#include <AngleConstraint.hh>

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

Collaboration diagram for core::scoring::constraints::AngleConstraint:

Public Member Functions
virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
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.
void	read_def (std::istream &data, pose::Pose const &pose, FuncFactory const &func_factory)
	read in constraint defiinition
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.
bool	operator== (Constraint const &other) const
	possibility to compare constraint according to data and not just pointers
Real	score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
	compute score
void	score (XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const
	compute score
void	fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
	compute atom deriv
	AngleConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, FuncOP func_in, ScoreType scotype=angle_constraint)
	Constructor.
	AngleConstraint (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!
Size	natoms () const
	number of atoms --- always 3 for angles
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.
AtomID const &	atom (Size const n) const
	return AtomID for atom 1,2,3
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 )
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.
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 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.
Real	func (Real const theta) const
	evaluate func at theta
Real	dfunc (Real const theta) const
	evaluate dfunc at theta
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
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)

Detailed Description

An Angular Constraint.

Constructor & Destructor Documentation

core::scoring::constraints::AngleConstraint::AngleConstraint	(	AtomID const &	a1,
		AtomID const &	a2,
		AtomID const &	a3,
		FuncOP	func_in,
		ScoreType	scotype = `angle_constraint`
	)		`[inline]`

Constructor.

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

core::scoring::constraints::AngleConstraint::AngleConstraint	(	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.

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

virtual ConstraintOP core::scoring::constraints::AngleConstraint::clone ( ) const [inline, 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.

References AngleConstraint(), and core::scoring::constraints::Constraint::score_type().

Real core::scoring::constraints::AngleConstraint::dfunc ( Real const theta ) const [inline]

evaluate dfunc at theta

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

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

compute atom deriv

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

Referenced by core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives().

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.

Referenced by score().

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 [inline, virtual]

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 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 make_table_of_pilot_apps::d, dfunc(), and p1_theta_deriv().

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

References make_table_of_pilot_apps::f, and helper().

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 make_table_of_pilot_apps::d, dfunc(), and p1_theta_deriv().

void core::scoring::constraints::AngleConstraint::read_def	(	std::istream &	data,
		pose::Pose const &	pose,
		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 core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::scoring::constraints::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(), core::id::AtomID::atomno(), 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(), core::conformation::atom_id_to_named_atom_id(), 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().

void core::scoring::constraints::AngleConstraint::score	(	XYZ_Func const &	xyz,
		EnergyMap const &	,
		EnergyMap &	emap
	)		const `[virtual]`

compute score

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

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

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

compute score

References func().

Referenced by score().

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(), 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 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(), 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 core::id::AtomID::atomno(), core::pose::Pose::conformation(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

virtual std::string core::scoring::constraints::AngleConstraint::type ( ) const [inline, virtual]

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

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

Referenced by read_def(), and show_def().

The documentation for this class was generated from the following files:

src/core/scoring/constraints/AngleConstraint.hh
src/core/scoring/constraints/AngleConstraint.cc

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation