vicinity sampling kinematic perturber More...

#include <KinematicPerturber.hh>

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

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

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 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 ()

Private Attributes
bool	vary_ca_bond_angles_

core::Real	degree_vicinity_

bool	sample_omega_for_pre_prolines_

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

core::Size	max_sample_iterations_

Detailed Description

vicinity sampling kinematic perturber

Author: Amelie Stein (just the refactoring)

Definition at line 172 of file KinematicPerturber.hh.

Member Typedef Documentation

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

Definition at line 176 of file KinematicPerturber.hh.

Constructor & Destructor Documentation

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

Definition at line 232 of file KinematicPerturber.cc.

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

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

Definition at line 239 of file KinematicPerturber.cc.

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.

Definition at line 243 of file KinematicPerturber.cc.

References degree_vicinity_, 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(), 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.

Definition at line 182 of file KinematicPerturber.hh.

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

inline

Definition at line 210 of file KinematicPerturber.hh.

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.

Definition at line 296 of file KinematicPerturber.cc.

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_.