Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) More...

#include <KinematicPerturber.hh>

Public Types
typedef KinematicPerturber	parent

Public Types inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
typedef KinematicPerturber	parent

Public Member Functions
	NeighborDependentTabooSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)

	~NeighborDependentTabooSamplingKinematicPerturber ()

std::string	perturber_type () const

Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber
	BaseTabooPerturber (KinematicMoverCAP kinmover_in)

virtual	~BaseTabooPerturber ()

void	perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &)
	function that perturbs the chain, i.e. sets new values for the torsions, bond angles and bond lengths note: the torsions/angles/lengths that are input to this function will be identical to the ones in the pose, i.e. only the dof values that are explicitly set by this function plus the pivots will have changed after loop closure More...

void	set_pose_after_closure (core::pose::Pose &pose, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bond_ang, utility::vector1< core::Real > const &bond_len, bool closure_successful) const
	after the kinmover has closed the loop, the perturber needs to put the solutions into the pose note: the base class version of this function sets the torsions, so any KinematicPerturber that only changes the torsions will not have to implement this function More...

void	set_vary_ca_bond_angles (bool vary_ca_bond_angles)

void	clear_torsion_string_stack ()

core::Size	num_strings () const

core::conformation::torsion_bin_string	next_torsion_string ()

Public Member Functions inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
	KinematicPerturber ()

virtual	~KinematicPerturber ()

void	set_kinmover (KinematicMoverCAP kinmover)

void	set_movemap (core::kinematics::MoveMapCOP mm)

core::kinematics::MoveMapCOP	get_movemap () const

virtual bool	perturber_exhausted () const

void	set_max_sample_iterations (core::Size sample_its)

core::Size	max_sample_iterations () const

void	clear_torsion_string_stack ()

KinematicMoverCAP	kinmover () const

Private Member Functions
virtual void	get_random_phi_psi_for_residue (core::pose::Pose const &pose, core::Size resid, core::conformation::ppo_torsion_bin torbin, core::Real &phi, core::Real &psi) const

virtual std::map < core::conformation::ppo_torsion_bin, core::Size >	get_entries_per_torsion_bin (utility::vector1< core::chemical::AA > loop_seq, core::Size resid) const
	This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector. More...

Private Attributes
core::scoring::Ramachandran2B const &	rama_

Detailed Description

Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b)

Author: Amelie Stein

Date: Mon May 21 11:39:26 PDT 2012

Member Typedef Documentation

typedef KinematicPerturber protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::parent

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::NeighborDependentTabooSamplingKinematicPerturber ( KinematicMoverCAP kinmover_in )

References scoring.

protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::~NeighborDependentTabooSamplingKinematicPerturber ( )

Member Function Documentation

std::map< core::conformation::ppo_torsion_bin, core::Size > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_entries_per_torsion_bin	(	utility::vector1< core::chemical::AA >	loop_seq,
		core::Size	resid
	)		const

privatevirtual

This function is implemented by the derived classes and is used to interface with the particular Ramachandran library that the derived classs relies upon it is invoked inside of refill_torsion_string_vector.

Implements protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber.

References core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left(), core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right(), and rama_.

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_random_phi_psi_for_residue	(	core::pose::Pose const &	pose,
		core::Size	resid,
		core::conformation::ppo_torsion_bin	torbin,
		core::Real &	phi,
		core::Real &	psi
	)		const