protocols::constraints_additional::SequenceCouplingConstraint Class Reference

#include <SequenceCouplingConstraint.hh>

Public Types
typedef core::sequence::SequenceCoupling	SequenceCoupling
typedef core::sequence::SequenceCouplingOP	SequenceCouplingOP
typedef core::sequence::SequenceCouplingCOP	SequenceCouplingCOP
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 Member Functions
	SequenceCouplingConstraint ()
	SequenceCouplingConstraint (Pose const &, core::Size, core::Size, SequenceCouplingOP profile=NULL)
	SequenceCouplingConstraint (core::Size, core::Size, SequenceCouplingOP profile=NULL)
virtual	~SequenceCouplingConstraint ()
virtual ConstraintOP	clone () const
virtual std::string	type () const
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
virtual void	show (std::ostream &out) const
core::Size	seqpos1 () const
core::Size	seqpos2 () const
void	set_sequence_coupling (SequenceCouplingOP)
SequenceCouplingOP	sequence_coupling ()
SequenceCouplingCOP	sequence_coupling () const
virtual core::Size	natoms () const
virtual AtomID const &	atom (Size const ) const
virtual utility::vector1 < core::Size >	residues () const
virtual void	score (XYZ_Func const &, EnergyMap const &, EnergyMap &) const
virtual void	fill_f1_f2 (AtomID const &, XYZ_Func const &, core::Vector &, core::Vector &, EnergyMap const &) const

Private Attributes
core::Size	seqpos1_
core::Size	seqpos2_
SequenceCouplingOP	sequence_coupling_

Member Typedef Documentation

typedef core::conformation::Conformation protocols::constraints_additional::SequenceCouplingConstraint::Conformation

typedef core::scoring::constraints::ConstraintOP protocols::constraints_additional::SequenceCouplingConstraint::ConstraintOP

typedef core::scoring::EnergyMap protocols::constraints_additional::SequenceCouplingConstraint::EnergyMap

typedef core::scoring::func::FuncFactory protocols::constraints_additional::SequenceCouplingConstraint::FuncFactory

typedef core::pose::Pose protocols::constraints_additional::SequenceCouplingConstraint::Pose

typedef core::sequence::SequenceCoupling protocols::constraints_additional::SequenceCouplingConstraint::SequenceCoupling

typedef core::sequence::SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingCOP

typedef core::sequence::SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingOP

typedef core::id::SequenceMapping protocols::constraints_additional::SequenceCouplingConstraint::SequenceMapping

typedef core::scoring::func::XYZ_Func protocols::constraints_additional::SequenceCouplingConstraint::XYZ_Func

Constructor & Destructor Documentation

protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint

(

)

References res_type_constraint.

Referenced by clone().

protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint	(	Pose const &	,
		core::Size	seqpos1,
		core::Size	seqpos2,
		SequenceCouplingOP	profile = NULL
	)

References res_type_constraint.

protocols::constraints_additional::SequenceCouplingConstraint::SequenceCouplingConstraint	(	core::Size	seqpos1,
		core::Size	seqpos2,
		SequenceCouplingOP	profile = NULL
	)

References res_type_constraint.

protocols::constraints_additional::SequenceCouplingConstraint::~SequenceCouplingConstraint ( )

virtual

Member Function Documentation

virtual AtomID const& protocols::constraints_additional::SequenceCouplingConstraint::atom ( Size  const ) const

inlinevirtual

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

References core::id::BOGUS_ATOM_ID, and utility_exit_with_message.

ConstraintOP protocols::constraints_additional::SequenceCouplingConstraint::clone ( ) const

virtual

References SequenceCouplingConstraint().

void protocols::constraints_additional::SequenceCouplingConstraint::fill_f1_f2 ( AtomID const &  , XYZ_Func const &  , core::Vector &  , core::Vector &  , EnergyMap const &    ) const

virtual

virtual core::Size protocols::constraints_additional::SequenceCouplingConstraint::natoms ( ) const

inlinevirtual

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

void protocols::constraints_additional::SequenceCouplingConstraint::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)

References file_exists(), seqpos1_, seqpos2_, sequence_coupling_, t_debug, core::pose::Pose::total_residue(), protocols::constraints_additional::TR, utility_exit, and utility_exit_with_message.

utility::vector1< core::Size > protocols::constraints_additional::SequenceCouplingConstraint::residues ( ) const

virtual

References seqpos1_, and seqpos2_.

void protocols::constraints_additional::SequenceCouplingConstraint::score ( XYZ_Func const &  xyz_func, EnergyMap const &  weights, EnergyMap &  emap  ) const

virtual

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

References aa1, aa2, core::scoring::func::XYZ_Func::residue(), runtime_assert, score_type, seqpos1_, seqpos2_, sequence_coupling_, t_trace, and protocols::constraints_additional::TR.

core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos1 ( ) const

inline

References seqpos1_.

core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos2 ( ) const

inline

References seqpos2_.

SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling

(

)

References sequence_coupling_.

SequenceCouplingCOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling

(

)

const

References sequence_coupling_.

void protocols::constraints_additional::SequenceCouplingConstraint::set_sequence_coupling

(

SequenceCouplingOP

profile

)

References sequence_coupling_.

void protocols::constraints_additional::SequenceCouplingConstraint::show ( std::ostream &  out ) const

virtual

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

References seqpos1_, seqpos2_, and sequence_coupling_.

Referenced by show_def().

void protocols::constraints_additional::SequenceCouplingConstraint::show_def ( std::ostream &  os, Pose const &    ) const

virtual

References show().

virtual std::string protocols::constraints_additional::SequenceCouplingConstraint::type ( ) const

inlinevirtual

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

Member Data Documentation

core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos1_

private

Referenced by read_def(), residues(), score(), seqpos1(), and show().

core::Size protocols::constraints_additional::SequenceCouplingConstraint::seqpos2_

private

Referenced by read_def(), residues(), score(), seqpos2(), and show().

SequenceCouplingOP protocols::constraints_additional::SequenceCouplingConstraint::sequence_coupling_

private

Referenced by read_def(), score(), sequence_coupling(), set_sequence_coupling(), and show().

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

• symlinks/rosetta/src/protocols/constraints_additional/SequenceCouplingConstraint.hh
• symlinks/rosetta/src/protocols/constraints_additional/SequenceCouplingConstraint.cc