This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location. More...

#include <BackboneStubConstraint.hh>

Inheritance diagram for core::scoring::constraints::BackboneStubConstraint:

[legend]

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

	BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, pose::Pose const &target_pose, Size const target_seqpos, core::Real const &superposition_bonus, core::Real const &force_constant)

	BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, conformation::Residue const &target_rsd, core::Real const &superposition_bonus, core::Real const &force_constant, std::string const &sidechain_atom_name, std::string const &primary_backbone_atom_name, std::string const &backbone_atom1_name, std::string const &backbone_atom2_name)

	BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, conformation::Residue const &target_rsd, core::Real const &superposition_bonus, core::Real const &force_constant)

	BackboneStubConstraint (BackboneStubConstraint const &src)
	Copy constructor – performs a deep copy. More...

	~BackboneStubConstraint () override

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 (Size const index) const override
	Returns the AtomID referred to by index. 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	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, 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...

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

void	fill_f1_f2 (AtomID const &atom, 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...

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::Size	seqpos () const
	returns the private member seqpos_ 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...

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

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_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 void	show_def (std::ostream &, pose::Pose const &) 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 void	read_def (std::istream &, pose::Pose const &, core::scoring::func::FuncFactory const &)
	Reads the definition of a Constraint from the given std::istream, 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. More...

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...

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

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

Private Attributes
core::Real	superposition_bonus_

core::Real	force_constant_

Size	seqpos_

AtomID	sidechain_atom_id_

AtomID	primary_atom_id_

AtomID	backbone_atom2_id_

AtomID	backbone_atom1_id_

utility::vector1< AtomID >	atom_ids_

core::Vector	sidechain_target_

core::Vector	primary_backbone_target_

core::Vector	backbone2_target_

core::Vector	backbone1_target_

core::Vector	primary_sidechain_target_

core::Vector	backbone1_2_target_

AtomID	fixed_atom_id_

core::Vector	fixed_reference_point_

utility::pointer::shared_ptr < AngleConstraint >	ang_cst_

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

Detailed Description

This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location.

Constructor & Destructor Documentation

core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint	(	pose::Pose const &	pose,
		Size const	seqpos,
		AtomID const &	fixed_atom_id,
		pose::Pose const &	target_pose,
		Size const	target_seqpos,
		core::Real const &	superposition_bonus,
		core::Real const &	force_constant
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, atom_ids_, core::scoring::constraints::auto_detect_atoms(), backbone1_2_target_, backbone1_target_, backbone2_target_, fixed_atom_id_, fixed_reference_point_, core::conformation::Residue::is_protein(), primary_backbone_target_, primary_sidechain_target_, core::pose::Pose::residue(), sidechain_target_, core::scoring::constraints::tr(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().

Referenced by clone().

core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint	(	pose::Pose const &	pose,
		Size const	seqpos,
		AtomID const &	fixed_atom_id,
		conformation::Residue const &	target_rsd,
		core::Real const &	superposition_bonus,
		core::Real const &	force_constant,
		std::string const &	sidechain_atom_name,
		std::string const &	primary_backbone_atom_name,
		std::string const &	backbone_atom1_name,
		std::string const &	backbone_atom2_name
	)

core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint	(	pose::Pose const &	pose,
		Size const	seqpos,
		AtomID const &	fixed_atom_id,
		conformation::Residue const &	target_rsd,
		core::Real const &	superposition_bonus,
		core::Real const &	force_constant
	)

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

Copy constructor – performs a deep copy.

core::scoring::constraints::BackboneStubConstraint::~BackboneStubConstraint ( )

inlineoverride

Member Function Documentation

AtomID const& core::scoring::constraints::BackboneStubConstraint::atom ( 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_ids_.

ConstraintOP core::scoring::constraints::BackboneStubConstraint::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.

References BackboneStubConstraint().

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

inlineoverridevirtual

"Distance" for BackboneStubConstraint isn't all that simple

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

void core::scoring::constraints::BackboneStubConstraint::fill_f1_f2	(	AtomID const &	atom,
		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 core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, backbone1_2_target_, backbone_atom1_id_, backbone_atom2_id_, force_constant_, core::conformation::Residue::is_protein(), primary_atom_id_, primary_sidechain_target_, core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, sidechain_atom_id_, sidechain_target_, superposition_bonus_, core::scoring::constraints::tr(), and core::conformation::Residue::xyz().

Size core::scoring::constraints::BackboneStubConstraint::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 atom_ids_.

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

overridevirtual

possibility to compare constraint according to data and not just pointers

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

References backbone1_2_target_, backbone1_target_, backbone2_target_, backbone_atom1_id_, backbone_atom2_id_, fixed_atom_id_, fixed_reference_point_, force_constant_, primary_atom_id_, primary_backbone_target_, primary_sidechain_target_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), seqpos_, sidechain_atom_id_, sidechain_target_, and superposition_bonus_.

ConstraintOP core::scoring::constraints::BackboneStubConstraint::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 backbone1_target_, backbone2_target_, core::conformation::ResidueFactory::create_residue(), fixed_atom_id_, force_constant_, primary_backbone_target_, core::id::AtomID::rsd(), seqpos_, sidechain_target_, and superposition_bonus_.

bool core::scoring::constraints::BackboneStubConstraint::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==().

void core::scoring::constraints::BackboneStubConstraint::score	(	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 core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, backbone1_2_target_, fixed_atom_id_, fixed_reference_point_, force_constant_, core::conformation::Residue::is_protein(), primary_sidechain_target_, core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, sidechain_target_, superposition_bonus_, core::scoring::constraints::tr(), and core::conformation::Residue::xyz().

core::Size core::scoring::constraints::BackboneStubConstraint::seqpos ( ) const

returns the private member seqpos_

References seqpos_.

void core::scoring::constraints::BackboneStubConstraint::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 force_constant_, seqpos_, and superposition_bonus_.

std::string core::scoring::constraints::BackboneStubConstraint::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.

Member Data Documentation

utility::pointer::shared_ptr< AngleConstraint > core::scoring::constraints::BackboneStubConstraint::ang_cst_

private

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

utility::vector1< AtomID > core::scoring::constraints::BackboneStubConstraint::atom_ids_

private

Referenced by atom(), BackboneStubConstraint(), and natoms().

core::Vector core::scoring::constraints::BackboneStubConstraint::backbone1_2_target_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), and score().

core::Vector core::scoring::constraints::BackboneStubConstraint::backbone1_target_

private

Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().

core::Vector core::scoring::constraints::BackboneStubConstraint::backbone2_target_

private

Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().

AtomID core::scoring::constraints::BackboneStubConstraint::backbone_atom1_id_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().

AtomID core::scoring::constraints::BackboneStubConstraint::backbone_atom2_id_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().

AtomID core::scoring::constraints::BackboneStubConstraint::fixed_atom_id_

private

Referenced by BackboneStubConstraint(), operator==(), remapped_clone(), and score().

core::Vector core::scoring::constraints::BackboneStubConstraint::fixed_reference_point_

private

Referenced by BackboneStubConstraint(), operator==(), and score().

core::Real core::scoring::constraints::BackboneStubConstraint::force_constant_

private

Referenced by fill_f1_f2(), operator==(), remapped_clone(), score(), and show().

AtomID core::scoring::constraints::BackboneStubConstraint::primary_atom_id_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().

core::Vector core::scoring::constraints::BackboneStubConstraint::primary_backbone_target_

private

Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().

core::Vector core::scoring::constraints::BackboneStubConstraint::primary_sidechain_target_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), and score().

Size core::scoring::constraints::BackboneStubConstraint::seqpos_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), remapped_clone(), score(), seqpos(), and show().

AtomID core::scoring::constraints::BackboneStubConstraint::sidechain_atom_id_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().

core::Vector core::scoring::constraints::BackboneStubConstraint::sidechain_target_

private

Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), remapped_clone(), and score().

core::Real core::scoring::constraints::BackboneStubConstraint::superposition_bonus_

private

Referenced by fill_f1_f2(), operator==(), remapped_clone(), score(), and show().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation