Rosetta 3.4
Public Types | Public Member Functions
protocols::constraints_additional::SequenceCoupling1BDConstraint Class Reference

#include <SequenceCoupling1BDConstraint.hh>

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List of all members.

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::constraints::FuncFactory 
FuncFactory
typedef
core::scoring::constraints::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
 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 (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.
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


Constructor & Destructor Documentation

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

Referenced by clone().

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

Member Function Documentation

ConstraintOP protocols::constraints_additional::SequenceCoupling1BDConstraint::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.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

References SequenceCoupling1BDConstraint().

void protocols::constraints_additional::SequenceCoupling1BDConstraint::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!)

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

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 core::pack::dunbrack::c, protocols::swa::rna::file_exists(), core::scoring::constraints::SequenceProfileConstraint::seqpos(), core::scoring::constraints::SequenceProfileConstraint::set_sequence_profile(), core::pose::Pose::total_residue(), and protocols::constraints_additional::TR().

void protocols::constraints_additional::SequenceCoupling1BDConstraint::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.

Reimplemented from core::scoring::constraints::SequenceProfileConstraint.

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

void protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.

References core::scoring::constraints::SequenceProfileConstraint::seqpos(), and core::scoring::constraints::SequenceProfileConstraint::sequence_profile().

virtual std::string protocols::constraints_additional::SequenceCoupling1BDConstraint::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::SequenceProfileConstraint.


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