#include <SequenceProfileConstraint.hh>

Inheritance diagram for core::scoring::constraints::SequenceProfileConstraint:

Public Types
typedef core::sequence::SequenceProfile	SequenceProfile

typedef core::sequence::SequenceProfileCOP	SequenceProfileCOP

typedef core::id::SequenceMapping	SequenceMapping

typedef core::pose::Pose	Pose

typedef core::conformation::Conformation	Conformation

typedef core::scoring::EnergyMap	EnergyMap

typedef core::scoring::func::FuncFactory	FuncFactory

typedef core::scoring::func::XYZ_Func	XYZ_Func

typedef core::scoring::constraints::ConstraintOP	ConstraintOP

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

Public Member Functions
	SequenceProfileConstraint ()

	SequenceProfileConstraint (Pose const &, core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL)

	SequenceProfileConstraint (core::Size, SequenceProfileCOP profile=NULL, core::id::SequenceMappingCOP mapping=NULL)

virtual	~SequenceProfileConstraint ()

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. 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...

virtual bool	operator== (Constraint const &) const
	Equality operator to test whether two constraints are functionally identical. More...

virtual bool	same_type_as_me (Constraint const &) const
	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...

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

virtual void	read_def (std::istream &, Pose const &, func::FuncFactory const &)
	used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file) More...

virtual void	show_def (std::ostream &, 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	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

void	seqpos (core::Size seqpos)

void	set_sequence_profile (SequenceProfileCOP profile, core::id::SequenceMappingCOP mapping=NULL)

SequenceProfileCOP	sequence_profile () const

core::id::SequenceMappingCOP	profile_mapping () const

virtual core::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 (core::Size const ) const
	Returns the AtomID referred to by index. 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 ConstraintOP	remap_resid (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 ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map) 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...

virtual void	score (XYZ_Func const &, EnergyMap const &, EnergyMap &) 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 &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const
	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	weight (core::Real const w)

core::Real	weight () 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 (func::FuncOP) const
	Clone the constraint, but where a new Func object is to be used instead. 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 &) const

virtual core::Real	dist (core::pose::Pose const &) const
	return the raw "distance" before that distance is 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	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

Protected Member Functions
	SequenceProfileConstraint (SequenceProfileConstraint const &src)

Private Attributes
core::Size	seqpos_

SequenceProfileCOP	sequence_profile_

core::id::SequenceMappingCOP	mapping_
	A mapping of current pose numbers onto profile numbers. More...

core::Real	weight_

Member Typedef Documentation

typedef core::conformation::Conformation core::scoring::constraints::SequenceProfileConstraint::Conformation

typedef core::scoring::constraints::ConstraintOP core::scoring::constraints::SequenceProfileConstraint::ConstraintOP

typedef core::scoring::EnergyMap core::scoring::constraints::SequenceProfileConstraint::EnergyMap

typedef core::scoring::func::FuncFactory core::scoring::constraints::SequenceProfileConstraint::FuncFactory

typedef core::pose::Pose core::scoring::constraints::SequenceProfileConstraint::Pose

typedef core::id::SequenceMapping core::scoring::constraints::SequenceProfileConstraint::SequenceMapping

typedef core::sequence::SequenceProfile core::scoring::constraints::SequenceProfileConstraint::SequenceProfile

typedef core::sequence::SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::SequenceProfileCOP

typedef core::scoring::func::XYZ_Func core::scoring::constraints::SequenceProfileConstraint::XYZ_Func

Constructor & Destructor Documentation

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint ( )

Referenced by clone().

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint	(	Pose const &	,
		core::Size	seqpos,
		SequenceProfileCOP	profile = `NULL`,
		core::id::SequenceMappingCOP	mapping = `NULL`
	)

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint	(	core::Size	seqpos,
		SequenceProfileCOP	profile = `NULL`,
		core::id::SequenceMappingCOP	mapping = `NULL`
	)

core::scoring::constraints::SequenceProfileConstraint::~SequenceProfileConstraint ( )

virtual

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

protected

Member Function Documentation

virtual AtomID const& core::scoring::constraints::SequenceProfileConstraint::atom ( core::Size 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 core::id::BOGUS_ATOM_ID.

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::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. 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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References SequenceProfileConstraint().

Referenced by remapped_clone().

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

virtual

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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

virtual core::Size core::scoring::constraints::SequenceProfileConstraint::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.

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

virtual

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References mapping_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), seqpos_, sequence_profile_, and weight_.

core::id::SequenceMappingCOP core::scoring::constraints::SequenceProfileConstraint::profile_mapping ( ) const

References mapping_.

void core::scoring::constraints::SequenceProfileConstraint::read_def	(	std::istream &	is,
		Pose const &	pose,
		func::FuncFactory const &
	)

virtual

used by ConstraintIO and ConstraintFactory to construct this constraint from a input file stream (constraint file)

one line definition "SequenceProfile resindex profilefilename" (profilefilename can also be set to "none" in the constraints file, and specified by -in::file::pssm)

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References protocols::stepwise::modeler::rna::file_exists(), mapping_, seqpos_, sequence_profile_, core::pose::Pose::total_residue(), and core::scoring::constraints::TR().

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::remap_resid ( 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 mapping_, seqpos_, sequence_profile_, and core::scoring::constraints::TR().

ConstraintOP core::scoring::constraints::SequenceProfileConstraint::remapped_clone	(	pose::Pose const &	,
		pose::Pose const &	,
		id::SequenceMappingCOP	map
	)		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 clone(), mapping_, seqpos_, sequence_profile_, and core::scoring::constraints::TR().

utility::vector1< core::Size > core::scoring::constraints::SequenceProfileConstraint::residues ( ) const

virtual

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

References seqpos_.

bool core::scoring::constraints::SequenceProfileConstraint::same_type_as_me ( Constraint const & other ) const

virtual

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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

Referenced by operator==().

void core::scoring::constraints::SequenceProfileConstraint::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.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References core::chemical::ResidueType::aa(), mapping_, core::scoring::func::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, sequence_profile_, core::scoring::constraints::TR(), core::conformation::Residue::type(), and weight().

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

inline

References seqpos_.

Referenced by protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), seqpos(), and protocols::constraints_additional::SequenceCoupling1BDConstraint::show().

void core::scoring::constraints::SequenceProfileConstraint::seqpos ( core::Size seqpos )

inline

References seqpos(), and seqpos_.

SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::sequence_profile ( ) const

References sequence_profile_.

Referenced by protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), and protocols::constraints_additional::SequenceCoupling1BDConstraint::show().

void core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile	(	SequenceProfileCOP	profile,
		core::id::SequenceMappingCOP	mapping = `NULL`
	)

References mapping_, and sequence_profile_.

Referenced by protocols::constraints_additional::SequenceCoupling1BDConstraint::read_def().

void core::scoring::constraints::SequenceProfileConstraint::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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

References mapping_, seqpos_, and sequence_profile_.

Referenced by show_def().

void core::scoring::constraints::SequenceProfileConstraint::show_def	(	std::ostream &	,
		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 show().

virtual std::string core::scoring::constraints::SequenceProfileConstraint::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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

void core::scoring::constraints::SequenceProfileConstraint::weight ( core::Real const w )

References weight_.

core::Real core::scoring::constraints::SequenceProfileConstraint::weight ( ) const

References weight_.

Referenced by score().

Member Data Documentation

core::id::SequenceMappingCOP core::scoring::constraints::SequenceProfileConstraint::mapping_

private

A mapping of current pose numbers onto profile numbers.

Referenced by operator==(), profile_mapping(), read_def(), remap_resid(), remapped_clone(), score(), set_sequence_profile(), and show().

core::Size core::scoring::constraints::SequenceProfileConstraint::seqpos_

private

Referenced by operator==(), read_def(), remap_resid(), remapped_clone(), residues(), score(), seqpos(), and show().

SequenceProfileCOP core::scoring::constraints::SequenceProfileConstraint::sequence_profile_

private

Referenced by operator==(), read_def(), remap_resid(), remapped_clone(), score(), sequence_profile(), set_sequence_profile(), and show().

core::Real core::scoring::constraints::SequenceProfileConstraint::weight_

private

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

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation