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core::scoring::constraints::LocalCoordinateConstraint Class Reference

#include <LocalCoordinateConstraint.hh>

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

 LocalCoordinateConstraint ()
 
 LocalCoordinateConstraint (id::AtomID const &a1, id::StubID const &fixed_stub_in, Vector const &xyz_target_in, func::FuncOP func, ScoreType scotype=coordinate_constraint)
 c-tor More...
 
 ~LocalCoordinateConstraint () override
 
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
 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 &rhs) 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 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 read_def (std::istream &, pose::Pose const &, func::FuncFactory const &) 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...
 
void steal_def (pose::Pose const &) override
 take coordinates, distances, angles, etc from given pose More...
 
Real score (Vector const &xyz, Vector const &s1, Vector const &s2, Vector const &s3) const
 
void score (func::XYZ_Func const &xyz, EnergyMap const &, EnergyMap &emap) const override
 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...
 
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...
 
void fill_f1_f2 (AtomID const &atom, func::XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const override
 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...
 
Size natoms () const override
 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...
 
AtomID const & atom (Size const n) const override
 Returns the AtomID referred to by index. More...
 
Size show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1) 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...
 
void set_fixed_stub (id::StubID new_stub)
 
Vector xyz_target (core::pose::Pose const &local_frame_pose) const
 
void set_xyz_target (Vector const &xyz_in, core::pose::Pose const &local_frame_pose)
 
- 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_scoring (core::scoring::func::XYZ_Func const &, ScoreFunction const &) const
 
virtual void setup_for_derivatives (core::scoring::func::XYZ_Func const &, ScoreFunction const &) 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
core::scoring::func::Func
const & 
get_func () const
 Returns the func::Func object associated with this Constraint object. 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

 LocalCoordinateConstraint (LocalCoordinateConstraint const &src)
 Explicit copy constructor so that derived classes will recieve a deep copy of the Func this class contains. More...
 

Private Member Functions

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

Private Attributes

id::AtomID atom_
 
id::StubID fixed_stub_
 
Vector xyz_target_
 
func::FuncOP func_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( )

Referenced by clone().

core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( id::AtomID const &  a1,
id::StubID const &  fixed_stub_in,
Vector const &  xyz_target_in,
func::FuncOP  func,
ScoreType  scotype = coordinate_constraint 
)
core::scoring::constraints::LocalCoordinateConstraint::~LocalCoordinateConstraint ( )
overridedefault
core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint ( LocalCoordinateConstraint const &  src)
protected

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

Member Function Documentation

id::AtomID const & core::scoring::constraints::LocalCoordinateConstraint::atom ( Size const  index) const
overridevirtual

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::StubID::atom(), atom_, and fixed_stub_.

Referenced by remapped_clone().

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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 LocalCoordinateConstraint().

Real core::scoring::constraints::LocalCoordinateConstraint::dfunc ( Real const  theta) const
private

References func_.

Referenced by fill_f1_f2().

Real core::scoring::constraints::LocalCoordinateConstraint::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

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

References core::id::StubID::atom(), atom_, fixed_stub_, core::kinematics::Stub::global2local(), protocols::kinmatch::xyz(), and xyz_target_.

Referenced by fill_f1_f2(), and show_violations().

void core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2 ( AtomID const &  atom,
func::XYZ_Func const &  xyz_func,
Vector F1,
Vector F2,
EnergyMap const &  weights 
) const
overridevirtual

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.

References atom_, dfunc(), dist(), core::scoring::constraints::Constraint::score_type(), protocols::kinmatch::xyz(), and xyz_target_.

Real core::scoring::constraints::LocalCoordinateConstraint::func ( Real const  theta) const
private

References func_.

Referenced by score().

Size core::scoring::constraints::LocalCoordinateConstraint::natoms ( ) const
overridevirtual

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::LocalCoordinateConstraint::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 atom_, fixed_stub_, func_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), core::scoring::constraints::Constraint::score_type(), and xyz_target_.

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

one line definition "LocalCoordinateConstraint Atom1_Name Atom1_ResNum Atom2_Name Atom3_Name Atom4_Name Atom234_ResNum Atom1_target_X_coordinate Atom1_target_Y_coordinate Atom1_target_Z_coordinate func::Func_Type func::Func_Def"

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

References atom_, fixed_stub_, func_, core::pose::named_atom_id_to_atom_id(), core::pose::named_stub_id_to_stub_id(), core::scoring::func::FuncFactory::new_func(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pose::Pose::size(), core::scoring::constraints::tr(), core::id::AtomID::valid(), core::id::StubID::valid(), and xyz_target_.

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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::id::StubID::atom(), atom_, core::id::AtomID::atomno(), fixed_stub_, func_, core::id::AtomID::rsd(), core::scoring::constraints::Constraint::score_type(), and xyz_target_.

ConstraintOP core::scoring::constraints::LocalCoordinateConstraint::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::Constraint.

References atom(), core::pose::atom_id_to_named_atom_id(), func_, core::pose::named_atom_id_to_atom_id(), core::id::AtomID::rsd(), core::id::NamedAtomID::rsd(), core::scoring::constraints::Constraint::score_type(), core::id::AtomID::valid(), and xyz_target_.

bool core::scoring::constraints::LocalCoordinateConstraint::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.

Referenced by operator==().

Real core::scoring::constraints::LocalCoordinateConstraint::score ( Vector const &  xyz,
Vector const &  s1,
Vector const &  s2,
Vector const &  s3 
) const
void core::scoring::constraints::LocalCoordinateConstraint::score ( func::XYZ_Func const &  xyz_func,
EnergyMap const &  weights,
EnergyMap emap 
) const
overridevirtual

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 core::id::StubID::atom(), atom_, fixed_stub_, score(), core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void core::scoring::constraints::LocalCoordinateConstraint::set_fixed_stub ( id::StubID  new_stub)

References fixed_stub_.

void core::scoring::constraints::LocalCoordinateConstraint::set_xyz_target ( Vector const &  xyz_in,
core::pose::Pose const &  local_frame_pose 
)
void core::scoring::constraints::LocalCoordinateConstraint::show ( std::ostream &  ) const
overridevirtual

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 atom_, core::id::AtomID::atomno(), fixed_stub_, func_, and core::id::AtomID::rsd().

void core::scoring::constraints::LocalCoordinateConstraint::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 core::id::NamedStubID::atom(), core::id::NamedAtomID::atom(), atom_, core::pose::atom_id_to_named_atom_id(), fixed_stub_, func_, core::id::NamedAtomID::rsd(), core::pose::stub_id_to_named_stub_id(), type(), and xyz_target_.

Size core::scoring::constraints::LocalCoordinateConstraint::show_violations ( std::ostream &  out,
pose::Pose const &  ,
Size  ,
Real  threshold = 1 
) 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 atom_, core::id::AtomID::atomno(), dist(), func_, core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

void core::scoring::constraints::LocalCoordinateConstraint::steal_def ( pose::Pose const &  )
overridevirtual

take coordinates, distances, angles, etc from given pose

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

References atom_, core::pose::Pose::conformation(), fixed_stub_, and xyz_target_.

std::string core::scoring::constraints::LocalCoordinateConstraint::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().

Vector core::scoring::constraints::LocalCoordinateConstraint::xyz_target ( core::pose::Pose const &  local_frame_pose) const

Member Data Documentation

id::AtomID core::scoring::constraints::LocalCoordinateConstraint::atom_
private
id::StubID core::scoring::constraints::LocalCoordinateConstraint::fixed_stub_
private
func::FuncOP core::scoring::constraints::LocalCoordinateConstraint::func_
private
Vector core::scoring::constraints::LocalCoordinateConstraint::xyz_target_
private

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