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protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber Class Reference

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

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::clear_torsion_string_stack ( )
inline
std::string protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::next_torsion_string ( )
protected
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.

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

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

References vary_ca_bond_angles_.

Member Data Documentation

core::Size protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::num_strings_
private
core::scoring::Ramachandran2B const& protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::rama_
private
utility::vector1< std::string > protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::random_torsion_strings_
private
bool protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::sample_omega_for_pre_prolines_
private

Referenced by perturb_chain().

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

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