#include <SequenceProfileConstraint.hh>

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

Collaboration 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::constraints::FuncFactory	FuncFactory

typedef core::scoring::constraints::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. 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 &, 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 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=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...

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 (FuncOP) const

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

virtual core::Real	dist (XYZ_Func const &) const

virtual void	setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const

virtual void	setup_for_derivatives (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 &)

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

virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison 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

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_

Detailed Description

Definition at line 35 of file SequenceProfileConstraint.hh.

Member Typedef Documentation

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

Definition at line 41 of file SequenceProfileConstraint.hh.

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

Definition at line 45 of file SequenceProfileConstraint.hh.

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

Definition at line 42 of file SequenceProfileConstraint.hh.

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

Definition at line 43 of file SequenceProfileConstraint.hh.

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

Definition at line 40 of file SequenceProfileConstraint.hh.

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

Definition at line 39 of file SequenceProfileConstraint.hh.

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

Definition at line 37 of file SequenceProfileConstraint.hh.

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

Definition at line 38 of file SequenceProfileConstraint.hh.

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

Definition at line 44 of file SequenceProfileConstraint.hh.

Constructor & Destructor Documentation

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

Definition at line 58 of file SequenceProfileConstraint.cc.

Referenced by core::scoring::constraints::SequenceProfileConstraintCreator::create_constraint().

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

Definition at line 66 of file SequenceProfileConstraint.cc.

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

Definition at line 79 of file SequenceProfileConstraint.cc.

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

virtual

Definition at line 91 of file SequenceProfileConstraint.cc.

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.

Definition at line 95 of file SequenceProfileConstraint.hh.

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.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

Definition at line 94 of file SequenceProfileConstraint.cc.

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.

Definition at line 301 of file SequenceProfileConstraint.cc.

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.

Definition at line 94 of file SequenceProfileConstraint.hh.

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

Definition at line 214 of file SequenceProfileConstraint.cc.

References mapping_.

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

Definition at line 100 of file SequenceProfileConstraint.cc.

References protocols::swa::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.

Definition at line 223 of file SequenceProfileConstraint.cc.

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 = `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.

Definition at line 241 of file SequenceProfileConstraint.cc.

References 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.

Definition at line 217 of file SequenceProfileConstraint.cc.

References seqpos_.

void core::scoring::constraints::SequenceProfileConstraint::score	(	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.

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

Definition at line 271 of file SequenceProfileConstraint.cc.

References core::chemical::ResidueType::aa(), mapping_, core::scoring::constraints::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

Definition at line 82 of file SequenceProfileConstraint.hh.

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

Definition at line 85 of file SequenceProfileConstraint.hh.

References seqpos(), and seqpos_.

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

Definition at line 211 of file SequenceProfileConstraint.cc.

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`
	)

Definition at line 204 of file SequenceProfileConstraint.cc.

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.

Definition at line 180 of file SequenceProfileConstraint.cc.

References mapping_, seqpos_, sequence_profile_, and core::io::serialization::size().

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 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.

Definition at line 174 of file SequenceProfileConstraint.cc.

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.

Definition at line 68 of file SequenceProfileConstraint.hh.

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

Definition at line 334 of file SequenceProfileConstraint.cc.

References weight_.