protocols::hybridization::FragmentBiasAssigner Class Reference

#include <FragmentBiasAssigner.hh>

Inheritance diagram for protocols::hybridization::FragmentBiasAssigner:

Public Member Functions
	FragmentBiasAssigner (core::pose::Pose &pose)
void	init (core::pose::Pose &pose)
void	compute_frag_bias (utility::vector1< numeric::random::WeightedSampler > &frag_bias, core::pose::Pose &pose, utility::vector1< core::fragment::FragSetOP > fragments)
void	include_residues (std::set< core::Size > residues_to_include)
void	exclude_residues (std::set< core::Size > residues_to_exclude)
void	uniform ()
void	automode (core::pose::Pose &pose, core::Real score_cut)
void	automode_scores (core::pose::Pose &pose, std::map< core::Size, core::Real > &scores)
void	user (std::set< core::Size > user_pos, protocols::loops::LoopsOP loops)
void	density_nbr (core::pose::Pose &pose)
void	rama (core::pose::Pose &pose, core::Real weight=0.2)
void	geometry (core::pose::Pose &pose, core::Real weight=1.0)
void	density (core::pose::Pose &pose)
void	chainbreak (core::pose::Pose &pose)
void	bfactors (core::pose::Pose &pose)
void	fragbias_reporter (core::pose::Pose &pose)
void	cumulate_probability ()
void	set_rsd_wdw_to_assign_prob (int wdw=0)
void	set_wdw_to_freeze (int wdw=0)
void	set_score_threshold (core::Real threshold)

Private Member Functions
void	cal_perrsd_score (core::pose::Pose &pose, core::scoring::ScoreType const &score_type, utility::vector1< core::Real > &perrsd_score, core::Real weight)
void	assign_fragprobs (std::map< core::Size, core::Real > const &perrsd_score, core::Real threshold)
void	assign_prob_with_rsd_wdw (int rsn)

Private Attributes
core::Size	nres_
core::Size	n_symm_subunit_
int	wdw_to_freeze_
int	rsd_wdw_size_
core::Real	score_threshold_
bool	cumulative_
bool	fragProbs_assigned_
core::conformation::symmetry::SymmetryInfoCOP	symminfo_
utility::vector1< core::Real >	fragmentProbs_
std::map< core::Size, core::Real >	perrsd_dens_
std::map< core::Size, core::Real >	perrsd_nbrdens_
std::map< core::Size, core::Real >	perrsd_rama_
std::map< core::Size, core::Real >	perrsd_geometry_

Constructor & Destructor Documentation

protocols::hybridization::FragmentBiasAssigner::FragmentBiasAssigner

(

core::pose::Pose &

pose

)

References core::init::init().

Member Function Documentation

void protocols::hybridization::FragmentBiasAssigner::assign_fragprobs ( std::map< core::Size, core::Real > const &  perrsd_score, core::Real  threshold  )

private

References protocols::hybridization::fragbias_tr().

void protocols::hybridization::FragmentBiasAssigner::assign_prob_with_rsd_wdw ( int  rsn )

private

References protocols::hybridization::fragbias_tr().

void protocols::hybridization::FragmentBiasAssigner::automode	(	core::pose::Pose &	pose,
		core::Real	score_cut
	)

References protocols::buns::geometry, core::scoring::rama, and protocols::hybridization::score.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::automode_scores	(	core::pose::Pose &	pose,
		std::map< core::Size, core::Real > &	scores
	)

References protocols::hybridization::fragbias_tr(), protocols::buns::geometry, core::scoring::rama, and protocols::hybridization::score.

void protocols::hybridization::FragmentBiasAssigner::bfactors

(

core::pose::Pose &

pose

)

References protocols::hybridization::fragbias_tr(), core::chemical::ResidueType::last_backbone_atom(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue_type().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::cal_perrsd_score ( core::pose::Pose &  pose, core::scoring::ScoreType const &  score_type, utility::vector1< core::Real > &  perrsd_score, core::Real  weight  )

private

References core::pose::Pose::energies(), and core::scoring::Energies::residue_total_energies().

void protocols::hybridization::FragmentBiasAssigner::chainbreak

(

core::pose::Pose &

pose

)

References core::conformation::Residue::atom(), core::pose::Pose::fold_tree(), protocols::hybridization::fragbias_tr(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Atom::xyz().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::compute_frag_bias	(	utility::vector1< numeric::random::WeightedSampler > &	frag_bias,
		core::pose::Pose &	pose,
		utility::vector1< core::fragment::FragSetOP >	fragments
	)

References core::pose::Pose::fold_tree(), protocols::hybridization::fragbias_tr(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::size().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::cumulate_probability ( )

inline

References cumulative_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::density

(

core::pose::Pose &

pose

)

References core::scoring::elec_dens_window, core::scoring::fa_rep, protocols::hybridization::fragbias_tr(), core::scoring::electron_density::getDensityMap(), core::pose::Pose::is_fullatom(), core::scoring::electron_density::ElectronDensity::matchRes(), core::pose::Pose::residue(), core::scoring::electron_density::ElectronDensity::setScoreWindowContext(), core::scoring::electron_density::ElectronDensity::setWindow(), and core::scoring::vdw.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::density_nbr

(

core::pose::Pose &

pose

)

References core::scoring::electron_density::calculate_density_nbr(), and protocols::hybridization::fragbias_tr().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::exclude_residues

(

std::set< core::Size >

residues_to_exclude

)

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::fragbias_reporter

(

core::pose::Pose &

pose

)

References protocols::hybridization::fragbias_tr().

void protocols::hybridization::FragmentBiasAssigner::geometry	(	core::pose::Pose &	pose,
		core::Real	weight = 1.0
	)

References core::scoring::electron_density::calculate_geometry().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::include_residues

(

std::set< core::Size >

residues_to_include

)

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::init

(

core::pose::Pose &

pose

)

References core::pose::Pose::conformation(), protocols::hybridization::fragbias_tr(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), and core::pose::Pose::size().

void protocols::hybridization::FragmentBiasAssigner::rama	(	core::pose::Pose &	pose,
		core::Real	weight = 0.2
	)

References core::scoring::electron_density::calculate_rama().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::set_rsd_wdw_to_assign_prob ( int  wdw = 0 )

inline

References rsd_wdw_size_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::set_score_threshold ( core::Real  threshold )

inline

References score_threshold_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::set_wdw_to_freeze ( int  wdw = 0 )

inline

References wdw_to_freeze_.

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::uniform

(

)

References protocols::hybridization::fragbias_tr().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

void protocols::hybridization::FragmentBiasAssigner::user	(	std::set< core::Size >	user_pos,
		protocols::loops::LoopsOP	loops
	)

References protocols::hybridization::fragbias_tr().

Referenced by protocols::hybridization::CartesianSampler::compute_fragment_bias().

Member Data Documentation

bool protocols::hybridization::FragmentBiasAssigner::cumulative_

private

Referenced by cumulate_probability().

utility::vector1<core::Real> protocols::hybridization::FragmentBiasAssigner::fragmentProbs_

private

bool protocols::hybridization::FragmentBiasAssigner::fragProbs_assigned_

private

core::Size protocols::hybridization::FragmentBiasAssigner::n_symm_subunit_

private

core::Size protocols::hybridization::FragmentBiasAssigner::nres_

private

std::map< core::Size, core::Real > protocols::hybridization::FragmentBiasAssigner::perrsd_dens_

private

std::map< core::Size, core::Real > protocols::hybridization::FragmentBiasAssigner::perrsd_geometry_

private

std::map< core::Size, core::Real > protocols::hybridization::FragmentBiasAssigner::perrsd_nbrdens_

private

std::map< core::Size, core::Real > protocols::hybridization::FragmentBiasAssigner::perrsd_rama_

private

int protocols::hybridization::FragmentBiasAssigner::rsd_wdw_size_

private

Referenced by set_rsd_wdw_to_assign_prob().

core::Real protocols::hybridization::FragmentBiasAssigner::score_threshold_

private

Referenced by set_score_threshold().

core::conformation::symmetry::SymmetryInfoCOP protocols::hybridization::FragmentBiasAssigner::symminfo_

private

int protocols::hybridization::FragmentBiasAssigner::wdw_to_freeze_

private

Referenced by set_wdw_to_freeze().

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

• src/protocols/hybridization/FragmentBiasAssigner.hh
• src/protocols/hybridization/FragmentBiasAssigner.cc