Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Attributes | List of all members
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

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

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

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