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

#include <BackboneStubLinearConstraint.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...

	BackboneStubLinearConstraint (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 &CB_force_constant)

virtual	~BackboneStubLinearConstraint ()

virtual Size	natoms () const
	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...

virtual AtomID const &	atom (Size const index) const
	Returns the AtomID referred to by index. More...

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

virtual void	score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const
	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 void	fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const

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...

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

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...

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 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 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	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 &)

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...

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
	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 Private Attributes
static utility::pointer::owning_ptr < AngleConstraint >	ang_cst_
	why is this static? More...

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::BackboneStubLinearConstraint::BackboneStubLinearConstraint	(	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 &	CB_force_constant
	)

virtual core::scoring::constraints::BackboneStubLinearConstraint::~BackboneStubLinearConstraint ( )

inlinevirtual

Member Function Documentation

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

inlinevirtual

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::BackboneStubLinearConstraint::clone ( ) const

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 BackboneStubLinearConstraint().

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

virtual

References core::conformation::Residue::aa(), core::chemical::aa_gly, C_atom_id_, C_target_, CA_atom_id_, CA_target_, CB_atom_id_, CB_force_constant_, CB_target_, core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length(), N_atom_id_, N_target_, core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, core::scoring::constraints::TR, and core::conformation::Residue::xyz().

virtual Size core::scoring::constraints::BackboneStubLinearConstraint::natoms ( ) const

inlinevirtual

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::BackboneStubLinearConstraint::operator== ( Constraint const & other ) const

virtual

possibility to compare constraint according to data and not just pointers

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

References C_atom_id_, C_N_target_, C_target_, CA_atom_id_, CA_target_, CB_atom_id_, CB_CA_target_, CB_force_constant_, CB_target_, fixed_atom_id_, fixed_reference_point_, N_atom_id_, N_target_, seqpos_, and superposition_bonus_.

ConstraintOP core::scoring::constraints::BackboneStubLinearConstraint::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 BackboneStubLinearConstraint(), C_target_, CA_target_, CB_force_constant_, CB_target_, core::conformation::ResidueFactory::create_residue(), fixed_atom_id_, core::chemical::ChemicalManager::get_instance(), N_target_, core::chemical::ChemicalManager::residue_type_set(), core::id::AtomID::rsd(), seqpos_, and superposition_bonus_.

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

virtual

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, C_target_, CA_target_, CB_force_constant_, CB_target_, numeric::xyzVector< class >::distance_squared(), fixed_atom_id_, fixed_reference_point_, core::conformation::Residue::is_protein(), N_target_, core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, core::scoring::constraints::TR, numeric::xyzVector< class >::x(), core::conformation::Residue::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

returns the private member seqpos_

References seqpos_.

void core::scoring::constraints::BackboneStubLinearConstraint::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 CB_force_constant_, seqpos_, and superposition_bonus_.

virtual std::string core::scoring::constraints::BackboneStubLinearConstraint::type ( ) const

inlinevirtual

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::owning_ptr< AngleConstraint > core::scoring::constraints::BackboneStubLinearConstraint::ang_cst_

staticprivate

why is this static?

Referenced by BackboneStubLinearConstraint().

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

private

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

AtomID core::scoring::constraints::BackboneStubLinearConstraint::C_atom_id_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::C_N_target_

private

Referenced by BackboneStubLinearConstraint(), and operator==().

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::C_target_

private

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

AtomID core::scoring::constraints::BackboneStubLinearConstraint::CA_atom_id_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::CA_target_

private

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

AtomID core::scoring::constraints::BackboneStubLinearConstraint::CB_atom_id_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::CB_CA_target_

private

Referenced by BackboneStubLinearConstraint(), and operator==().

core::Real core::scoring::constraints::BackboneStubLinearConstraint::CB_force_constant_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::CB_target_

private

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

AtomID core::scoring::constraints::BackboneStubLinearConstraint::fixed_atom_id_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::fixed_reference_point_

private

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

AtomID core::scoring::constraints::BackboneStubLinearConstraint::N_atom_id_

private

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

core::Vector core::scoring::constraints::BackboneStubLinearConstraint::N_target_

private

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

Size core::scoring::constraints::BackboneStubLinearConstraint::seqpos_

private

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

core::Real core::scoring::constraints::BackboneStubLinearConstraint::superposition_bonus_

private

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

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

symlinks/rosetta/src/core/scoring/constraints/BackboneStubLinearConstraint.hh
symlinks/rosetta/src/core/scoring/constraints/BackboneStubLinearConstraint.cc

Private Attributes
core::Real	superposition_bonus_

core::Real	CB_force_constant_

Size	seqpos_

AtomID	CB_atom_id_

AtomID	CA_atom_id_

AtomID	C_atom_id_

AtomID	N_atom_id_

utility::vector1< AtomID >	atom_ids_

core::Vector	CB_target_

core::Vector	CA_target_

core::Vector	C_target_

core::Vector	N_target_

core::Vector	CB_CA_target_

core::Vector	C_N_target_

AtomID	fixed_atom_id_

core::Vector	fixed_reference_point_

Public Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation