Rosetta Protocols  2014.35
Public Types | Public Member Functions | List of all members
protocols::constraints_additional::SequenceCoupling1BDConstraint Class Reference

#include <SequenceCoupling1BDConstraint.hh>

Public Types

typedef
core::sequence::SequenceCoupling 
SequenceCoupling
 
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 Types inherited from core::scoring::constraints::SequenceProfileConstraint
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 Member Functions

 SequenceCoupling1BDConstraint ()
 
 SequenceCoupling1BDConstraint (Pose const &, core::Size, SequenceProfileCOP profile)
 
 SequenceCoupling1BDConstraint (core::Size, SequenceProfileCOP profile)
 
virtual ~SequenceCoupling1BDConstraint ()
 
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 (std::ostream &out) 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
 
- Public Member Functions inherited from core::scoring::constraints::SequenceProfileConstraint
 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 void show_def (std::ostream &, Pose const &) const
 
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
 
virtual AtomID const & atom (core::Size const ) const
 
virtual utility::vector1
< core::Size
residues () const
 
virtual ConstraintOP remap_resid (SequenceMapping const &) const
 
virtual ConstraintOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=NULL) const
 
void weight (core::Real const w)
 
core::Real weight () const
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( )

References constraints, and scoring.

Referenced by clone().

protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( Pose const &  pose,
core::Size  numpos,
SequenceProfileCOP  profile 
)

References constraints, and scoring.

protocols::constraints_additional::SequenceCoupling1BDConstraint::SequenceCoupling1BDConstraint ( core::Size  numpos,
SequenceProfileCOP  profile 
)

References constraints, and scoring.

protocols::constraints_additional::SequenceCoupling1BDConstraint::~SequenceCoupling1BDConstraint ( )
virtual

Member Function Documentation

ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::clone ( ) const
virtual
void protocols::constraints_additional::SequenceCoupling1BDConstraint::fill_f1_f2 ( AtomID const &  ,
XYZ_Func const &  ,
core::Vector ,
core::Vector ,
EnergyMap const &   
) const
virtual
void protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.

References c, file_exists(), core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile(), t_debug, core::pose::Pose::total_residue(), protocols::constraints_additional::TR, utility_exit, and utility_exit_with_message.

void protocols::constraints_additional::SequenceCoupling1BDConstraint::score ( XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
virtual
void protocols::constraints_additional::SequenceCoupling1BDConstraint::show ( std::ostream &  out) const
virtual
virtual std::string protocols::constraints_additional::SequenceCoupling1BDConstraint::type ( ) const
inlinevirtual

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