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core::scoring::constraints::ResidueTypeConstraint Class Reference

This class favors a particular residue identity at a particular position by reducing its res_type energy. More...

#include <ResidueTypeConstraint.hh>

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Public Types

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

Public Member Functions

 ResidueTypeConstraint ()
 
 ResidueTypeConstraint (pose::Pose const &pose, Size seqpos, Real native_residue_bonus)
 
 ResidueTypeConstraint (pose::Pose const &pose, Size seqpos, std::string AAname, Real favor_native_bonus)
 
 ResidueTypeConstraint (Size seqpos, std::string aa_in, std::string name3_in, core::Real bonus_in)
 
virtual ~ResidueTypeConstraint ()
 
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 ) const
 Returns the AtomID referred to by index. More...
 
virtual utility::vector1
< core::Size
residues () const
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
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. More...
 
virtual ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) 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...
 
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers More...
 
virtual ConstraintOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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 void score (XYZ_Func const &xyz_func, EnergyMap const &weights, 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, XYZ_Func const &xyz, Vector &F1, Vector &F2, 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 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...
 
- 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 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 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 std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
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...
 
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 AAname
 
std::string rsd_type_name3_
 
core::Real favor_native_bonus_
 

Detailed Description

This class favors a particular residue identity at a particular position by reducing its res_type energy.

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::constraints::ResidueTypeConstraint::ResidueTypeConstraint ( )

Referenced by clone(), remap_resid(), and remapped_clone().

core::scoring::constraints::ResidueTypeConstraint::ResidueTypeConstraint ( pose::Pose const &  pose,
Size  seqpos,
core::Real  favor_native_bonus 
)
core::scoring::constraints::ResidueTypeConstraint::ResidueTypeConstraint ( pose::Pose const &  pose,
Size  seqpos,
std::string  AAname,
core::Real  favor_native_bonus 
)
core::scoring::constraints::ResidueTypeConstraint::ResidueTypeConstraint ( Size  seqpos,
std::string  aa_in,
std::string  name3_in,
core::Real  bonus_in 
)
core::scoring::constraints::ResidueTypeConstraint::~ResidueTypeConstraint ( )
virtual

Member Function Documentation

virtual AtomID const& core::scoring::constraints::ResidueTypeConstraint::atom ( Size  index) const
inlinevirtual

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 core::id::BOGUS_ATOM_ID.

ConstraintOP core::scoring::constraints::ResidueTypeConstraint::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.

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

References ResidueTypeConstraint().

void core::scoring::constraints::ResidueTypeConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz_func,
Vector F1,
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!)

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

virtual Size core::scoring::constraints::ResidueTypeConstraint::natoms ( ) const
inlinevirtual

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.

bool core::scoring::constraints::ResidueTypeConstraint::operator== ( Constraint const &  other) const
virtual

possibility to compare constraint according to data and not just pointers

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

References AAname, favor_native_bonus_, rsd_type_name3_, core::scoring::constraints::Constraint::score_type(), and seqpos_.

ConstraintOP core::scoring::constraints::ResidueTypeConstraint::remap_resid ( core::id::SequenceMapping const &  ) const
virtual

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.

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

References AAname, favor_native_bonus_, ResidueTypeConstraint(), rsd_type_name3_, and seqpos_.

ConstraintOP core::scoring::constraints::ResidueTypeConstraint::remapped_clone ( pose::Pose const &  ,
pose::Pose const &  ,
id::SequenceMappingCOP  map = NULL 
) const
virtual

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.

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

References AAname, favor_native_bonus_, ResidueTypeConstraint(), rsd_type_name3_, and seqpos_.

utility::vector1< core::Size > core::scoring::constraints::ResidueTypeConstraint::residues ( ) const
virtual

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

References seqpos_.

void core::scoring::constraints::ResidueTypeConstraint::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.

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

References favor_native_bonus_, core::scoring::constraints::XYZ_Func::residue(), rsd_type_name3_, core::scoring::constraints::Constraint::score_type(), and seqpos_.

void core::scoring::constraints::ResidueTypeConstraint::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::Constraint.

References AAname, favor_native_bonus_, rsd_type_name3_, and seqpos_.

Member Data Documentation

std::string core::scoring::constraints::ResidueTypeConstraint::AAname
private
core::Real core::scoring::constraints::ResidueTypeConstraint::favor_native_bonus_
private
std::string core::scoring::constraints::ResidueTypeConstraint::rsd_type_name3_
private
Size core::scoring::constraints::ResidueTypeConstraint::seqpos_
private

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