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core::scoring::constraints::NamedAngleConstraint Class Reference

#include <NamedAngleConstraint.hh>

Inheritance diagram for core::scoring::constraints::NamedAngleConstraint:
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Public Member Functions

 NamedAngleConstraint (id::NamedAtomID const &a1, id::NamedAtomID const &a2, id::NamedAtomID const &a3, func::FuncOP func, ScoreType scoretype=angle_constraint)
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
ConstraintOP clone () const override
 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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned. More...
 
ConstraintOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=nullptr) const override
 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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes. More...
 
ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) const override
 This overrride updates the sequence numbering but not the atom names. More...
 
bool operator== (Constraint const &rhs) const override
 possibility to compare constraint according to data and not just pointers More...
 
bool same_type_as_me (Constraint const &other) const override
 Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it. More...
 
void show_def (std::ostream &out, pose::Pose const &pose) const override
 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
 
void read_def (std::istream &in, pose::Pose const &pose, func::FuncFactory const &func_factory) override
 
void score (func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override
 compute score More...
 
void setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override
 
core::Real dist (core::scoring::func::XYZ_Func const &xyz) const override
 return the raw "distance" before that distance is handed to the FUNC object More...
 
- Public Member Functions inherited from core::scoring::constraints::AngleConstraint
 AngleConstraint (AtomID const &a1, AtomID const &a2, AtomID const &a3, core::scoring::func::FuncOP func_in, ScoreType scotype=angle_constraint)
 Constructor. More...
 
 AngleConstraint (core::scoring::func::FuncOP func_in, ScoreType scoretype=angle_constraint)
 Constructor without atom IDs – if you create an AngleConstraint with this constructor, you must never call its score( XYZFunc ) method! Dangerous and stupid! More...
 
Real score (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
 compute score More...
 
virtual core::Real score (conformation::Conformation const &) const
 
Real angle (Vector const &xyz1, Vector const &xyz2, Vector const &xyz3) const
 compute More...
 
void fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
 compute atom deriv More...
 
Size natoms () const override
 number of atoms — always 3 for angles More...
 
AtomID const & atom (Size const n) const override
 return AtomID for atom 1,2,3 More...
 
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, core::Real threshold=1) const override
 output violation of constraint to out - returns 1 if violated ( i.e., func.show_violations() > 0 ) More...
 
void show (std::ostream &out) const override
 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...
 
core::scoring::func::Func const & get_func () const override
 Returns the func::Func object associated with this Constraint object. More...
 
Real func (Real const theta) const
 evaluate func at theta More...
 
Real dfunc (Real const theta) const
 evaluate dfunc at theta More...
 
void p1_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const
 
void p2_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &F1, Vector &F2) const
 
AtomID const & atom1 () const
 
AtomID const & atom2 () const
 
AtomID const & atom3 () const
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
 ~Constraint () override
 Virtual destructor. More...
 
virtual ConstraintOP clone (func::FuncOP) const
 Clone the constraint, but where a new Func object is to be used instead. 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 DON'T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL. 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 Real score (pose::Pose const &pose) const
 Returns the unweighted score of this constraint computed over the given pose. More...
 
virtual Real score (pose::Pose const &pose, EnergyMap const &weights) const
 Returns the weighted score of this constraint computed over the given pose. More...
 
virtual Real dist (core::pose::Pose const &) const
 return the raw "distance" before that distance is handed to the FUNC object More...
 
virtual void setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual void steal_def (pose::Pose const &)
 take coordinates, distances, angles, etc from given pose More...
 
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
 Inequality operator to test whether two constraints are not functionally identical. 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
 

Protected Member Functions

 NamedAngleConstraint (NamedAngleConstraint const &src)
 
- Protected Member Functions inherited from core::scoring::constraints::AngleConstraint
 AngleConstraint (AngleConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...
 
func::FuncCOP func () const
 const access to func More...
 
void set_func (func::FuncOP f)
 set func More...
 
void atom1 (AtomID newid) const
 
void atom2 (AtomID newid) const
 
void atom3 (AtomID newid) const
 

Private Attributes

id::NamedAtomID named_atom1_
 
id::NamedAtomID named_atom2_
 
id::NamedAtomID named_atom3_
 
core::Size type1_id_
 
core::Size type2_id_
 
core::Size type3_id_
 

Additional Inherited Members

- Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID AtomID
 
- Static Public Member Functions inherited from core::scoring::constraints::AngleConstraint
static void p1_theta_deriv (Vector const &p1, Vector const &p2, Vector const &p3, Vector &f1, Vector &f2)
 
static void helper (Vector const &M, Vector const &w, Vector &F1, Vector &F2)
 

Constructor & Destructor Documentation

core::scoring::constraints::NamedAngleConstraint::NamedAngleConstraint ( id::NamedAtomID const &  a1,
id::NamedAtomID const &  a2,
id::NamedAtomID const &  a3,
func::FuncOP  func,
ScoreType  scoretype = angle_constraint 
)

Referenced by clone(), and remap_resid().

core::scoring::constraints::NamedAngleConstraint::NamedAngleConstraint ( NamedAngleConstraint const &  src)
protecteddefault

Member Function Documentation

ConstraintOP core::scoring::constraints::NamedAngleConstraint::clone ( ) const
overridevirtual

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. This function must return a deep copy of itself – meaning that if this Constraint holds pointers to other Constraints that it must invoke clone on those Constraints as well. If the Constraint holds a FuncOP, then the Func should also be cloned.

Reimplemented from core::scoring::constraints::AngleConstraint.

References NamedAngleConstraint().

Referenced by remap_resid().

core::Real core::scoring::constraints::NamedAngleConstraint::dist ( core::scoring::func::XYZ_Func const &  ) const
overridevirtual

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

  • If such a distance doesn't make sense for this constraint, just return 0

Reimplemented from core::scoring::constraints::AngleConstraint.

References core::scoring::constraints::AngleConstraint::angle(), core::id::NamedAtomID::atom(), named_atom1_, named_atom2_, named_atom3_, core::scoring::func::XYZ_Func::residue(), core::id::NamedAtomID::rsd(), and protocols::kinmatch::xyz().

bool core::scoring::constraints::NamedAngleConstraint::operator== ( Constraint const &  other) const
overridevirtual

possibility to compare constraint according to data and not just pointers

Reimplemented from core::scoring::constraints::AngleConstraint.

References named_atom1_, named_atom2_, named_atom3_, type1_id_, type2_id_, and type3_id_.

void core::scoring::constraints::NamedAngleConstraint::read_def ( std::istream &  data,
pose::Pose const &  pose,
func::FuncFactory const &  func_factory 
)
overridevirtual
ConstraintOP core::scoring::constraints::NamedAngleConstraint::remap_resid ( core::id::SequenceMapping const &  seqmap) const
overridevirtual
ConstraintOP core::scoring::constraints::NamedAngleConstraint::remapped_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
id::SequenceMappingCOP  map = nullptr 
) const
overridevirtual

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 .. nullptr = identity mapping to the new object. Intended to be implemented by derived classes.

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::AngleConstraint.

References core::scoring::constraints::AngleConstraint::atom1(), core::scoring::constraints::AngleConstraint::atom2(), core::scoring::constraints::AngleConstraint::atom3(), core::scoring::constraints::AngleConstraint::func(), named_atom1_, named_atom2_, named_atom3_, core::pose::named_atom_id_to_atom_id(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and core::id::AtomID::valid().

bool core::scoring::constraints::NamedAngleConstraint::same_type_as_me ( Constraint const &  other) const
overridevirtual

Determine if the calling class has the same type as the input class, using dynamic casts. This is important in ensuring that two constraints are equal: both this and other must check that the other is the same as it. This is not an optional method and every class should implement it, regaurdless of whether a parent class implements it.

Reimplemented from core::scoring::constraints::AngleConstraint.

void core::scoring::constraints::NamedAngleConstraint::score ( func::XYZ_Func const &  xyz,
EnergyMap const &  ,
EnergyMap emap 
) const
overridevirtual
void core::scoring::constraints::NamedAngleConstraint::setup_for_scoring ( func::XYZ_Func const &  xyz,
ScoreFunction const &   
) const
overridevirtual
void core::scoring::constraints::NamedAngleConstraint::show_def ( std::ostream &  ,
pose::Pose const &   
) const
overridevirtual

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::AngleConstraint.

References show_def_nopose().

void core::scoring::constraints::NamedAngleConstraint::show_def_nopose ( std::ostream &  out) const
std::string core::scoring::constraints::NamedAngleConstraint::type ( ) const
overridevirtual

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

Reimplemented from core::scoring::constraints::AngleConstraint.

Referenced by setup_for_scoring(), and show_def_nopose().

Member Data Documentation

id::NamedAtomID core::scoring::constraints::NamedAngleConstraint::named_atom1_
private
id::NamedAtomID core::scoring::constraints::NamedAngleConstraint::named_atom2_
private
id::NamedAtomID core::scoring::constraints::NamedAngleConstraint::named_atom3_
private
core::Size core::scoring::constraints::NamedAngleConstraint::type1_id_
private

Referenced by operator==(), and setup_for_scoring().

core::Size core::scoring::constraints::NamedAngleConstraint::type2_id_
private

Referenced by operator==(), and setup_for_scoring().

core::Size core::scoring::constraints::NamedAngleConstraint::type3_id_
private

Referenced by operator==(), and setup_for_scoring().


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