This constraint favors creating a pocket suitable for a small-molecule. More...

#include <PocketConstraint.hh>

Inheritance diagram for protocols::pockets::PocketConstraint:

Public Member Functions
std::string	type () const override
	Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More...

	PocketConstraint ()

	PocketConstraint (core::pose::Pose const &pose)

	PocketConstraint (const PocketConstraint &old)

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

core::Size	target_res () const

	~PocketConstraint () override

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::id::AtomID const &	atom (core::Size const index) const override
	Returns the AtomID referred to by index. 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
	Reads the definition of a Constraint from the given std::istream, 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. More...

void	score (core::scoring::func::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, 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	fill_f1_f2 (core::id::AtomID const &, core::scoring::func::XYZ_Func const &, core::Vector &, core::Vector &, core::scoring::EnergyMap const &weights) const override

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	set_target_res (core::pose::Pose const &pose, core::Size new_seqpos)

void	set_target_res_pdb (core::pose::Pose const &pose, std::string resid)

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 ConstraintOP	remap_resid (core::id::SequenceMapping const &) 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...

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

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	show (std::ostream &) 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...

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 Size	show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) 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...

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

Private Attributes
core::Size	seqpos_

core::Size	totalres_

core::Size	angles_

core::Real	weight_

protocols::pockets::PocketGridOP	pocketgrid_

utility::vector1< AtomID >	atom_ids_

bool	dumppdb_

std::vector < core::conformation::ResidueCOP >	residues_

Additional Inherited Members
Public Types inherited from core::scoring::constraints::Constraint
typedef id::AtomID	AtomID

Detailed Description

This constraint favors creating a pocket suitable for a small-molecule.

Constructor & Destructor Documentation

protocols::pockets::PocketConstraint::PocketConstraint ( )

Referenced by clone().

protocols::pockets::PocketConstraint::PocketConstraint ( core::pose::Pose const & pose )

References core::pose::Pose::conformation(), init(), core::pose::Pose::pdb_info(), pocketgrid_, core::conformation::Conformation::residue(), seqpos_, and core::pose::Pose::size().

protocols::pockets::PocketConstraint::PocketConstraint ( const PocketConstraint & old )

References dumppdb_, pocketgrid_, seqpos_, and totalres_.

protocols::pockets::PocketConstraint::~PocketConstraint ( )

overridedefault

Member Function Documentation

core::id::AtomID const& protocols::pockets::PocketConstraint::atom ( core::Size const index ) const

inlineoverridevirtual

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 atom_ids_.

core::scoring::constraints::ConstraintOP protocols::pockets::PocketConstraint::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 PocketConstraint().

core::Real protocols::pockets::PocketConstraint::dist ( core::scoring::func::XYZ_Func const & ) const

inlineoverridevirtual

PocketConstraints don't have a single distance

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

void protocols::pockets::PocketConstraint::fill_f1_f2	(	core::id::AtomID const &	,
		core::scoring::func::XYZ_Func const &	,
		core::Vector &	,
		core::Vector &	,
		core::scoring::EnergyMap const &	weights
	)		const

override

References core::scoring::constraints::Constraint::score_type(), and protocols::pockets::TR().

void protocols::pockets::PocketConstraint::init ( core::pose::Pose const & pose )

References angles_, dumppdb_, seqpos_, core::pose::Pose::size(), totalres_, and weight_.

Referenced by PocketConstraint(), and read_def().

core::Size protocols::pockets::PocketConstraint::natoms ( ) const

inlineoverridevirtual

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 atom_ids_.

bool protocols::pockets::PocketConstraint::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 angles_, atom_ids_, dumppdb_, pocketgrid_, residues_, same_type_as_me(), core::scoring::constraints::Constraint::same_type_as_me(), seqpos_, totalres_, and weight_.

void protocols::pockets::PocketConstraint::read_def	(	std::istream &	,
		core::pose::Pose const &	,
		core::scoring::func::FuncFactory const &
	)

overridevirtual

Reads the definition of a Constraint from the given std::istream, 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.

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

References protocols::pockets::PocketGrid::getRelaxResidues(), init(), pocketgrid_, residues_, and weight_.

bool protocols::pockets::PocketConstraint::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::pockets::PocketConstraint::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 angles_, core::pack::interaction_graph::debug, dumppdb_, pocketgrid_, core::scoring::func::XYZ_Func::residue(), residues_, core::scoring::constraints::Constraint::score_type(), seqpos_, totalres_, protocols::pockets::TR(), and weight_.

void protocols::pockets::PocketConstraint::set_target_res	(	core::pose::Pose const &	pose,
		core::Size	new_seqpos
	)

References core::pose::Pose::conformation(), pocketgrid_, core::conformation::Conformation::residue(), seqpos_, and core::pose::Pose::size().

void protocols::pockets::PocketConstraint::set_target_res_pdb	(	core::pose::Pose const &	pose,
		std::string	resid
	)

References core::pose::Pose::conformation(), core::pose::Pose::pdb_info(), pocketgrid_, core::conformation::Conformation::residue(), seqpos_, and core::pose::Pose::size().

void protocols::pockets::PocketConstraint::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::pockets::PocketConstraint::target_res ( ) const

inline

References seqpos_.

std::string protocols::pockets::PocketConstraint::type ( ) const

inlineoverridevirtual

Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.

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