#include <DecoySetEvaluation.hh>

Inheritance diagram for protocols::toolbox::DecoySetEvaluation:

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::Real >	all_energies_

bool	store_energies_

Static Private Attributes
static bool	options_registered_

Constructor & Destructor Documentation

◆ DecoySetEvaluation()

protocols::toolbox::DecoySetEvaluation::DecoySetEvaluation ( )

◆ ~DecoySetEvaluation()

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

overridedefault

Member Function Documentation

◆ all_energies()

utility::vector1< core::Real > const& protocols::toolbox::DecoySetEvaluation::all_energies ( ) const

inline

References all_energies_.

Referenced by protocols::toolbox::cluster_silent_structs(), and set_all_energies().

◆ center_all()

void protocols::toolbox::DecoySetEvaluation::center_all ( ObjexxFCL::FArray1_double const & weights )

References center_structure(), and n_decoys_.

◆ center_structure() [1/2]

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

References n_atoms_.

Referenced by center_all().

◆ center_structure() [2/2]

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

◆ clear()

void protocols::toolbox::DecoySetEvaluation::clear ( )

inline

References n_atoms_, n_decoys_, and n_decoys_max_.

◆ compute_average_structure()

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

References coords_, n_atoms_, and n_decoys_.

Referenced by wRMSD().

◆ compute_distance_matrix()

void protocols::toolbox::DecoySetEvaluation::compute_distance_matrix ( ObjexxFCL::FArray2D_double & dist ) const

References coords_, core::chemical::element::F, protocols::toolbox::fit_centered_coords(), n_atoms(), n_atoms_, n_decoys(), protocols::toolbox::reset_x(), rmsd(), protocols::toolbox::tr(), and weights_.

Referenced by protocols::toolbox::cluster_silent_structs().

◆ coords() [1/2]

ObjexxFCL::FArray3D_double const& protocols::toolbox::DecoySetEvaluation::coords ( ) const

inline

References coords_.

Referenced by protocols::toolbox::KClusterData::coords(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::coords(), protocols::toolbox::KClusterData::dist_square(), and protocols::toolbox::KClusterData::load_silent_files().

◆ coords() [2/2]

ObjexxFCL::FArray2P_double protocols::toolbox::DecoySetEvaluation::coords ( core::Size i ) const

inline

References coords_, and n_atoms_.

◆ create_dist_constraints()

void protocols::toolbox::DecoySetEvaluation::create_dist_constraints ( core::scoring::constraints::ConstraintSet & cst_set ) const

References core::scoring::constraints::ConstraintSet::add_constraint(), coords_, create_dist_constraints_median(), n_atoms(), n_decoys(), options_registered_, and protocols::toolbox::tr().

◆ create_dist_constraints_median()

void protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median ( core::scoring::constraints::ConstraintSet & cst_set ) const

References core::scoring::constraints::ConstraintSet::add_constraint(), coords_, protocols::loops::PoseNumberedLoopFileReader::hijack_loop_reading_code_set_loop_line_begin_token(), protocols::loops::Loops::is_loop_residue(), n_atoms(), n_decoys(), protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), protocols::loops::Loops::size(), and protocols::toolbox::tr().

Referenced by create_dist_constraints().

◆ create_xyz_constraints_median()

void protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median	(	core::scoring::constraints::ConstraintSet &	cst_set,
		core::pose::Pose const &	ref_pose,
		core::Size	root
	)		const

References core::scoring::constraints::ConstraintSet::add_constraint(), core::conformation::Residue::atom_index(), coords_, n_atoms(), n_decoys(), core::pose::named_stub_id_to_stub_id(), ref_pose(), core::pose::Pose::residue(), and protocols::toolbox::tr().

◆ find_closest_to_average()

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().

◆ n_atoms()

core::Size protocols::toolbox::DecoySetEvaluation::n_atoms ( ) const

inline

References n_atoms_.

Referenced by compute_distance_matrix(), create_dist_constraints(), create_dist_constraints_median(), create_xyz_constraints_median(), protocols::toolbox::KClusterData::load_silent_file(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::natom(), push_back_CA_xyz_from_silent_file(), rmsd(), set_n_atom(), and wRMSD().

◆ n_decoys()

core::Size protocols::toolbox::DecoySetEvaluation::n_decoys ( ) const

inline

References n_decoys_.

Referenced by protocols::toolbox::cluster_silent_structs(), compute_distance_matrix(), create_dist_constraints(), create_dist_constraints_median(), create_xyz_constraints_median(), protocols::toolbox::KClusterData::load_silent_file(), push_back_CA_xyz_from_silent_file(), rmsf(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::size(), and wRMSD().

◆ n_decoys_max()

core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_max ( ) const

inline

References n_decoys_max_.

Referenced by protocols::toolbox::KClusterData::load_silent_file(), and push_back_CA_xyz_from_silent_file().

◆ pop_back_CA_xyz()

void protocols::toolbox::DecoySetEvaluation::pop_back_CA_xyz ( )

References coords_, n_atoms_, and n_decoys_.

◆ prepare_push_back()

void protocols::toolbox::DecoySetEvaluation::prepare_push_back ( core::Size nres )

private

References coords_, n_atoms_, n_decoys_, n_decoys_max_, ref_structure_, and weights_.

Referenced by push_back(), and push_back_CA_xyz().

◆ push_back()

void protocols::toolbox::DecoySetEvaluation::push_back ( core::pose::Pose & pose )

References coords_, core::chemical::ResidueTypeBase::is_protein(), n_decoys_, prepare_push_back(), ref_pose_, core::pose::Pose::residue_type(), core::pose::Pose::size(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

◆ push_back_CA_xyz()

void protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz	(	ObjexxFCL::FArray2_double const &	xyz,
		core::Size	nres
	)

References coords_, n_decoys_, prepare_push_back(), and protocols::kinmatch::xyz().

Referenced by protocols::toolbox::KClusterData::load_silent_file(), and push_back_CA_xyz_from_silent_file().

◆ push_back_CA_xyz_from_silent_file() [1/2]

void protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file	(	core::io::silent::SilentFileData const &	sfd,
		bool	store_energies
	)

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), and core::io::silent::SilentFileData::size().

Referenced by protocols::toolbox::cluster_silent_structs().

◆ push_back_CA_xyz_from_silent_file() [2/2]

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
	)

References protocols::toolbox::_impl_tr(), all_energies_, core::sequence::end, core::conformation::Residue::is_protein(), n_atoms(), n_decoys(), n_decoys_max(), push_back_CA_xyz(), reserve(), core::pose::Pose::residue(), set_n_atom(), core::pose::Pose::size(), and store_energies_.

◆ ref_pose()

core::pose::Pose const& protocols::toolbox::DecoySetEvaluation::ref_pose ( )

inline

References ref_pose_.

Referenced by create_xyz_constraints_median().

◆ register_options()

void protocols::toolbox::DecoySetEvaluation::register_options ( )

static

References options_registered_.

◆ reserve()

void protocols::toolbox::DecoySetEvaluation::reserve ( core::Size n_decoys_ )

References coords_, n_atoms_, and n_decoys_max_.

Referenced by protocols::toolbox::KClusterData::load_silent_file(), and push_back_CA_xyz_from_silent_file().

◆ rmsd()

core::Real protocols::toolbox::DecoySetEvaluation::rmsd	(	ObjexxFCL::FArray1_double const &	weights,
		ObjexxFCL::FArray2_double &	xx_ref,
		ObjexxFCL::FArray2_double &	xx
	)		const

References protocols::toolbox::fit_centered_coords(), n_atoms(), n_atoms_, protocols::toolbox::reset_x(), and weights_.

Referenced by compute_distance_matrix().

◆ rmsf() [1/3]

Real protocols::toolbox::DecoySetEvaluation::rmsf ( core::Size pos )

private

References coords_, n_decoys(), and core::scoring::rms.

◆ rmsf() [2/3]

void protocols::toolbox::DecoySetEvaluation::rmsf ( ObjexxFCL::FArray1_double & result )

◆ rmsf() [3/3]

void protocols::toolbox::DecoySetEvaluation::rmsf ( utility::vector1< core::Real > & results )

References n_atoms_.

Referenced by wRMSD().

◆ set_all_energies()

void protocols::toolbox::DecoySetEvaluation::set_all_energies ( utility::vector1< core::Real > const & all_energies )

inline

References all_energies(), all_energies_, and store_energies_.

◆ set_n_atom()

void protocols::toolbox::DecoySetEvaluation::set_n_atom ( core::Size natoms )

References n_atoms(), n_atoms_, and protocols::toolbox::tr().

Referenced by push_back_CA_xyz_from_silent_file().

◆ set_weights()

void protocols::toolbox::DecoySetEvaluation::set_weights ( ObjexxFCL::FArray1_double const & weights )

References n_atoms_, and weights_.

◆ superimpose() [1/2]

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

References n_atoms_.

Referenced by wRMSD().

◆ superimpose() [2/2]

void protocols::toolbox::DecoySetEvaluation::superimpose	(	ObjexxFCL::FArray1_double const &	weights,
		core::Size	icenter = `1`
	)

private

◆ wRMSD()

Size protocols::toolbox::DecoySetEvaluation::wRMSD	(	core::Real	sigma2,
		core::Real	tolerance,
		ObjexxFCL::FArray1_double &	weights
	)

References compute_average_structure(), find_closest_to_average(), n_atoms(), n_atoms_, n_decoys(), rmsf(), superimpose(), and protocols::toolbox::tr().

Member Data Documentation

◆ all_energies_

utility::vector1< core::Real > protocols::toolbox::DecoySetEvaluation::all_energies_

private

Referenced by all_energies(), push_back_CA_xyz_from_silent_file(), and set_all_energies().

◆ COM

ObjexxFCL::FArray1D_double protocols::toolbox::DecoySetEvaluation::COM

private

◆ coords_

ObjexxFCL::FArray3D_double protocols::toolbox::DecoySetEvaluation::coords_

private

Referenced by compute_average_structure(), compute_distance_matrix(), coords(), create_dist_constraints(), create_dist_constraints_median(), create_xyz_constraints_median(), find_closest_to_average(), pop_back_CA_xyz(), prepare_push_back(), push_back(), push_back_CA_xyz(), reserve(), and rmsf().

◆ n_atoms_

core::Size protocols::toolbox::DecoySetEvaluation::n_atoms_

private

Referenced by center_structure(), clear(), compute_average_structure(), compute_distance_matrix(), coords(), find_closest_to_average(), n_atoms(), pop_back_CA_xyz(), prepare_push_back(), reserve(), rmsd(), rmsf(), set_n_atom(), set_weights(), superimpose(), and wRMSD().

◆ n_decoys_

core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_

private

Referenced by center_all(), clear(), compute_average_structure(), find_closest_to_average(), n_decoys(), pop_back_CA_xyz(), prepare_push_back(), push_back(), and push_back_CA_xyz().

◆ n_decoys_max_

core::Size protocols::toolbox::DecoySetEvaluation::n_decoys_max_

private

Referenced by clear(), n_decoys_max(), prepare_push_back(), and reserve().

◆ options_registered_

bool protocols::toolbox::DecoySetEvaluation::options_registered_

staticprivate

Referenced by create_dist_constraints(), and register_options().

◆ ref_pose_

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

private

Referenced by push_back(), and ref_pose().

◆ ref_structure_

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

private

Referenced by prepare_push_back().

◆ store_energies_

bool protocols::toolbox::DecoySetEvaluation::store_energies_

private

Referenced by push_back_CA_xyz_from_silent_file(), and set_all_energies().

◆ weights_

ObjexxFCL::FArray1D_double protocols::toolbox::DecoySetEvaluation::weights_

private

Referenced by compute_distance_matrix(), prepare_push_back(), rmsd(), and set_weights().

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

src/protocols/toolbox/DecoySetEvaluation.hh
src/protocols/toolbox/DecoySetEvaluation.cc
src/protocols/toolbox/DecoySetEvaluation.impl.hh

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

◆ DecoySetEvaluation()

◆ ~DecoySetEvaluation()

Member Function Documentation

◆ all_energies()

◆ center_all()

◆ center_structure() [1/2]

◆ center_structure() [2/2]

◆ clear()

◆ compute_average_structure()

◆ compute_distance_matrix()

◆ coords() [1/2]

◆ coords() [2/2]

◆ create_dist_constraints()

◆ create_dist_constraints_median()

◆ create_xyz_constraints_median()

◆ find_closest_to_average()

◆ n_atoms()

◆ n_decoys()

◆ n_decoys_max()

◆ pop_back_CA_xyz()

◆ prepare_push_back()

◆ push_back()

◆ push_back_CA_xyz()

◆ push_back_CA_xyz_from_silent_file() [1/2]

◆ push_back_CA_xyz_from_silent_file() [2/2]

◆ ref_pose()

◆ register_options()

◆ reserve()

◆ rmsd()

◆ rmsf() [1/3]

◆ rmsf() [2/3]

◆ rmsf() [3/3]

◆ set_all_energies()

◆ set_n_atom()

◆ set_weights()

◆ superimpose() [1/2]

◆ superimpose() [2/2]

◆ wRMSD()

Member Data Documentation

◆ all_energies_

◆ COM

◆ coords_

◆ n_atoms_

◆ n_decoys_

◆ n_decoys_max_

◆ options_registered_

◆ ref_pose_

◆ ref_structure_

◆ store_energies_

◆ weights_