neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup More...

#include <KinematicPerturber.hh>

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

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Collaboration diagram for protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber:

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Public Types
typedef KinematicPerturber	parent

Public Member Functions
	NeighborDependentTorsionSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)

	~NeighborDependentTorsionSamplingKinematicPerturber ()

std::string	perturber_type () const

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

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 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 ()

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 ()

Private Attributes
bool	vary_ca_bond_angles_

bool	sample_omega_for_pre_prolines_

core::scoring::Ramachandran2B const &	rama_

Additional Inherited Members
Protected Attributes inherited from protocols::loops::loop_closure::kinematic_closure::KinematicPerturber
KinematicMoverCAP	kinmover_

core::Size	max_sample_iterations_

Detailed Description

neighbor-dependent torsion sampling kinematic perturber – uses rama2b for phi/psi lookup

Author: Amelie Stein

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

References protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_kinmover().

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

Member Function Documentation

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

virtual

randomly varies the torsions (and possibly the bond angles) for the loop, using phi/psi combinations based on rama2b

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(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, rama_, core::scoring::Ramachandran2B::random_phipsi_from_rama_left(), core::scoring::Ramachandran2B::random_phipsi_from_rama_right(), protocols::loops::loop_closure::kinematic_closure::RG(), sample_omega_for_pre_prolines_, and vary_ca_bond_angles_.

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

inlinevirtual

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

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::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

virtual

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(), 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_.

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::set_vary_ca_bond_angles ( bool vary_ca_bond_angles)

inline

References vary_ca_bond_angles_.