protocols::pockets::PocketConstraint Class Reference

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

#include <PocketConstraint.hh>

Public Member Functions
virtual std::string	type () const
	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
virtual core::id::AtomID const &	atom (core::Size const index) const
void	show_def (std::ostream &out, core::pose::Pose const &pose) const
void	read_def (std::istream &in, core::pose::Pose const &pose, core::scoring::func::FuncFactory const &func_factory)
virtual void	score (core::scoring::func::XYZ_Func const &xyz_func, core::scoring::EnergyMap const &weights, core::scoring::EnergyMap &emap) const
virtual void	fill_f1_f2 (core::id::AtomID const &, core::scoring::func::XYZ_Func const &, core::Vector &, core::Vector &, core::scoring::EnergyMap const &weights) const
virtual core::scoring::constraints::ConstraintOP	clone () const
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
virtual void	show (std::ostream &) 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_

Detailed Description

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

Constructor & Destructor Documentation

protocols::pockets::PocketConstraint::PocketConstraint

(

)

References pocket_constraint, and scoring.

Referenced by clone().

protocols::pockets::PocketConstraint::PocketConstraint

(

core::pose::Pose const &

pose

)

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

protocols::pockets::PocketConstraint::PocketConstraint

(

const PocketConstraint &

old

)

References dumppdb_, pocket_constraint, pocketgrid_, scoring, seqpos_, and totalres_.

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

virtual

Member Function Documentation

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

inlinevirtual

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

References atom_ids_.

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

virtual

References PocketConstraint().

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

virtual

References option, score_type, and protocols::pockets::TR.

void protocols::pockets::PocketConstraint::init

(

core::pose::Pose const &

pose

)

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

Referenced by PocketConstraint(), and read_def().

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

inlinevirtual

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

References atom_ids_.

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

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

void protocols::pockets::PocketConstraint::score ( core::scoring::func::XYZ_Func const &  xyz_func, core::scoring::EnergyMap const &  weights, core::scoring::EnergyMap &  emap  ) const

virtual

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

References angles_, debug, dumppdb_, exit, option, pocketgrid_, core::scoring::func::XYZ_Func::residue(), residues_, 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(), exit, 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
	)

References chain, core::pose::Pose::conformation(), exit, 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 &	out,
		core::pose::Pose const &	pose
	)		const

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

inline

References seqpos_.

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

inlinevirtual

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

Member Data Documentation

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

private

Referenced by init(), and score().

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

private

Referenced by atom(), and natoms().

bool protocols::pockets::PocketConstraint::dumppdb_

private

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

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

mutableprivate

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

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

private

Referenced by read_def(), and score().

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

private

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

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

private

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

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

private

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