom3_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), show_def_nopose(), core::scoring::constraints::TR(), type(), type1_id_, type2_id_, and type3_id_.

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

overridevirtual

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 from core::scoring::constraints::AngleConstraint.

References show_def_nopose().

void core::scoring::constraints::NamedAngleConstraint::show_def_nopose ( std::ostream & out ) const

References core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, and type().

Referenced by setup_for_scoring(), and show_def().

std::string core::scoring::constraints::NamedAngleConstraint::type ( ) const

overridevirtual

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

Reimplemented from core::scoring::constraints::AngleConstraint.

Referenced by setup_for_scoring(), and show_def_nopose().