#include <BindingSiteConstraint.hh>

Inheritance diagram for protocols::constraints_additional::BindingSiteConstraint:

Public Member Functions
	BindingSiteConstraint ()
	null constructor More...

	BindingSiteConstraint (utility::vector1< AtomID > const &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 > const &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...

virtual core::scoring::constraints::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. 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
	Equality operator to test whether two constraints are functionally identical. More...

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

void	setup_for_scoring (core::scoring::func::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const

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

virtual 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
	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 core::scoring::constraints::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...

void	show_def (std::ostream &out, core::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	read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory)
	Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_. More...

Size	show_violations (std::ostream &out, core::pose::Pose const &pose, core::Size verbose_level, core::Real threshold=1.0) 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...

Public Member Functions inherited from core::scoring::constraints::Constraint
	Constraint (ScoreType const &t)
	Constructor for Constraint class. More...

virtual	~Constraint ()
	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 &) const

virtual core::Real	dist (core::pose::Pose const &) const
	return the raw "distance" before that distance is handed to the FUNC object More...

virtual core::Real	dist (core::scoring::func::XYZ_Func 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 &)
	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< AtomID >	atms_

ObjexxFCL::FArray2D< core::Real >	tgt_pos_

ObjexxFCL::FArray2D< core::Real >	tgt_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

Referenced by clone(), and remap_resid().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint	(	utility::vector1< AtomID > const &	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 > const &	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 ( Size const index ) const

virtual

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().

virtual core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::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. 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_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

void protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2	(	AtomID const &	atom,
		core::scoring::func::XYZ_Func const &	xyz_func,
		core::Vector &	F1,
		core::Vector &	F2,
		core::scoring::EnergyMap const &	weights
	)		const

virtual

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 atms_, atom(), rot_db, core::scoring::constraints::Constraint::score_type(), and protocols::kinmatch::xyz().

void protocols::constraints_additional::BindingSiteConstraint::init ( core::pose::Pose const & start_pose )

protected

References atms_, core::chemical::CENTROID, protocols::membrane::com(), natoms(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::util::switch_to_residue_type_set(), tgt_pos_, tgt_pos_centroid_, and core::pose::Pose::xyz().

Referenced by BindingSiteConstraint(), and read_def().

core::Size protocols::constraints_additional::BindingSiteConstraint::natoms ( ) const

virtual

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

virtual

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

References atms_, protocols::membrane::com(), natoms(), rot_db, tgt_pos_, and tgt_pos_centroid_.

Referenced by setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::read_def	(	std::istream &	in,
		core::pose::Pose const &	pose,
		core::scoring::func::FuncFactory const &	func_factory
	)

virtual

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::total_residue(), and tr().

core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::remap_resid ( core::id::SequenceMapping const & ) const

virtual

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_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

bool protocols::constraints_additional::BindingSiteConstraint::same_type_as_me ( core::scoring::constraints::Constraint const & other ) const

virtual

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

virtual

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.

Reimplemented from 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

virtual

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

References setup_for_scoring().

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

virtual

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

References atms_, core::chemical::CENTROID, natoms(), pre_align(), core::scoring::func::XYZ_Func::residue(), core::chemical::ResidueType::residue_type_set(), core::conformation::Residue::type(), and protocols::kinmatch::xyz().

Referenced by setup_for_derivatives().

void protocols::constraints_additional::BindingSiteConstraint::show ( std::ostream & ) const

virtual

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

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::Constraint.

core::Size protocols::constraints_additional::BindingSiteConstraint::show_violations	(	std::ostream &	out,
		core::pose::Pose const &	,
		core::Size	,
		core::Real	threshold = `1.0`
	)		const

virtual

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

virtual

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

Referenced by atom(), clone(), fill_f1_f2(), init(), natoms(), operator==(), pre_align(), read_def(), remap_resid(), score(), and setup_for_scoring().

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

Referenced by clone(), init(), operator==(), pre_align(), and remap_resid().

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

private

Referenced by clone(), init(), operator==(), pre_align(), and remap_resid().

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

src/protocols/constraints_additional/BindingSiteConstraint.hh
src/protocols/constraints_additional/BindingSiteConstraint.cc

Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation