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protocols::toolbox::DecoySetEvaluation Class Reference

#include <DecoySetEvaluation.hh>

Inheritance diagram for protocols::toolbox::DecoySetEvaluation:
Inheritance graph
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Public Member Functions

 DecoySetEvaluation ()
 
 ~DecoySetEvaluation () override
 
void reserve (core::Size n_decoys_)
 
void push_back (core::pose::Pose &pose)
 
void push_back_CA_xyz (ObjexxFCL::FArray2_double const &, core::Size nres)
 
void pop_back_CA_xyz ()
 
void push_back_CA_xyz_from_silent_file (core::io::silent::SilentFileData const &sfd, bool store_energies)
 
template<typename SilentStructIterator >
void push_back_CA_xyz_from_silent_file (core::Size n_decoys, SilentStructIterator begin, SilentStructIterator end, bool store_energies)
 
void rmsf (utility::vector1< core::Real > &results)
 
core::Size n_decoys_max () const
 
core::Size n_decoys () const
 
core::Size n_atoms () const
 
void set_n_atom (core::Size natoms)
 
ObjexxFCL::FArray3D_double const & coords () const
 
void compute_distance_matrix (ObjexxFCL::FArray2D_double &) const
 
ObjexxFCL::FArray2P_double coords (core::Size i) const
 
void rmsf (ObjexxFCL::FArray1_double &result)
 
core::Real rmsd (ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &xx_ref, ObjexxFCL::FArray2_double &xx) const
 
core::Size wRMSD (core::Real sigma2, core::Real tolerance, ObjexxFCL::FArray1_double &weights)
 
void set_weights (ObjexxFCL::FArray1_double const &weights)
 
void superimpose (core::Size icenter=1)
 
core::pose::Pose const & ref_pose ()
 
void clear ()
 
void center_structure (core::Size i)
 
void center_structure (core::Size i, ObjexxFCL::FArray1_double const &weights)
 
void center_all (ObjexxFCL::FArray1_double const &weights)
 
void create_dist_constraints_median (core::scoring::constraints::ConstraintSet &cst_set) const
 
void create_dist_constraints (core::scoring::constraints::ConstraintSet &cst_set) const
 
void create_xyz_constraints_median (core::scoring::constraints::ConstraintSet &cst_set, core::pose::Pose const &ref_pose, core::Size root) const
 
core::Size find_closest_to_average (ObjexxFCL::FArray2_double &average_structure) const
 
void compute_average_structure (ObjexxFCL::FArray2_double &average_structure) const
 
utility::vector1< core::Real >
const & 
all_energies () const
 
void set_all_energies (utility::vector1< core::Real > const &all_energies)
 

Static Public Member Functions

static void register_options ()
 

Private Member Functions

void superimpose (ObjexxFCL::FArray1_double const &weights, core::Size icenter=1)
 
core::Real rmsf (core::Size pos)
 
void prepare_push_back (core::Size nres)
 

Private Attributes

core::pose::Pose ref_pose_
 
ObjexxFCL::FArray1D_double COM
 
core::Size n_decoys_
 
core::Size n_atoms_
 
ObjexxFCL::FArray3D_double coords_
 
ObjexxFCL::FArray2D_double ref_structure_
 
core::Size n_decoys_max_
 
ObjexxFCL::FArray1D_double weights_
 
utility::vector1< core::Realall_energies_
 
bool store_energies_
 

Static Private Attributes

static bool options_registered_
 

Constructor & Destructor Documentation

protocols::toolbox::DecoySetEvaluation::DecoySetEvaluation ( )
protocols::toolbox::DecoySetEvaluation::~DecoySetEvaluation ( )
overridedefault

Member Function Documentation

utility::vector1< core::Real > const& protocols::toolbox::DecoySetEvaluation::all_energies ( ) const
inline
void protocols::toolbox::DecoySetEvaluation::center_all ( ObjexxFCL::FArray1_double const &  weights)

References center_structure(), and n_decoys_.

void protocols::toolbox::DecoySetEvaluation::center_structure ( core::Size  i)

References n_atoms_.

Referenced by center_all().

void protocols::toolbox::DecoySetEvaluation::center_structure ( core::Size  i,
ObjexxFCL::FArray1_double const &  weights 
)
void protocols::toolbox::DecoySetEvaluation::clear ( )
inline

References n_atoms_, and n_decoys_max_.

void protocols::toolbox::DecoySetEvaluation::compute_average_structure ( ObjexxFCL::FArray2_double &  average_structure) const

References coords_, n_atoms_, and n_decoys_.

Referenced by wRMSD().

void protocols::toolbox::DecoySetEvaluation::compute_distance_matrix ( ObjexxFCL::FArray2D_double &  dist) const
ObjexxFCL::FArray3D_double const& protocols::toolbox::DecoySetEvaluation::coords ( ) const
inline
ObjexxFCL::FArray2P_double protocols::toolbox::DecoySetEvaluation::coords ( core::Size  i) const
inline

References coords_, and n_atoms_.

void protocols::toolbox::DecoySetEvaluation::create_dist_constraints ( core::scoring::constraints::ConstraintSet cst_set) const
void protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median ( core::scoring::constraints::ConstraintSet cst_set) const
void protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median ( core::scoring::constraints::ConstraintSet cst_set,
core::pose::Pose const &  ref_pose,
core::Size  root 
) const
Size protocols::toolbox::DecoySetEvaluation::find_closest_to_average ( ObjexxFCL::FArray2_double &  average_structure) const

References coords_, n_atoms_, n_decoys_, and protocols::toolbox::tr().

Referenced by wRMSD().

core::Size protocols::toolbox::DecoySetEvaluation::n_atoms ( ) const
inline
core::Size protocols::toolbox::DecoySetEvaluation::n_decoys ( ) const
inline
core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_max ( ) const
inline
void protocols::toolbox::DecoySetEvaluation::pop_back_CA_xyz ( )

References coords_, n_atoms_, and n_decoys_.

void protocols::toolbox::DecoySetEvaluation::prepare_push_back ( core::Size  nres)
private
void protocols::toolbox::DecoySetEvaluation::push_back ( core::pose::Pose pose)
void protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz ( ObjexxFCL::FArray2_double const &  xyz,
core::Size  nres 
)
void protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file ( core::io::silent::SilentFileData const &  sfd,
bool  store_energies 
)
template<typename SilentStructIterator >
void protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file ( core::Size  n_decoys,
SilentStructIterator  begin,
SilentStructIterator  end,
bool  store_energies 
)
core::pose::Pose const& protocols::toolbox::DecoySetEvaluation::ref_pose ( )
inline

References ref_pose_.

Referenced by create_xyz_constraints_median().

void protocols::toolbox::DecoySetEvaluation::register_options ( )
static
void protocols::toolbox::DecoySetEvaluation::reserve ( core::Size  n_decoys_)
core::Real protocols::toolbox::DecoySetEvaluation::rmsd ( ObjexxFCL::FArray1_double const &  weights,
ObjexxFCL::FArray2_double &  xx_ref,
ObjexxFCL::FArray2_double &  xx 
) const
void protocols::toolbox::DecoySetEvaluation::rmsf ( utility::vector1< core::Real > &  results)

References n_atoms_.

Referenced by protocols::abinitio::get_core(), and wRMSD().

void protocols::toolbox::DecoySetEvaluation::rmsf ( ObjexxFCL::FArray1_double &  result)
Real protocols::toolbox::DecoySetEvaluation::rmsf ( core::Size  pos)
private
void protocols::toolbox::DecoySetEvaluation::set_all_energies ( utility::vector1< core::Real > const &  all_energies)
inline
void protocols::toolbox::DecoySetEvaluation::set_n_atom ( core::Size  natoms)
void protocols::toolbox::DecoySetEvaluation::set_weights ( ObjexxFCL::FArray1_double const &  weights)

References n_atoms_, and weights_.

void protocols::toolbox::DecoySetEvaluation::superimpose ( core::Size  icenter = 1)

References n_atoms_.

Referenced by protocols::abinitio::get_core(), and wRMSD().

void protocols::toolbox::DecoySetEvaluation::superimpose ( ObjexxFCL::FArray1_double const &  weights,
core::Size  icenter = 1 
)
private
Size protocols::toolbox::DecoySetEvaluation::wRMSD ( core::Real  sigma2,
core::Real  tolerance,
ObjexxFCL::FArray1_double &  weights 
)

Member Data Documentation

utility::vector1< core::Real > protocols::toolbox::DecoySetEvaluation::all_energies_
private
ObjexxFCL::FArray1D_double protocols::toolbox::DecoySetEvaluation::COM
private
ObjexxFCL::FArray3D_double protocols::toolbox::DecoySetEvaluation::coords_
private
core::Size protocols::toolbox::DecoySetEvaluation::n_atoms_
private
core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_
private
core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_max_
private
bool protocols::toolbox::DecoySetEvaluation::options_registered_
staticprivate

Referenced by create_dist_constraints().

core::pose::Pose protocols::toolbox::DecoySetEvaluation::ref_pose_
private

Referenced by push_back(), and ref_pose().

ObjexxFCL::FArray2D_double protocols::toolbox::DecoySetEvaluation::ref_structure_
private

Referenced by prepare_push_back().

bool protocols::toolbox::DecoySetEvaluation::store_energies_
private
ObjexxFCL::FArray1D_double protocols::toolbox::DecoySetEvaluation::weights_
private

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