#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 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.
virtual std::string	type () const
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
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)
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.
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.
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.
virtual AtomID const &	atom (core::Size const ) const
	Returns the AtomID referred to by index.
virtual utility::vector1 < core::Size >	residues () const
	Returns the pose numbers of the residues involved in this constraint, in no particular order.
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.
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.
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.
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!)

Member Typedef Documentation

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

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

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

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

Reimplemented in protocols::constraints_additional::SequenceCoupling1BDConstraint.

Constructor & Destructor Documentation

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

Referenced by clone(), core::scoring::constraints::SequenceProfileConstraintCreator::create_constraint(), remap_resid(), and remapped_clone().

core::scoring::constraints::SequenceProfileConstraint::SequenceProfileConstraint	(	Pose const &	pose,
		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]

Member Function Documentation

virtual AtomID const& core::scoring::constraints::SequenceProfileConstraint::atom ( core::Size index ) const [inline, virtual]

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.

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.

References SequenceProfileConstraint().

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 [inline, virtual]

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.

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

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.

References protocols::swa::rna::file_exists(), 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 SequenceProfileConstraint(), 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.

References SequenceProfileConstraint(), 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.

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.

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

void core::scoring::constraints::SequenceProfileConstraint::seqpos ( core::Size seqpos ) [inline]

References seqpos().

core::Size core::scoring::constraints::SequenceProfileConstraint::seqpos ( ) const [inline]

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

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

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`
	)

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.

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.

References show().

virtual std::string core::scoring::constraints::SequenceProfileConstraint::type ( ) const [inline, virtual]

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.

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation