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core::scoring::constraints::AmbiguousNMRConstraint Class Reference

#include <AmbiguousNMRConstraint.hh>

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

 AmbiguousNMRConstraint (func::FuncOP func=nullptr)
 default Constructor More...
 
 AmbiguousNMRConstraint (ConstraintCOPs const &cst_in, func::FuncOP func)
 Constructor. 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 clone (func::FuncOP func) const override
 Clone the constraint, but where a new Func object is to be used instead. More...
 
MultiConstraintOP empty_clone () const override
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
bool operator== (Constraint const &other) const override
 Equality operator to test whether two constraints are functionally identical. 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 score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override
 compute score More...
 
core::Real dist (func::XYZ_Func const &xyz) const override
 return the raw "distance" before that distance is handed to the FUNC object More...
 
void add_individual_constraint (ConstraintCOP cst_in) override
 add individual constraint into AmbiguousNMRConstraint More...
 
ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) const override
 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...
 
void fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
 compute atom deriv More...
 
func::Func const & get_func () const override
 Returns the func::Func object associated with this Constraint object. More...
 
void read_def (std::istream &data, core::pose::Pose const &pose, func::FuncFactory const &func_factory) override
 
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...
 
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) const override
 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...
 
- Public Member Functions inherited from core::scoring::constraints::MultiConstraint
 MultiConstraint (ScoreType const &t=dof_constraint)
 default Constructor More...
 
 MultiConstraint (ConstraintCOPs const &cst_in, ScoreType const &t=dof_constraint)
 Constructor – performs a shallow copy of the input ConstraintCOPs. More...
 
ConstraintOP clone () const override
 Creates a deep copy of this MultiConstaint, cloning all constraints that it holds. More...
 
Size natoms () const override
 number of atoms involved in this MultiConstraint container More...
 
Size size () const
 number of constraints that are held by this MultiConstraint More...
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
void read_def (std::istream &data, pose::Pose const &pose, func::FuncFactory const &func_factory) override
 read in constraint defiinition More...
 
bool operator== (Constraint const &other) 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 score (func::XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const override
 compute score More...
 
core::Real dist (core::scoring::func::XYZ_Func const &) const override
 
AtomID const & atom (Size const n) const override
 Returns the AtomID referred to by index. More...
 
utility::vector1< core::Sizeresidues () const override
 Returns the pose numbers of the residues involved in this constraint, in no particular order. More...
 
void setup_for_scoring (func::XYZ_Func const &, ScoreFunction const &) const override
 
ConstraintOP remap_resid (core::id::SequenceMapping const &seqmap) const override
 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...
 
void fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
 compute atom deriv 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...
 
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...
 
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) const override
 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...
 
ConstraintCOPs const & member_constraints () const
 
ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, 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 .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More...
 
void set_effective_sequence_separation (core::Size setting)
 
core::Size choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &) override
 
core::Size effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const override
 
- Public Member Functions inherited from core::scoring::constraints::Constraint
 Constraint (ScoreType const &t)
 Constructor for Constraint class. More...
 
 ~Constraint () override
 Virtual destructor. 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...
 

Protected Member Functions

 AmbiguousNMRConstraint (AmbiguousNMRConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...
 
- Protected Member Functions inherited from core::scoring::constraints::MultiConstraint
 MultiConstraint (MultiConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the member constraints held in this class. More...
 
 MultiConstraint (MultiConstraint const &src, dont_copy_constraints const &)
 non-public key for special constructor More...
 
ConstraintCOPs cloned_member_constraints () const
 Return a vector of Constraints that are clones of the member constraints. More...
 

Private Attributes

func::FuncOP func_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint ( func::FuncOP  func = nullptr)
core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint ( ConstraintCOPs const &  cst_in,
func::FuncOP  func 
)
core::scoring::constraints::AmbiguousNMRConstraint::AmbiguousNMRConstraint ( AmbiguousNMRConstraint const &  src)
protected

Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains.

References add_individual_constraint(), and core::scoring::constraints::MultiConstraint::member_constraints().

Member Function Documentation

void core::scoring::constraints::AmbiguousNMRConstraint::add_individual_constraint ( ConstraintCOP  cst_in)
overridevirtual
ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::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.

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

References AmbiguousNMRConstraint().

Referenced by empty_clone().

ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::clone ( func::FuncOP  ) const
overridevirtual

Clone the constraint, but where a new Func object is to be used instead.

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

References AmbiguousNMRConstraint(), and core::scoring::constraints::MultiConstraint::cloned_member_constraints().

core::Real core::scoring::constraints::AmbiguousNMRConstraint::dist ( 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

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

References core::scoring::constraints::MultiConstraint::member_constraints().

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

MultiConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::empty_clone ( ) const
overridevirtual
void core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2 ( AtomID const &  atom,
func::XYZ_Func const &  xyz,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
overridevirtual
func::Func const & core::scoring::constraints::AmbiguousNMRConstraint::get_func ( ) const
overridevirtual

Returns the func::Func object associated with this Constraint object.

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

References func_.

Referenced by empty_clone(), fill_f1_f2(), remap_resid(), and score().

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

Equality operator to test whether two constraints are functionally identical.

This operator should use floating point comparison and should not decide that two floats are identical if they are within some epsilon > 0. This method allows developes to remove specific constraints from Poses, even if the constraints have been cloned. Remapped constraints should not be considered identical – i.e., if cst1 is between residues i and j and cst2 is between residues i+1 and j+1. All subclasses of Constraint must implement this method.

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

References func_, core::scoring::constraints::MultiConstraint::operator==(), and core::scoring::constraints::Constraint::same_type_as_me().

void core::scoring::constraints::AmbiguousNMRConstraint::read_def ( std::istream &  data,
core::pose::Pose const &  pose,
func::FuncFactory const &  func_factory 
)
overridevirtual

read definition of a multiconstraint. Since a MultiConstraint is essentially a vector of

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

References func_, core::scoring::func::FuncFactory::new_func(), and core::scoring::constraints::MultiConstraint::read_def().

ConstraintOP core::scoring::constraints::AmbiguousNMRConstraint::remap_resid ( core::id::SequenceMapping const &  ) const
overridevirtual

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 core::scoring::func::Func::clone(), get_func(), and core::scoring::constraints::MultiConstraint::member_constraints().

bool core::scoring::constraints::AmbiguousNMRConstraint::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.

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

void core::scoring::constraints::AmbiguousNMRConstraint::score ( func::XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
overridevirtual

compute score

ScoreFunction, scores all member constraints but only reports the lowest one.

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

References dist(), core::scoring::func::Func::func(), get_func(), and core::scoring::constraints::Constraint::score_type().

void core::scoring::constraints::AmbiguousNMRConstraint::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::Constraint.

References func_, core::scoring::constraints::MultiConstraint::member_constraints(), and type().

Size core::scoring::constraints::AmbiguousNMRConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1.0 
) const
overridevirtual

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 dist(), func_, and core::scoring::constraints::MultiConstraint::member_constraints().

std::string core::scoring::constraints::AmbiguousNMRConstraint::type ( ) const
overridevirtual

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_def().

Member Data Documentation

func::FuncOP core::scoring::constraints::AmbiguousNMRConstraint::func_
private

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