An Angular Constraint. More...

#include <AngleConstraint.hh>

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...

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...

void	read_def (std::istream &data, pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory)
	read in constraint defiinition More...

virtual ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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...

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

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

	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...

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

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

AtomID const &	atom (Size const n) const
	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
	output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 ) More...

virtual 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...

void	show_def (std::ostream &out, pose::Pose const &pose) 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 core::scoring::func::Func const &	get_func () const
	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

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 (core::scoring::func::FuncOP) const

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 core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object More...

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

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 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	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	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...

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

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)

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`
	)

inline

Constructor.

Referenced by clone(), remap_resid(), and remapped_clone().

core::scoring::constraints::AngleConstraint::AngleConstraint	(	core::scoring::func::FuncOP	func_in,
		ScoreType	scoretype = `angle_constraint`
	)

inline

Constructor without atom IDs – if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid!

Member Function Documentation

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

virtual

return AtomID for atom 1,2,3

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

References atom1_, atom2_, atom3_, and utility_exit_with_message.

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

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

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

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

inline

evaluate dfunc at theta

References func_.

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

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

compute atom deriv

References numeric::deriv::angle_p1_deriv(), angle_p1_deriv(), numeric::deriv::angle_p2_deriv(), angle_p2_deriv(), atom1_, atom2_, atom3_, dfunc(), and core::scoring::constraints::Constraint::score_type().

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

inline

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_.

Referenced by score().

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

inlinevirtual

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

References cross().

Referenced by p1_theta_deriv().

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

inlinevirtual

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

virtual

possibility to compare constraint according to data and not just pointers

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

References atom1_, atom2_, atom3_, func_, 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 numeric::arccos(), dfunc(), dot(), numeric::xyzVector< class >::length(), and p1_theta_deriv().

Referenced by core::scoring::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 ASSERT_ONLY, cross(), dot(), helper(), numeric::xyzVector< class >::length(), numeric::xyzVector< class >::normalized(), radians(), and numeric::conversions::radians().

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 numeric::arccos(), cross(), dfunc(), dot(), numeric::xyzVector< class >::length(), and p1_theta_deriv().

Referenced by core::scoring::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
	)

virtual

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.

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::total_residue(), core::scoring::constraints::TRACER, and type().

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

References AngleConstraint(), 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 = `NULL`
	)		const

virtual

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.

References AngleConstraint(), atom(), atom1_, atom2_, 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().

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

compute score

References numeric::arccos(), dot(), func(), numeric::xyzVector< class >::length(), and runtime_assert.

Referenced by score().

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

virtual

compute score

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

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

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

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

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

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

virtual

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 numeric::arccos(), atom1_, atom2_, atom3_, core::id::AtomID::atomno(), core::pose::Pose::conformation(), dot(), func_, numeric::xyzVector< class >::length(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().