protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber Class Reference

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:

Public Types
typedef KinematicPerturber	parent

Public Member Functions
	NeighborDependentTorsionSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)
	~NeighborDependentTorsionSamplingKinematicPerturber () 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_
bool	sample_omega_for_pre_prolines_
core::scoring::Ramachandran2B const &	rama_

Detailed Description

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

Author

Amelie Stein

Member Typedef Documentation

parent

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

Constructor & Destructor Documentation

NeighborDependentTorsionSamplingKinematicPerturber()

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

(

KinematicMoverCAP

kinmover_in

)

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

~NeighborDependentTorsionSamplingKinematicPerturber()

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

overridedefault

Member Function Documentation

perturb_chain()

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 > &    )

overridevirtual

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(), core::conformation::Residue::has_property(), 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(), core::pose::Pose::residue(), core::scoring::rg, sample_omega_for_pre_prolines_, and vary_ca_bond_angles_.

perturber_type()

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

inlineoverridevirtual

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

set_pose_after_closure()

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

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_.

set_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_.

Member Data Documentation

rama_

core::scoring::Ramachandran2B const& protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::rama_

private

Referenced by perturb_chain().

sample_omega_for_pre_prolines_

bool protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::sample_omega_for_pre_prolines_

private

Referenced by perturb_chain().

vary_ca_bond_angles_

bool protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber::vary_ca_bond_angles_

private

Referenced by perturb_chain(), set_pose_after_closure(), and set_vary_ca_bond_angles().

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The documentation for this class was generated from the following files:

• src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.hh
• src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc