core::scoring::loop_graph Namespace Reference

Namespaces
	evaluator

Classes
class	Loop
class	LoopCycle
struct	cycle_printer
class	LoopGraph

Typedefs
typedef utility::pointer::shared_ptr< Loop >	LoopOP
typedef utility::pointer::shared_ptr< Loop const >	LoopCOP
typedef utility::pointer::shared_ptr< LoopCycle >	LoopCycleOP
typedef utility::pointer::shared_ptr< LoopCycle const >	LoopCycleCOP
typedef utility::pointer::shared_ptr< LoopGraph >	LoopGraphOP
typedef utility::pointer::shared_ptr< LoopGraph const >	LoopGraphCOP
typedef utility::pointer::shared_ptr< util >	utilOP
typedef utility::pointer::shared_ptr< util const >	utilCOP

Functions
std::ostream &	operator<< (std::ostream &os, Loop const &loop)
std::ostream &	operator<< (std::ostream &os, LoopCycle const &loop_cycle)
	Test IO operator for debug and Python bindings. More...
void	get_loop_atom (Size const res, core::pose::Pose const &pose, id::AtomID &atom_id, Vector &xyz, bool const takeoff)
void	get_loop_atom (core::Size const res, core::pose::Pose const &pose, std::string const &atom_name, id::AtomID &atom_id, Vector &xyz)
LoopClosePotentialEvaluatorCOP	get_loop_close_potential (pose::Pose const &pose, LoopCycle const &loop_cycle, core::Real const &loop_fixed_cost, bool const use_6D_potential)
LoopClosePotentialEvaluatorCOP	get_6D_trans_rot_potential_evaluator (LoopCycle const &loop_cycle, core::Real const &loop_fixed_cost, pose::Pose const &pose)

Typedef Documentation

LoopCOP

typedef utility::pointer::shared_ptr< Loop const > core::scoring::loop_graph::LoopCOP

LoopCycleCOP

typedef utility::pointer::shared_ptr< LoopCycle const > core::scoring::loop_graph::LoopCycleCOP

LoopCycleOP

typedef utility::pointer::shared_ptr< LoopCycle > core::scoring::loop_graph::LoopCycleOP

LoopGraphCOP

typedef utility::pointer::shared_ptr< LoopGraph const > core::scoring::loop_graph::LoopGraphCOP

LoopGraphOP

typedef utility::pointer::shared_ptr< LoopGraph > core::scoring::loop_graph::LoopGraphOP

LoopOP

typedef utility::pointer::shared_ptr< Loop > core::scoring::loop_graph::LoopOP

utilCOP

typedef utility::pointer::shared_ptr< util const > core::scoring::loop_graph::utilCOP

utilOP

typedef utility::pointer::shared_ptr< util > core::scoring::loop_graph::utilOP

Function Documentation

get_6D_trans_rot_potential_evaluator()

evaluator::LoopClosePotentialEvaluatorCOP core::scoring::loop_graph::get_6D_trans_rot_potential_evaluator	(	LoopCycle const &	loop_cycle,
		core::Real const &	loop_fixed_cost,
		pose::Pose const &	pose
	)

References core::pose::full_model_info::get_residue(), core::conformation::Residue::is_NA(), core::scoring::loop_graph::Loop::landing_pos(), core::scoring::loop_graph::LoopCycle::loop(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), core::scoring::loop_graph::Loop::takeoff_pos(), and core::scoring::TR().

Referenced by get_loop_close_potential().

get_loop_atom() [1/2]

void core::scoring::loop_graph::get_loop_atom	(	core::Size const	res,
		core::pose::Pose const &	pose,
		std::string const &	atom_name,
		id::AtomID &	atom_id,
		Vector &	xyz
	)

References core::conformation::Residue::atom_index(), core::pose::full_model_info::get_residue(), core::conformation::Residue::seqpos(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

get_loop_atom() [2/2]

void core::scoring::loop_graph::get_loop_atom	(	Size const	res,
		core::pose::Pose const &	pose,
		id::AtomID &	atom_id,
		Vector &	xyz,
		bool const	takeoff
	)

References core::pose::full_model_info::get_residue(), core::conformation::Residue::has(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_TNA(), and protocols::kinmatch::xyz().

Referenced by core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::evaluate(), and core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize().

get_loop_close_potential()

evaluator::LoopClosePotentialEvaluatorCOP core::scoring::loop_graph::get_loop_close_potential	(	pose::Pose const &	pose,
		LoopCycle const &	loop_cycle,
		core::Real const &	loop_fixed_cost,
		bool const	use_6D_potential
	)

References get_6D_trans_rot_potential_evaluator(), and core::scoring::loop_graph::LoopCycle::size().

Referenced by core::scoring::loop_graph::LoopGraph::update().

operator<<() [1/2]

std::ostream& core::scoring::loop_graph::operator<<	(	std::ostream &	os,
		Loop const &	loop
	)

operator<<() [2/2]

std::ostream& core::scoring::loop_graph::operator<<	(	std::ostream &	os,
		LoopCycle const &	loop_cycle
	)

Test IO operator for debug and Python bindings.