Neighbor-dependent Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b) More...

#include <KinematicPerturber.hh>

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

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

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Public Types
typedef KinematicPerturber	parent

Public Member Functions
	NeighborDependentTabooSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)

	~NeighborDependentTabooSamplingKinematicPerturber ()

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 > &)
	function that perturbs the chain, i.e. sets new values 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	clear_torsion_string_stack ()

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 ()

Protected Member Functions
void	refill_torsion_string_vector ()

std::string	next_torsion_string ()

Private Attributes
bool	vary_ca_bond_angles_

bool	sample_omega_for_pre_prolines_

core::Size	num_strings_

utility::vector1< std::string >	random_torsion_strings_

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 Taboo-sampling kinematic perturber (still samples randomly, but only within a given torsion bin; the Taboo sampler ensures that this torsion bin is varied in each iteration) that uses neighbor-dependent Ramachandran distributions (rama2b)

Author: Amelie Stein

Date: Mon May 21 11:39:26 PDT 2012

Definition at line 444 of file KinematicPerturber.hh.

Member Typedef Documentation

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

Definition at line 448 of file KinematicPerturber.hh.

Constructor & Destructor Documentation

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

Definition at line 901 of file KinematicPerturber.cc.

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

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

Definition at line 910 of file KinematicPerturber.cc.

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::clear_torsion_string_stack ( )

inline

Definition at line 480 of file KinematicPerturber.hh.

References random_torsion_strings_.

std::string protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::next_torsion_string ( )

protected

Definition at line 978 of file KinematicPerturber.cc.

References protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, random_torsion_strings_, and refill_torsion_string_vector().

Referenced by perturb_chain().

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

virtual

function that perturbs the chain, i.e. sets new values

for the torsions, bond angles and bond lengths note: the torsions/angles/lengths that are input to this function will be identical to the ones in the pose, i.e. only the dof values that are explicitly set by this function plus the pivots will have changed after loop closure

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

Definition at line 1010 of file KinematicPerturber.cc.

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_, next_torsion_string(), rama_, core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_left(), core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_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::NeighborDependentTabooSamplingKinematicPerturber::perturber_type ( ) const

inlinevirtual

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

Definition at line 454 of file KinematicPerturber.hh.

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::refill_torsion_string_vector ( )

protected

Definition at line 913 of file KinematicPerturber.cc.

References core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left(), core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover_, num_strings_, rama_, random_torsion_strings_, and RG().

Referenced by next_torsion_string().

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::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 1118 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_.

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

inline

Definition at line 476 of file KinematicPerturber.hh.

References vary_ca_bond_angles_.

Member Data Documentation

core::Size protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::num_strings_

private

Definition at line 498 of file KinematicPerturber.hh.

Referenced by refill_torsion_string_vector().

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

private

Definition at line 501 of file KinematicPerturber.hh.

Referenced by perturb_chain(), and refill_torsion_string_vector().

utility::vector1< std::string > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::random_torsion_strings_

private

Definition at line 499 of file KinematicPerturber.hh.

Referenced by clear_torsion_string_stack(), next_torsion_string(), and refill_torsion_string_vector().

bool protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::sample_omega_for_pre_prolines_

private

Definition at line 495 of file KinematicPerturber.hh.

Referenced by perturb_chain().

bool protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::vary_ca_bond_angles_

private

Definition at line 494 of file KinematicPerturber.hh.

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

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