protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber Class Reference

vicinity sampling kinematic perturber More...

#include <KinematicPerturber.hh>

Public Types
typedef KinematicPerturber	parent

Public Member Functions
	VicinitySamplingKinematicPerturber (KinematicMoverCAP kinmover_in)
	~VicinitySamplingKinematicPerturber ()
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 > &)
	varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. – note that the analytic closure and pivot selection currently do not respect movemaps though 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	set_degree_vicinity (core::Real degree_vicinity)
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::Real	degree_vicinity_
bool	sample_omega_for_pre_prolines_

Detailed Description

vicinity sampling kinematic perturber

Author

Amelie Stein (just the refactoring)

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::VicinitySamplingKinematicPerturber

(

KinematicMoverCAP

kinmover_in

)

References loops, option, options, sample_omega_at_pre_prolines, protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_kinmover(), and vicinity_degree.

protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::~VicinitySamplingKinematicPerturber

(

)

Member Function Documentation

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

virtual

varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. – note that the analytic closure and pivot selection currently do not respect movemaps though

small variation around the starting phi/psi angles – order of magnitude is determined by degree_vicinity_

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

References degree_vicinity_, numeric::random::RandomGenerator::gaussian(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::get_movemap(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::loops::loop_closure::kinematic_closure::RG, numeric::random::RandomGenerator::uniform(), and vary_ca_bond_angles_.

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

inlinevirtual

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

void protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::set_degree_vicinity ( core::Real  degree_vicinity )

inline

References degree_vicinity_.

void protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::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(), numeric::conversions::radians(), 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::VicinitySamplingKinematicPerturber::set_vary_ca_bond_angles ( bool  vary_ca_bond_angles )

inline

References vary_ca_bond_angles_.

Member Data Documentation

core::Real protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::degree_vicinity_

private

Referenced by perturb_chain(), and set_degree_vicinity().

bool protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::sample_omega_for_pre_prolines_

private

bool protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber::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