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protocols::constraints_additional::BindingSiteConstraint Class Reference

#include <BindingSiteConstraint.hh>

Inheritance diagram for protocols::constraints_additional::BindingSiteConstraint:
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Public Member Functions

 BindingSiteConstraint ()
 null constructor More...
 
 BindingSiteConstraint (utility::vector1< AtomID > atms, core::pose::Pose const &start_pose, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
 ctor from atom list + input pose More...
 
 BindingSiteConstraint (utility::vector1< AtomID > atms, ObjexxFCL::FArray2D< core::Real > tgt_pos, ObjexxFCL::FArray2D< core::Real > tgt_pos_centroid, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
 ctor from a vector of atom positions (in lieu of a pose) More...
 
core::scoring::constraints::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...
 
bool operator== (core::scoring::constraints::Constraint const &other) const override
 Equality operator to test whether two constraints are functionally identical. More...
 
bool same_type_as_me (core::scoring::constraints::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 (core::scoring::func::XYZ_Func const &xyz, core::scoring::EnergyMap const &, core::scoring::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 &) const override
 
void setup_for_scoring (core::scoring::func::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const override
 
void pre_align (utility::vector1< numeric::xyzVector< core::Real > > const &templ_atms, utility::vector1< bool > const &) const
 
void setup_for_derivatives (core::scoring::func::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const override
 
void fill_f1_f2 (AtomID const &atom, core::scoring::func::XYZ_Func const &xyz, core::Vector &F1, core::Vector &F2, core::scoring::EnergyMap const &weights) const override
 
std::string type () const override
 Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...
 
core::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...
 
core::scoring::constraints::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...
 
AtomID const & atom (core::Size const n) const override
 Returns the AtomID referred to by index. 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, core::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 read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory) override
 Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_. More...
 
core::Size show_violations (std::ostream &out, core::pose::Pose const &pose, core::Size verbose_level, core::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::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 ConstraintOP remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map) 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 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 fill_f1_f2 (AtomID const &atom, core::scoring::func::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 &)
 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...
 
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

void init (core::pose::Pose const &start_pose)
 

Private Attributes

utility::vector1< AtomIDatms_
 
ObjexxFCL::FArray2D< core::Realtgt_pos_
 
ObjexxFCL::FArray2D< core::Realtgt_pos_centroid_
 

Static Private Attributes

static std::map< AtomID,
numeric::xyzVector< core::Real > > 
rot_db
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( )
inline

null constructor

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( utility::vector1< AtomID atms,
core::pose::Pose const &  start_pose,
core::scoring::ScoreType  scoretype = core::scoring::atom_pair_constraint 
)

ctor from atom list + input pose

c-tor

Parameters
scoretype? TO DO – give own scoretype

References init().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( utility::vector1< AtomID atms,
ObjexxFCL::FArray2D< core::Real tgt_pos,
ObjexxFCL::FArray2D< core::Real tgt_pos_centroid,
core::scoring::ScoreType  scoretype = core::scoring::atom_pair_constraint 
)

ctor from a vector of atom positions (in lieu of a pose)

Parameters
scoretype? TO DO – give own scoretype

Member Function Documentation

core::id::AtomID const & protocols::constraints_additional::BindingSiteConstraint::atom ( core::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 atms_.

Referenced by fill_f1_f2().

core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::clone ( ) const
inlineoverridevirtual

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 atms_, core::scoring::constraints::Constraint::score_type(), tgt_pos_, and tgt_pos_centroid_.

core::Real protocols::constraints_additional::BindingSiteConstraint::dist ( core::scoring::func::XYZ_Func const &  ) const
inlineoverridevirtual

BindingSiteConstraints don't have a single distance

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

void protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2 ( AtomID const &  atom,
core::scoring::func::XYZ_Func const &  xyz,
core::Vector F1,
core::Vector F2,
core::scoring::EnergyMap const &  weights 
) const
override
void protocols::constraints_additional::BindingSiteConstraint::init ( core::pose::Pose const &  start_pose)
protected
core::Size protocols::constraints_additional::BindingSiteConstraint::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.

References atms_.

Referenced by init(), pre_align(), and setup_for_scoring().

bool protocols::constraints_additional::BindingSiteConstraint::operator== ( core::scoring::constraints::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 atms_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), tgt_pos_, and tgt_pos_centroid_.

void protocols::constraints_additional::BindingSiteConstraint::pre_align ( utility::vector1< numeric::xyzVector< core::Real > > const &  templ_atms,
utility::vector1< bool > const &  align_centroid 
) const
void protocols::constraints_additional::BindingSiteConstraint::read_def ( std::istream &  in,
core::pose::Pose const &  pose,
core::scoring::func::FuncFactory const &  func_factory 
)
overridevirtual

Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.

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

References atms_, core::chemical::ResidueType::atom_index(), init(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and tr().

core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::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 atms_, tgt_pos_, and tgt_pos_centroid_.

bool protocols::constraints_additional::BindingSiteConstraint::same_type_as_me ( core::scoring::constraints::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==().

void protocols::constraints_additional::BindingSiteConstraint::score ( core::scoring::func::XYZ_Func const &  xyz_func,
core::scoring::EnergyMap const &  weights,
core::scoring::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 atms_, rot_db, and core::scoring::constraints::Constraint::score_type().

void protocols::constraints_additional::BindingSiteConstraint::setup_for_derivatives ( core::scoring::func::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const
overridevirtual
void protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring ( core::scoring::func::XYZ_Func const &  xyz,
core::scoring::ScoreFunction const &  scfxn 
) const
overridevirtual
void protocols::constraints_additional::BindingSiteConstraint::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.

void protocols::constraints_additional::BindingSiteConstraint::show_def ( std::ostream &  ,
core::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.

core::Size protocols::constraints_additional::BindingSiteConstraint::show_violations ( std::ostream &  out,
core::pose::Pose const &  ,
core::Size  ,
core::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.

std::string protocols::constraints_additional::BindingSiteConstraint::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.

Member Data Documentation

utility::vector1< AtomID > protocols::constraints_additional::BindingSiteConstraint::atms_
private
std::map< core::id::AtomID, numeric::xyzVector< core::Real > > protocols::constraints_additional::BindingSiteConstraint::rot_db
staticprivate

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

ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_
private
ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_centroid_
private

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