#include <AngleConstraint.hh>

Inheritance diagram for core::scoring::constraints::AngleConstraint:

Public Member Functions
	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...

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...

bool	operator== (Constraint const &other) 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	read_def (std::istream &data, pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory) override
	read in constraint defiinition 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...

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

void	score (core::scoring::func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override
	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...

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

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...

ConstraintOP	remap_resid (core::id::SequenceMapping const &seqmap) 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...

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...

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...

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

Static Public Member Functions
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)

Protected Member Functions
	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
AtomID	atom1_

AtomID	atom2_

AtomID	atom3_

core::scoring::func::FuncOP	func_

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

Detailed Description

An Angular Constraint.

Constructor & Destructor Documentation

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.

Referenced by clone().

core::scoring::constraints::AngleConstraint::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!

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

protected

Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains.

Member Function Documentation

Real core::scoring::constraints::AngleConstraint::angle	(	Vector const &	xyz1,
		Vector const &	xyz2,
		Vector const &	xyz3
	)		const

compute

References core::scoring::constraints::TR().

Referenced by core::scoring::constraints::NamedAngleConstraint::dist(), dist(), and score().

id::AtomID const & core::scoring::constraints::AngleConstraint::atom ( Size const n ) const

overridevirtual

return AtomID for atom 1,2,3

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

References atom1_, atom2_, and atom3_.

Referenced by remapped_clone(), show(), and show_def().

AtomID const& core::scoring::constraints::AngleConstraint::atom1 ( ) const

inline

References atom1_.

Referenced by core::scoring::constraints::NamedAngleConstraint::remapped_clone(), remapped_clone(), and core::scoring::constraints::NamedAngleConstraint::setup_for_scoring().

void core::scoring::constraints::AngleConstraint::atom1 ( AtomID newid ) const

protected

References atom1_.

AtomID const& core::scoring::constraints::AngleConstraint::atom2 ( ) const

inline

References atom2_.

Referenced by core::scoring::constraints::NamedAngleConstraint::remapped_clone(), remapped_clone(), and core::scoring::constraints::NamedAngleConstraint::setup_for_scoring().

void core::scoring::constraints::AngleConstraint::atom2 ( AtomID newid ) const

protected

References atom2_.

AtomID const& core::scoring::constraints::AngleConstraint::atom3 ( ) const

inline

References atom3_.

Referenced by core::scoring::constraints::NamedAngleConstraint::remapped_clone(), remapped_clone(), and core::scoring::constraints::NamedAngleConstraint::setup_for_scoring().

void core::scoring::constraints::AngleConstraint::atom3 ( AtomID newid ) const

protected

References atom3_.

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

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References AngleConstraint().

Real core::scoring::constraints::AngleConstraint::dfunc ( Real const theta ) const

evaluate dfunc at theta

References func_.

Referenced by fill_f1_f2(), p1_deriv(), and p2_deriv().

core::Real core::scoring::constraints::AngleConstraint::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

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References angle(), atom1_, atom2_, atom3_, and protocols::kinmatch::xyz().

void core::scoring::constraints::AngleConstraint::fill_f1_f2	(	AtomID const &	atom,
		core::scoring::func::XYZ_Func const &	xyz,
		Vector &	F1,
		Vector &	F2,
		EnergyMap const &	weights
	)		const

overridevirtual

compute atom deriv

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

References atom1_, atom2_, atom3_, dfunc(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

Real core::scoring::constraints::AngleConstraint::func ( Real const theta ) const

evaluate func at theta

Previously private member functions made public so that in the absence of atom_ids, these functions could still be called externally.

References func_.

func::FuncCOP core::scoring::constraints::AngleConstraint::func ( ) const

protected

const access to func

References func_.

Referenced by core::scoring::constraints::NamedAngleConstraint::read_def(), core::scoring::constraints::NamedAngleConstraint::remap_resid(), core::scoring::constraints::NamedAngleConstraint::remapped_clone(), score(), and core::scoring::constraints::NamedAngleConstraint::show_def_nopose().

core::scoring::func::Func const& core::scoring::constraints::AngleConstraint::get_func ( ) const

inlineoverridevirtual

Returns the func::Func object associated with this Constraint object.

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

References func_.

void core::scoring::constraints::AngleConstraint::helper	(	Vector const &	M,
		Vector const &	w,
		Vector &	F1,
		Vector &	F2
	)

static

Referenced by p1_theta_deriv().

Size core::scoring::constraints::AngleConstraint::natoms ( ) const

inlineoverridevirtual

number of atoms — always 3 for angles

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

Referenced by show(), and show_def().

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

overridevirtual

possibility to compare constraint according to data and not just pointers

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom1_, atom2_, atom3_, func_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AngleConstraint::p1_deriv	(	Vector const &	p1,
		Vector const &	p2,
		Vector const &	p3,
		Vector &	F1,
		Vector &	F2
	)		const

References dfunc(), and p1_theta_deriv().

Referenced by core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair().

void core::scoring::constraints::AngleConstraint::p1_theta_deriv	(	Vector const &	p1,
		Vector const &	p2,
		Vector const &	p3,
		Vector &	f1,
		Vector &	f2
	)

static

References helper(), protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by p1_deriv(), and p2_deriv().

void core::scoring::constraints::AngleConstraint::p2_deriv	(	Vector const &	p1,
		Vector const &	p2,
		Vector const &	p3,
		Vector &	F1,
		Vector &	F2
	)		const

References dfunc(), and p1_theta_deriv().

Referenced by core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair().

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

overridevirtual

read in constraint defiinition

one line definition "Angle atom1 res1 atom2 res2 atom3 res3 function_type function_definition" SML: It appears to be reading the angle in radians, because score ultimately uses std:acos, which returns radians.

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom1_, atom2_, atom3_, core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), func_, core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::constraints::TR().

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

overridevirtual

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom1_, atom2_, atom3_, core::id::AtomID::atomno(), func_, and core::id::AtomID::rsd().

ConstraintOP core::scoring::constraints::AngleConstraint::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::Constraint.

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom(), atom1(), atom1_, atom2(), atom2_, atom3(), atom3_, core::conformation::atom_id_to_named_atom_id(), func_, core::conformation::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

bool core::scoring::constraints::AngleConstraint::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.

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

Referenced by operator==().

Real core::scoring::constraints::AngleConstraint::score	(	Vector const &	xyz1,
		Vector const &	xyz2,
		Vector const &	xyz3
	)		const

compute score

References angle(), and func().

Referenced by core::scoring::constraints::NamedAngleConstraint::score(), and score().

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

overridevirtual

compute score

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom1_, atom2_, atom3_, score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

core::Real core::scoring::constraints::AngleConstraint::score ( conformation::Conformation const & conf ) const

virtual

References atom1_, atom2_, atom3_, score(), and core::conformation::Conformation::xyz().

void core::scoring::constraints::AngleConstraint::set_func ( func::FuncOP f )

protected

set func

References func_.

Referenced by core::scoring::constraints::NamedAngleConstraint::read_def().

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

overridevirtual

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

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

void core::scoring::constraints::AngleConstraint::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::Constraint.

References atom(), func_, natoms(), and type().

void core::scoring::constraints::AngleConstraint::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::Constraint.

Reimplemented in core::scoring::constraints::NamedAngleConstraint.

References atom(), core::conformation::atom_id_to_named_atom_id(), func_, natoms(), and type().

Size core::scoring::constraints::AngleConstraint::show_violations	(	std::ostream &	out,
		pose::Pose const &	pose,
		Size	verbose_level,
		core::Real	threshold = `1`
	)		const

overridevirtual

output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 )

show violations of angular constraint. Control verbosity level between 1 .. 100 >80 : write MET 4 CA otherwise: compute angle and call func_->show_violations

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

References atom1_, atom2_, atom3_, core::id::AtomID::atomno(), core::pose::Pose::conformation(), func_, core::pose::Pose::residue_type(), and core::id::AtomID::rsd().