protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber Class Reference

torsion sampling kinematic perturber More...

#include <KinematicPerturber.hh>

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

Public Types
typedef KinematicPerturber	parent

Public Member Functions
	TorsionSamplingKinematicPerturber (KinematicMoverCAP kinmover_in)
	~TorsionSamplingKinematicPerturber () override
std::string	perturber_type () const override
void	perturb_beta_residue (core::Real &phi, core::Real &theta, core::Real &psi, const core::Size beta_residue_type) const
	Varies torsions of a beta-amino acid residue based on minimia in the beta-amino acid Ramachandran cube. This randomly picks a minimum, then chooses phi/theta/psi values randomly in a Gaussian centered in that minimum. More...
void	initialize_betaresidue_minima (utility::vector1< core::Real > &philist, utility::vector1< core::Real > &thetalist, utility::vector1< core::Real > &psilist, const core::Size mode) const
	Initialize positions of minima in the beta-amino acid Ramachandran cube. More...
void	perturb_chain (core::pose::Pose const &pose, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bond_ang, utility::vector1< core::Real > &) override
	varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap. 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 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::Ramachandran const &	rama_

Detailed Description

torsion sampling kinematic perturber

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::TorsionSamplingKinematicPerturber

(

KinematicMoverCAP

kinmover_in

)

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

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

overridedefault

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::initialize_betaresidue_minima	(	utility::vector1< core::Real > &	philist,
		utility::vector1< core::Real > &	thetalist,
		utility::vector1< core::Real > &	psilist,
		const core::Size	mode
	)		const

Initialize positions of minima in the beta-amino acid Ramachandran cube.

Helper function for TorsionSamplingKinematicPerturber::perturb_beta_residue. This initializes the list of minima in the Ramachandran cube for beta-3-amino acids.

Referenced by perturb_beta_residue().

void protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_beta_residue	(	core::Real &	phi,
		core::Real &	theta,
		core::Real &	psi,
		const core::Size	beta_residue_type
	)		const

Varies torsions of a beta-amino acid residue based on minimia in the beta-amino acid Ramachandran cube. This randomly picks a minimum, then chooses phi/theta/psi values randomly in a Gaussian centered in that minimum.

This randomly picks a minimum from the enumerated minimia of the beta-amino acid Ramachandran cube, then chooses phi/theta/psi values randomly in a Gaussian centered in that minimum. The behaviour depends on beta_residue_type (0=pick everything randomly, 1=pick using beta-3-alanine Ramachandran cube).

References initialize_betaresidue_minima(), and core::scoring::rg.

Referenced by perturb_chain().

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

overridevirtual

varies torsions always and bond angles sometimes. Currently torsion varying will respect a movemap if present; angles do NOT look for a movemap.

randomly varies the torsions (and possibly the bond angles) for the loop. Respects a MoveMap, if present, for torsions. Does NOT respect the movemap for angles; does NOT cause any sort of interactions between the MoveMap and the KinematicMover's pivot residues.

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

References core::pose::Pose::aa(), core::conformation::Residue::aa(), core::chemical::aa_dpr, core::chemical::aa_pro, protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::get_movemap(), core::conformation::Residue::has_property(), core::chemical::is_canonical_D_aa(), core::conformation::Residue::is_lower_terminus(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), perturb_beta_residue(), rama_, core::scoring::Ramachandran::random_phipsi_from_rama(), core::pose::Pose::residue(), core::scoring::rg, sample_omega_for_pre_prolines_, and vary_ca_bond_angles_.

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

inlineoverridevirtual

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

void protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::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(), core::conformation::Residue::is_lower_terminus(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::kinmover(), core::pose::Pose::residue(), core::pose::Pose::set_dof(), protocols::loops::loop_closure::kinematic_closure::KinematicPerturber::set_pose_after_closure(), core::pose::Pose::update_residue_neighbors(), and vary_ca_bond_angles_.

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

inline

References vary_ca_bond_angles_.

Member Data Documentation

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

private

Referenced by perturb_chain().

bool protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::sample_omega_for_pre_prolines_

private

Referenced by perturb_chain().

bool protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::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