#include <BindingSiteConstraint.hh>

Inheritance diagram for protocols::constraints_additional::BindingSiteConstraint:

Collaboration 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. More...

void	score (core::scoring::constraints::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::constraints::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::constraints::XYZ_Func const &xyz, core::scoring::ScoreFunction const &scfxn) const

virtual void	fill_f1_f2 (AtomID const &atom, core::scoring::constraints::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 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::constraints::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 (FuncOP) const

virtual ConstraintOP	remapped_clone (pose::Pose const &, pose::Pose const &, id::SequenceMappingCOP map=NULL) 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. 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 core::Real	dist (core::pose::Pose const &) const
	return the "raw" distance before handed to the FUNC object More...

virtual core::Real	dist (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 &)

std::string	to_string () const
	Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More...

virtual Func const &	get_func () const
	Returns the Func object associated with this Constraint object. More...

virtual bool	operator== (Constraint const &) const
	possibility to do object comparison instead of pointer comparison More...

bool	operator!= (Constraint const &other) const
	possibility to do object comparison instead of pointer comparison 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

Detailed Description

Definition at line 42 of file BindingSiteConstraint.hh.

Constructor & Destructor Documentation

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

inline

null constructor

Definition at line 46 of file BindingSiteConstraint.hh.

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

Definition at line 60 of file BindingSiteConstraint.cc.

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

Definition at line 116 of file BindingSiteConstraint.cc.

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.

Definition at line 325 of file BindingSiteConstraint.cc.

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.

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

Definition at line 65 of file BindingSiteConstraint.hh.

References atms_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

void protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2	(	AtomID const &	atom,
		core::scoring::constraints::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.

Definition at line 271 of file BindingSiteConstraint.cc.

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

Definition at line 70 of file BindingSiteConstraint.cc.

References atms_, core::chemical::CENTROID, natoms(), core::pose::Pose::residue(), 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.

Definition at line 301 of file BindingSiteConstraint.cc.

References atms_.

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

void protocols::constraints_additional::BindingSiteConstraint::pre_align	(	utility::vector1< numeric::xyzVector< core::Real > > const &	templ_atms,
		utility::vector1< bool > const &	align_centroid
	)		const

Definition at line 179 of file BindingSiteConstraint.cc.

References atms_, 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::constraints::FuncFactory const &	func_factory
	)

virtual

Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.

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

Definition at line 397 of file BindingSiteConstraint.cc.

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.

Definition at line 307 of file BindingSiteConstraint.cc.

References atms_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

void protocols::constraints_additional::BindingSiteConstraint::score	(	core::scoring::constraints::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.

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

Definition at line 130 of file BindingSiteConstraint.cc.

References atms_, rot_db, and core::scoring::constraints::Constraint::score_type().

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

virtual

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

Definition at line 263 of file BindingSiteConstraint.cc.

References setup_for_scoring().

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

virtual

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

Definition at line 147 of file BindingSiteConstraint.cc.

References atms_, core::chemical::CENTROID, core::chemical::ResidueTypeSet::name(), natoms(), pre_align(), core::scoring::constraints::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.

Definition at line 336 of file BindingSiteConstraint.cc.

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 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.

Definition at line 341 of file BindingSiteConstraint.cc.

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.

Definition at line 346 of file BindingSiteConstraint.cc.

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.

Definition at line 295 of file BindingSiteConstraint.cc.

Member Data Documentation

utility::vector1< AtomID > protocols::constraints_additional::BindingSiteConstraint::atms_

private

Definition at line 121 of file BindingSiteConstraint.hh.

Referenced by atom(), clone(), fill_f1_f2(), init(), natoms(), 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

Definition at line 126 of file BindingSiteConstraint.hh.

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

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

private

Definition at line 122 of file BindingSiteConstraint.hh.

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

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

private

Definition at line 123 of file BindingSiteConstraint.hh.

Referenced by clone(), init(), 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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation