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core::pack::dunbrack::RotamerConstraint Class Reference

This class favors a particular rotamer at a particular position by reducing its Dunbrack energy. More...

#include <RotamerConstraint.hh>

Inheritance diagram for core::pack::dunbrack::RotamerConstraint:
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Public Member Functions

virtual std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
 RotamerConstraint (pose::Pose const &pose, Size seqpos)
 
virtual ~RotamerConstraint ()
 
virtual void add_residue (conformation::Residue const &rsd)
 
virtual
scoring::constraints::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. More...
 
virtual 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. More...
 
virtual AtomID const & atom (Size const index) const
 Returns the AtomID referred to by index. More...
 
virtual void score (scoring::constraints::XYZ_Func const &xyz_func, scoring::EnergyMap const &weights, scoring::EnergyMap &emap) 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. More...
 
virtual void fill_f1_f2 (AtomID const &atom, scoring::constraints::XYZ_Func const &xyz, Vector &F1, Vector &F2, scoring::EnergyMap const &weights) 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!) More...
 
virtual void show (std::ostream &out) const
 This gets used to compare one constraint to another, so it should uniquely reflect all the parameters. More...
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
virtual ~Constraint ()
 Virtual destructor. More...
 
virtual ConstraintOP clone (FuncOP) const
 
virtual ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, 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. More...
 
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
virtual void read_constraint (std::istream &, core::pose::Pose const &)
 This method is totally redundant with read_def YAY. More...
 
ScoreType const & score_type () const
 Returns the ScoreType that this Constraint object will use. More...
 
virtual void read_data (std::istream &)
 initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More...
 
virtual ConstraintOP remap_resid (core::id::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. More...
 
virtual core::Real dist (core::pose::Pose const &) const
 return the "raw" distance before handed to the FUNC object More...
 
virtual core::Real dist (XYZ_Func const &) const
 
virtual void setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (XYZ_Func const &, ScoreFunction const &) const
 
virtual Real score (conformation::Conformation const &) const
 Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. More...
 
virtual void show_def (std::ostream &, pose::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. More...
 
virtual void read_def (std::istream &, pose::Pose const &, FuncFactory const &)
 
virtual void steal_def (pose::Pose const &)
 
std::string to_string () const
 Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...
 
virtual Size show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) const
 Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ... More...
 
virtual Func const & get_func () const
 Returns the Func object associated with this Constraint object. More...
 
virtual bool operator== (Constraint const &) const
 possibility to do object comparison instead of pointer comparison More...
 
bool operator!= (Constraint const &other) const
 possibility to do object comparison instead of pointer comparison More...
 
virtual core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &)
 
virtual core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const
 

Private Attributes

Size seqpos_
 
std::string rsd_type_name_
 
utility::vector1< AtomIDatom_ids_
 
SingleResidueRotamerLibraryCAP rotlib_
 
utility::vector1< ChiVectorfavored_rotamers_
 
utility::vector1< RotVectorfavored_rotamer_numbers_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 

Detailed Description

This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.

Specifically, the given rotamer well(s) receive a bonus equal to the difference between their minimum energy (for the ideal rotamer in this well) and the minimum energy of any rotamer (at the current phi,psi). This class is used to implement the scoring component of the -unboundrot flag; actually adding those rotamers to the library occurs in core/pack/rotamer_set/UnboundRotamersOperation.

Constructor & Destructor Documentation

core::pack::dunbrack::RotamerConstraint::RotamerConstraint ( pose::Pose const &  pose,
Size  seqpos 
)
core::pack::dunbrack::RotamerConstraint::~RotamerConstraint ( )
virtual

Member Function Documentation

void core::pack::dunbrack::RotamerConstraint::add_residue ( conformation::Residue const &  rsd)
virtual
id::AtomID const & core::pack::dunbrack::RotamerConstraint::atom ( Size const  index) const
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.

References atom_ids_.

virtual scoring::constraints::ConstraintOP core::pack::dunbrack::RotamerConstraint::clone ( ) const
inlinevirtual

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.

References RotamerConstraint().

void core::pack::dunbrack::RotamerConstraint::fill_f1_f2 ( AtomID const &  atom,
scoring::constraints::XYZ_Func const &  xyz_func,
Vector F1,
Vector F2,
scoring::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.

Size core::pack::dunbrack::RotamerConstraint::natoms ( ) const
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.

References atom_ids_.

void core::pack::dunbrack::RotamerConstraint::score ( scoring::constraints::XYZ_Func const &  xyz_func,
scoring::EnergyMap const &  weights,
scoring::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.

References favored_rotamer_numbers_, core::scoring::constraints::XYZ_Func::residue(), rot(), core::pack::dunbrack::rotamer_from_chi(), rotlib_, rsd_type_name_, core::scoring::constraints::Constraint::score_type(), seqpos_, and core::pack::dunbrack::TR().

void core::pack::dunbrack::RotamerConstraint::show ( std::ostream &  out) const
virtual

This gets used to compare one constraint to another, so it should uniquely reflect all the parameters.

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

References favored_rotamer_numbers_, rsd_type_name_, seqpos_, core::io::serialization::size(), and type().

virtual std::string core::pack::dunbrack::RotamerConstraint::type ( ) const
inlinevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

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

Referenced by show().

Member Data Documentation

utility::vector1< AtomID > core::pack::dunbrack::RotamerConstraint::atom_ids_
private

Referenced by atom(), natoms(), and RotamerConstraint().

utility::vector1< RotVector > core::pack::dunbrack::RotamerConstraint::favored_rotamer_numbers_
private

Referenced by add_residue(), score(), and show().

utility::vector1< ChiVector > core::pack::dunbrack::RotamerConstraint::favored_rotamers_
private

Referenced by add_residue().

SingleResidueRotamerLibraryCAP core::pack::dunbrack::RotamerConstraint::rotlib_
private

Referenced by score().

std::string core::pack::dunbrack::RotamerConstraint::rsd_type_name_
private

Referenced by add_residue(), score(), and show().

Size core::pack::dunbrack::RotamerConstraint::seqpos_
private

Referenced by RotamerConstraint(), score(), and show().


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