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

#include <PocketConstraint.hh>

Inheritance diagram for protocols::pockets::PocketConstraint:

Collaboration diagram for protocols::pockets::PocketConstraint:

Public Member Functions
virtual std::string	type () const
	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

virtual	~PocketConstraint ()

virtual core::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::id::AtomID const &	atom (core::Size const index) const
	Returns the AtomID referred to by index. 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)

virtual void	score (core::scoring::constraints::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, 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...

virtual void	fill_f1_f2 (core::id::AtomID const &, core::scoring::constraints::XYZ_Func const &, core::Vector &, core::Vector &, 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...

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	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...

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 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 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 void	setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const

virtual void	setup_for_derivatives (XYZ_Func const &, ScoreFunction 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	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 &)

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 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

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::ResidueOP >	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.

Definition at line 43 of file PocketConstraint.hh.

Constructor & Destructor Documentation

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

Definition at line 113 of file PocketConstraint.cc.

Referenced by clone().

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

Definition at line 115 of file PocketConstraint.cc.

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

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

Definition at line 167 of file PocketConstraint.cc.

References dumppdb_, pocketgrid_, seqpos_, and totalres_.

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

virtual

Definition at line 177 of file PocketConstraint.cc.

Member Function Documentation

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

inlinevirtual

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 61 of file PocketConstraint.hh.

References atom_ids_.

core::scoring::constraints::ConstraintOP protocols::pockets::PocketConstraint::clone ( ) const

virtual

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 326 of file PocketConstraint.cc.

References PocketConstraint().

void protocols::pockets::PocketConstraint::fill_f1_f2	(	core::id::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 304 of file PocketConstraint.cc.

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

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

Definition at line 70 of file PocketConstraint.cc.

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

Referenced by PocketConstraint(), and read_def().

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

inlinevirtual

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 59 of file PocketConstraint.hh.

References atom_ids_.

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

virtual

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

Definition at line 85 of file PocketConstraint.cc.

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

void protocols::pockets::PocketConstraint::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 239 of file PocketConstraint.cc.

References angles_, dumppdb_, pocketgrid_, core::scoring::constraints::XYZ_Func::residue(), residues_, core::scoring::constraints::Constraint::score_type(), seqpos_, totalres_, and weight_.

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

Definition at line 180 of file PocketConstraint.cc.

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

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

Definition at line 195 of file PocketConstraint.cc.

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

void protocols::pockets::PocketConstraint::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 108 of file PocketConstraint.cc.

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

inline

Definition at line 56 of file PocketConstraint.hh.

References seqpos_.

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

inlinevirtual

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 46 of file PocketConstraint.hh.

Member Data Documentation

core::Size protocols::pockets::PocketConstraint::angles_

private

Definition at line 89 of file PocketConstraint.hh.

Referenced by init(), and score().

utility::vector1< AtomID > protocols::pockets::PocketConstraint::atom_ids_

private

Definition at line 92 of file PocketConstraint.hh.

Referenced by atom(), and natoms().

bool protocols::pockets::PocketConstraint::dumppdb_

private

Definition at line 93 of file PocketConstraint.hh.

Referenced by init(), PocketConstraint(), and score().

protocols::pockets::PocketGridOP protocols::pockets::PocketConstraint::pocketgrid_

mutableprivate

Definition at line 91 of file PocketConstraint.hh.

Referenced by PocketConstraint(), read_def(), score(), set_target_res(), and set_target_res_pdb().

std::vector< core::conformation::ResidueOP > protocols::pockets::PocketConstraint::residues_

private

Definition at line 94 of file PocketConstraint.hh.

Referenced by read_def(), and score().

core::Size protocols::pockets::PocketConstraint::seqpos_

private

Definition at line 87 of file PocketConstraint.hh.

Referenced by init(), PocketConstraint(), score(), set_target_res(), set_target_res_pdb(), and target_res().

core::Size protocols::pockets::PocketConstraint::totalres_

private

Definition at line 88 of file PocketConstraint.hh.

Referenced by init(), PocketConstraint(), and score().

core::Real protocols::pockets::PocketConstraint::weight_

private

Definition at line 90 of file PocketConstraint.hh.

Referenced by init(), read_def(), and score().

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

src/protocols/pockets/PocketConstraint.hh
src/protocols/pockets/PocketConstraint.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation