#include <AtomToAxisConstraint.hh>

Inheritance diagram for core::scoring::constraints::AtomToAxisConstraint:

Public Member Functions
	AtomToAxisConstraint ()

	AtomToAxisConstraint (AtomID const &a, utility::vector1< AtomID > const &axis1, utility::vector1< AtomID > const &axis2, core::scoring::func::FuncOP const &func, ScoreType scoretype=atom_pair_constraint)
	c-tor More...

	AtomToAxisConstraint (AtomToAxisConstraint const &)=default

ConstraintOP	clone () const override
	Create a deep copy of this AtomToAxisConstraint, cloning its Func. More...

ConstraintOP	clone (func::FuncOP func) const override
	Create a deep copy of this AtomToAxisConstraint except that the copy should use the input Func instead of its existing one. 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...

bool	operator== (Constraint const &other) const override
	Compare a) the class types (w/ same_type_as_me), b) the atoms being constrained, c) the score_type being used, and d) the Func objects (the FuncOPs may point at different objects, but as long as those objects are equal, that counts) 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...

Real	score (Vector const &xyz1, Vector const &xyz2) const

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

Real	score (pose::Pose const &pose) const override
	Returns the unweighted score of this constraint computed over the given pose. More...

XYZs	calc_xyzs (pose::Pose const &pose) const

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

XYZs	calc_xyzs (core::scoring::func::XYZ_Func const &xyz) const

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

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

Size	natoms () const override
	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...

AtomID const &	atom (core::Size const ii) const override
	Returns the AtomID referred to by index. 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 &	get_atom () const

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...

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

Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1) const override
	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...

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

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

virtual void	score (core::scoring::func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const=0
	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 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 core::Real	dist (core::scoring::func::XYZ_Func const &) const=0
	return the raw "distance" before that distance is handed to the FUNC object More...

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

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

	~Constraint () override
	Virtual destructor. 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, EnergyMap const &weights) const
	Returns the weighted score of this constraint computed over the given pose. 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
void	set_func (func::FuncOP setting)
	Setter for the derived class. More...

void	atom (AtomID const &newid)

void	add_atom_to_axis1 (AtomID const &newid)

void	add_atom_to_axis2 (AtomID const &newid)

Private Member Functions
Real	func (Real const theta) const

Real	dfunc (Real const theta) const

Private Attributes
AtomID	atom_

utility::vector1< AtomID >	axis1_

utility::vector1< AtomID >	axis2_

core::scoring::func::FuncOP	func_

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

Constructor & Destructor Documentation

◆ AtomToAxisConstraint() [1/3]

core::scoring::constraints::AtomToAxisConstraint::AtomToAxisConstraint ( )

◆ AtomToAxisConstraint() [2/3]

core::scoring::constraints::AtomToAxisConstraint::AtomToAxisConstraint	(	AtomID const &	a,
		utility::vector1< AtomID > const &	axis1,
		utility::vector1< AtomID > const &	axis2,
		core::scoring::func::FuncOP const &	func,
		ScoreType	scoretype = `atom_pair_constraint`
	)

c-tor

◆ AtomToAxisConstraint() [3/3]

core::scoring::constraints::AtomToAxisConstraint::AtomToAxisConstraint ( AtomToAxisConstraint const & )

default

Member Function Documentation

◆ add_atom_to_axis1()

void core::scoring::constraints::AtomToAxisConstraint::add_atom_to_axis1 ( AtomID const & newid )

inlineprotected

References axis1_.

◆ add_atom_to_axis2()

void core::scoring::constraints::AtomToAxisConstraint::add_atom_to_axis2 ( AtomID const & newid )

inlineprotected

References axis2_.

◆ atom() [1/2]

void core::scoring::constraints::AtomToAxisConstraint::atom ( AtomID const & newid )

inlineprotected

References atom_.

◆ atom() [2/2]

AtomID const& core::scoring::constraints::AtomToAxisConstraint::atom ( core::Size const index ) const

inlineoverridevirtual

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.

References atom_, axis1_, and axis2_.

Referenced by dist(), fill_f1_f2(), and remapped_clone().

◆ calc_xyzs() [1/2]

XYZs core::scoring::constraints::AtomToAxisConstraint::calc_xyzs ( core::scoring::func::XYZ_Func const & xyz ) const

References core::scoring::constraints::XYZs::atom, atom_, core::scoring::constraints::XYZs::axis1, axis1_, core::scoring::constraints::XYZs::axis2, axis2_, and protocols::kinmatch::xyz().

◆ calc_xyzs() [2/2]

XYZs core::scoring::constraints::AtomToAxisConstraint::calc_xyzs ( pose::Pose const & pose ) const

References core::scoring::constraints::XYZs::atom, atom_, core::scoring::constraints::XYZs::axis1, axis1_, core::scoring::constraints::XYZs::axis2, axis2_, and core::pose::Pose::xyz().

Referenced by dist(), fill_f1_f2(), and score().

◆ clone() [1/2]

ConstraintOP core::scoring::constraints::AtomToAxisConstraint::clone ( ) const

overridevirtual

Create a deep copy of this AtomToAxisConstraint, cloning its Func.

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

◆ clone() [2/2]

ConstraintOP core::scoring::constraints::AtomToAxisConstraint::clone ( func::FuncOP func ) const

overridevirtual

Create a deep copy of this AtomToAxisConstraint except that the copy should use the input Func instead of its existing one.

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

References atom_, axis1_, axis2_, func(), and core::scoring::constraints::Constraint::score_type().

◆ dfunc()

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

private

References func_.

Referenced by fill_f1_f2().

◆ dist() [1/4]

Real core::scoring::constraints::Constraint::dist

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

◆ dist() [2/4]

virtual core::Real core::scoring::constraints::Constraint::dist

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

Referenced by fill_f1_f2(), score(), and show_violations().

◆ dist() [3/4]

Real core::scoring::constraints::AtomToAxisConstraint::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.

References atom_, calc_xyzs(), core::scoring::constraints::closest_point_on_line(), and protocols::kinmatch::xyz().

◆ dist() [4/4]

Real core::scoring::constraints::AtomToAxisConstraint::dist ( pose::Pose const & pose ) 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::Constraint.

References atom(), atom_, core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), axis1_, axis2_, calc_xyzs(), core::scoring::constraints::closest_point_on_line(), core::kinematics::AtomTree::has(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::scoring::constraints::TR(), and core::pose::Pose::xyz().

◆ fill_f1_f2()

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

overridevirtual

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.

References atom(), atom_, calc_xyzs(), core::scoring::constraints::closest_point_on_line(), dfunc(), dist(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

◆ func()

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

private

References func_.

Referenced by clone(), and score().

◆ get_atom()

AtomID const& core::scoring::constraints::AtomToAxisConstraint::get_atom ( ) const

inline

References atom_.

◆ get_func()

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

overridevirtual

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

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

References func_.

◆ natoms()

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

inlineoverridevirtual

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.

References axis1_, and axis2_.

◆ operator==()

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

overridevirtual

Compare a) the class types (w/ same_type_as_me), b) the atoms being constrained, c) the score_type being used, and d) the Func objects (the FuncOPs may point at different objects, but as long as those objects are equal, that counts)

Beware of noise in our floating point comparison checks

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

References atom_, axis1_, axis2_, func_, core::scoring::constraints::Constraint::same_type_as_me(), same_type_as_me(), and core::scoring::constraints::Constraint::score_type().

◆ read_def()

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

overridevirtual

one line definition "AtomPairs atom1 res1 atom2 res2 function_type function_definition"

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

◆ remap_resid()

ConstraintOP core::scoring::constraints::AtomToAxisConstraint::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.

◆ remapped_clone()

ConstraintOP core::scoring::constraints::AtomToAxisConstraint::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.

References atom(), atom_, core::conformation::atom_id_to_named_atom_id(), axis1_, axis2_, func_, core::conformation::named_atom_id_to_atom_id(), protocols::denovo_design::movers::new_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::scoring::constraints::TR().

◆ same_type_as_me()

bool core::scoring::constraints::AtomToAxisConstraint::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.

Referenced by operator==().

◆ score() [1/6]

void core::scoring::constraints::AtomToAxisConstraint::score	(	core::scoring::func::XYZ_Func const &	xyz_func,
		EnergyMap const &	weights,
		EnergyMap &	emap
	)		const

overridevirtual

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.

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

◆ score() [2/6]

virtual void core::scoring::constraints::Constraint::score

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.

Referenced by score().

◆ score() [3/6]

Real core::scoring::constraints::Constraint::score

Returns the unweighted score of this constraint computed over the given pose.

◆ score() [4/6]

Real core::scoring::constraints::AtomToAxisConstraint::score ( pose::Pose const & pose ) const

overridevirtual

Returns the unweighted score of this constraint computed over the given pose.

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

References dist(), and func_.

◆ score() [5/6]

Real core::scoring::constraints::Constraint::score

Returns the weighted score of this constraint computed over the given pose.

◆ score() [6/6]

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

References func().

◆ set_func()

void core::scoring::constraints::AtomToAxisConstraint::set_func ( func::FuncOP setting )

protected

Setter for the derived class.

References func_.

◆ setup_for_scoring()

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

overridevirtual

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

◆ show()

void core::scoring::constraints::AtomToAxisConstraint::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_, core::id::AtomID::atomno(), func_, core::conformation::membrane::out, and core::id::AtomID::rsd().

◆ show_def()

void core::scoring::constraints::AtomToAxisConstraint::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.

References atom_, core::conformation::atom_id_to_named_atom_id(), func_, core::conformation::membrane::out, and type().

◆ show_violations()

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

overridevirtual

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 ...

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

References dist(), func_, and core::conformation::membrane::out.

◆ type()

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

inlineoverridevirtual

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

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

Referenced by show_def().

Member Data Documentation

◆ atom_

AtomID core::scoring::constraints::AtomToAxisConstraint::atom_

private

Referenced by atom(), calc_xyzs(), clone(), dist(), fill_f1_f2(), get_atom(), operator==(), remapped_clone(), score(), show(), and show_def().

◆ axis1_

utility::vector1< AtomID > core::scoring::constraints::AtomToAxisConstraint::axis1_

private

Referenced by add_atom_to_axis1(), atom(), calc_xyzs(), clone(), dist(), natoms(), operator==(), and remapped_clone().

◆ axis2_

utility::vector1< AtomID > core::scoring::constraints::AtomToAxisConstraint::axis2_

private

Referenced by add_atom_to_axis2(), atom(), calc_xyzs(), clone(), dist(), natoms(), operator==(), and remapped_clone().

◆ func_

core::scoring::func::FuncOP core::scoring::constraints::AtomToAxisConstraint::func_

private

Referenced by dfunc(), func(), get_func(), operator==(), remapped_clone(), score(), set_func(), show(), show_def(), and show_violations().

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

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ AtomToAxisConstraint() [1/3]

◆ AtomToAxisConstraint() [2/3]

◆ AtomToAxisConstraint() [3/3]

Member Function Documentation

◆ add_atom_to_axis1()

◆ add_atom_to_axis2()

◆ atom() [1/2]

◆ atom() [2/2]

◆ calc_xyzs() [1/2]

◆ calc_xyzs() [2/2]

◆ clone() [1/2]

◆ clone() [2/2]

◆ dfunc()

◆ dist() [1/4]

◆ dist() [2/4]

◆ dist() [3/4]

◆ dist() [4/4]

◆ fill_f1_f2()

◆ func()

◆ get_atom()

◆ get_func()

◆ natoms()

◆ operator==()

◆ read_def()

◆ remap_resid()

◆ remapped_clone()

◆ same_type_as_me()

◆ score() [1/6]

◆ score() [2/6]

◆ score() [3/6]

◆ score() [4/6]

◆ score() [5/6]

◆ score() [6/6]

◆ set_func()

◆ setup_for_scoring()

◆ show()

◆ show_def()

◆ show_violations()

◆ type()

Member Data Documentation

◆ atom_

◆ axis1_

◆ axis2_

◆ func_