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core::scoring::constraints::AtomPairConstraint Class Reference

#include <AtomPairConstraint.hh>

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Public Member Functions

 AtomPairConstraint ()
 
 AtomPairConstraint (AtomID const &a1, AtomID const &a2, FuncOP func, ScoreType scoretype=atom_pair_constraint)
 c-tor 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...
 
virtual ConstraintOP clone (FuncOP func) const
 
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...
 
bool operator== (Constraint const &other) const
 possibility to compare constraint according to data and not just pointers More...
 
Real score (Vector const &xyz1, Vector const &xyz2) const
 
void score (XYZ_Func const &xyz, EnergyMap const &, 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...
 
Real score (pose::Pose const &pose) const
 
virtual void fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const
 
std::string type () const
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
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 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...
 
AtomID const & atom (Size const n) const
 Returns the AtomID referred to by index. 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...
 
void show_def (std::ostream &out, pose::Pose const &pose) 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...
 
void read_def (std::istream &in, pose::Pose const &pose, FuncFactory const &func_factory)
 
virtual Real dist (pose::Pose const &pose) const
 return the "raw" distance before handed to the FUNC object More...
 
Real dist (core::conformation::Conformation const &conformation) const
 
virtual Real dist (XYZ_Func const &xyz) const
 
virtual Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, 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 core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp) const
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
virtual ~Constraint ()
 Virtual destructor. 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 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 fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0
 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 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...
 
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 &)
 

Protected Attributes

AtomID atom1_
 
AtomID atom2_
 
FuncOP func_
 

Private Member Functions

Real func (Real const theta) const
 
Real dfunc (Real const theta) const
 

Additional Inherited Members

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

Constructor & Destructor Documentation

core::scoring::constraints::AtomPairConstraint::AtomPairConstraint ( )
inline

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

core::scoring::constraints::AtomPairConstraint::AtomPairConstraint ( AtomID const &  a1,
AtomID const &  a2,
FuncOP  func,
ScoreType  scoretype = atom_pair_constraint 
)
inline

c-tor

Member Function Documentation

AtomID const& core::scoring::constraints::AtomPairConstraint::atom ( Size const  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 atom1_, and atom2_.

Referenced by remapped_clone().

virtual ConstraintOP core::scoring::constraints::AtomPairConstraint::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.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom1_, atom2_, AtomPairConstraint(), func_, and core::scoring::constraints::Constraint::score_type().

virtual ConstraintOP core::scoring::constraints::AtomPairConstraint::clone ( FuncOP  func) const
inlinevirtual
Real core::scoring::constraints::AtomPairConstraint::dfunc ( Real const  theta) const
inlineprivate

References func_.

Referenced by fill_f1_f2().

Real core::scoring::constraints::AtomPairConstraint::dist ( pose::Pose const &  ) const
virtual

return the "raw" distance before handed to the FUNC object

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

References core::pose::Pose::conformation().

Referenced by dist(), fill_f1_f2(), score(), and show_violations().

Real core::scoring::constraints::AtomPairConstraint::dist ( core::conformation::Conformation const &  conformation) const
Real core::scoring::constraints::AtomPairConstraint::dist ( XYZ_Func const &  xyz) const
virtual
core::Size core::scoring::constraints::AtomPairConstraint::effective_sequence_separation ( core::kinematics::ShortestPathInFoldTree const &  sp) const
virtual
void core::scoring::constraints::AtomPairConstraint::fill_f1_f2 ( AtomID const &  atom,
XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
virtual
Real core::scoring::constraints::AtomPairConstraint::func ( Real const  theta) const
inlineprivate

References func_.

Referenced by score().

virtual Func const& core::scoring::constraints::AtomPairConstraint::get_func ( ) const
inlinevirtual

Returns the Func object associated with this Constraint object.

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

References func_.

Size core::scoring::constraints::AtomPairConstraint::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::AtomPairConstraint::operator== ( Constraint const &  other) const
virtual

possibility to compare constraint according to data and not just pointers

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

References atom1_, atom2_, func_, and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AtomPairConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
FuncFactory const &  func_factory 
)
virtual
ConstraintOP core::scoring::constraints::AtomPairConstraint::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 atom1_, atom2_, core::id::AtomID::atomno(), AtomPairConstraint(), func_, and core::id::AtomID::rsd().

ConstraintOP core::scoring::constraints::AtomPairConstraint::remapped_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
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.

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom(), atom1_, atom2_, core::conformation::atom_id_to_named_atom_id(), AtomPairConstraint(), func_, core::conformation::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

Real core::scoring::constraints::AtomPairConstraint::score ( Vector const &  xyz1,
Vector const &  xyz2 
) const

References func().

Referenced by score().

void core::scoring::constraints::AtomPairConstraint::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 atom1_, atom2_, score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

Real core::scoring::constraints::AtomPairConstraint::score ( pose::Pose const &  pose) const
inline

References dist(), and func_.

void core::scoring::constraints::AtomPairConstraint::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 atom1_, atom2_, core::id::AtomID::atomno(), func_, and core::id::AtomID::rsd().

void core::scoring::constraints::AtomPairConstraint::show_def ( std::ostream &  ,
pose::Pose const &   
) const
virtual

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.

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

Reimplemented in core::scoring::constraints::NamedAtomPairConstraint.

References atom1_, atom2_, core::conformation::atom_id_to_named_atom_id(), func_, and type().

Size core::scoring::constraints::AtomPairConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1 
) const
virtual

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 ...

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

References atom1_, atom2_, core::id::AtomID::atomno(), core::pose::Pose::conformation(), dist(), func_, core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

std::string core::scoring::constraints::AtomPairConstraint::type ( ) const
inlinevirtual

Member Data Documentation

AtomID core::scoring::constraints::AtomPairConstraint::atom1_
mutableprotected
AtomID core::scoring::constraints::AtomPairConstraint::atom2_
mutableprotected
FuncOP core::scoring::constraints::AtomPairConstraint::func_
protected

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