torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin) More...

#include <KinematicPerturber.hh>

Inheritance diagram for protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber:

Public Types
typedef KinematicPerturber	parent

Public Member Functions
	TorsionRestrictedKinematicPerturber (KinematicMoverCAP kinmover_in, core::conformation::torsion_bin_string const &torsion_bins)

	~TorsionRestrictedKinematicPerturber () override

std::string	perturber_type () const override

void	perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &) override

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 override
	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)

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

	~KinematicPerturber () override

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 Attributes
bool	vary_ca_bond_angles_

core::conformation::torsion_bin_string	predefined_torsions_

core::scoring::Ramachandran const &	rama_

Detailed Description

torsion-restricted kinematic perturber (still samples randomly, but only within a given torsion bin)

Author: Amelie Stein

Member Typedef Documentation

◆ parent

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

Constructor & Destructor Documentation

◆ TorsionRestrictedKinematicPerturber()

protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::TorsionRestrictedKinematicPerturber	(	KinematicMoverCAP	kinmover_in,
		core::conformation::torsion_bin_string const &	torsion_bins
	)

References predefined_torsions_, and protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_kinmover().

◆ ~TorsionRestrictedKinematicPerturber()

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

overridedefault

Member Function Documentation

◆ perturb_chain()

void protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	torsions,
		utility::vector1< core::Real > &	bond_ang,
		utility::vector1< core::Real > &
	)

overridevirtual

randomly varies the torsions within the given torsion bin

Implements protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

References core::pose::Pose::aa(), core::chemical::aa_pro, protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::get_movemap(), core::conformation::Residue::has_property(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), core::conformation::ppo_torbin_a, core::conformation::ppo_torbin_X, predefined_torsions_, rama_, core::scoring::Ramachandran::random_phipsi_from_rama_by_torsion_bin(), core::conformation::remap_cis_omega_torsion_bins_to_trans(), core::pose::Pose::residue(), core::scoring::rg, and vary_ca_bond_angles_.

◆ perturber_type()

std::string protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturber_type ( ) const

inlineoverridevirtual

Implements protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

◆ set_pose_after_closure()

void protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::set_pose_after_closure	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	,
		utility::vector1< core::Real > const &	,
		bool
	)		const

overridevirtual

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

Reimplemented from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber.

References core::pose::Pose::atom_tree(), core::kinematics::AtomTree::bond_angle_dof_id(), core::kinematics::AtomTree::bond_length_dof_id(), core::pose::Pose::has_dof(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), core::pose::Pose::set_dof(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), and vary_ca_bond_angles_.