Rosetta Core  2014.35
Public Member Functions | Private Attributes | List of all members
core::scoring::constraints::NamedAtomPairConstraint Class Reference

#include <NamedAtomPairConstraint.hh>

Public Member Functions

 NamedAtomPairConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, func::FuncOP func, ScoreType scoretype=atom_pair_constraint)
 
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 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 setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const
 
virtual 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 func::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 show_def_nopose (std::ostream &out) const
 
virtual void read_def (std::istream &in, pose::Pose const &pose, func::FuncFactory const &func_factory)
 
- Public Member Functions inherited from core::scoring::constraints::AtomPairConstraint
 AtomPairConstraint ()
 
 AtomPairConstraint (AtomID const &a1, AtomID const &a2, core::scoring::func::FuncOP func, ScoreType scoretype=atom_pair_constraint)
 c-tor More...
 
virtual ConstraintOP clone (core::scoring::func::FuncOP func) const
 
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 (core::scoring::func::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, core::scoring::func::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...
 
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...
 
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 (core::scoring::func::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::Func const & get_func () const
 Returns the func::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_derivatives (core::scoring::func::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 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 &)
 

Private Attributes

id::NamedAtomID named_atom1_
 
id::NamedAtomID named_atom2_
 
core::Size type1_id_
 
core::Size type2_id_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 
- Protected Attributes inherited from core::scoring::constraints::AtomPairConstraint
AtomID atom1_
 
AtomID atom2_
 
core::scoring::func::FuncOP func_
 

Constructor & Destructor Documentation

core::scoring::constraints::NamedAtomPairConstraint::NamedAtomPairConstraint ( id::NamedAtomID const &  a1,
id::NamedAtomID const &  a2,
func::FuncOP  func,
ScoreType  scoretype = atom_pair_constraint 
)
inline

Referenced by clone(), and remapped_clone().

Member Function Documentation

virtual ConstraintOP core::scoring::constraints::NamedAtomPairConstraint::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.

Reimplemented from core::scoring::constraints::AtomPairConstraint.

References core::scoring::constraints::AtomPairConstraint::func_, named_atom1_, named_atom2_, NamedAtomPairConstraint(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::NamedAtomPairConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
func::FuncFactory const &  func_factory 
)
virtual
ConstraintOP core::scoring::constraints::NamedAtomPairConstraint::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::AtomPairConstraint.

References core::scoring::constraints::AtomPairConstraint::atom1_, core::scoring::constraints::AtomPairConstraint::atom2_, core::scoring::constraints::AtomPairConstraint::func_, named_atom1_, named_atom2_, core::pose::named_atom_id_to_atom_id(), NamedAtomPairConstraint(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

void core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring ( func::XYZ_Func const &  xyz,
ScoreFunction const &   
) const
virtual
void core::scoring::constraints::NamedAtomPairConstraint::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 func::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::AtomPairConstraint.

References show_def_nopose().

void core::scoring::constraints::NamedAtomPairConstraint::show_def_nopose ( std::ostream &  out) const

Member Data Documentation

id::NamedAtomID core::scoring::constraints::NamedAtomPairConstraint::named_atom1_
private
id::NamedAtomID core::scoring::constraints::NamedAtomPairConstraint::named_atom2_
private
core::Size core::scoring::constraints::NamedAtomPairConstraint::type1_id_
private

Referenced by setup_for_scoring().

core::Size core::scoring::constraints::NamedAtomPairConstraint::type2_id_
private

Referenced by setup_for_scoring().


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