protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber Class Reference

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 ()
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 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 ()
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 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

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

Constructor & Destructor Documentation

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().

protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::~TorsionRestrictedKinematicPerturber

(

)

Member Function Documentation

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 > &    )

virtual

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_.

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

inlinevirtual

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

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

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(), 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_.

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

inline

References vary_ca_bond_angles_.

Member Data Documentation

core::conformation::torsion_bin_string protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::predefined_torsions_

private

Referenced by perturb_chain(), and TorsionRestrictedKinematicPerturber().

core::scoring::Ramachandran const& protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::rama_

private

Referenced by perturb_chain().

bool protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::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