Rosetta
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::hybridization::FragmentBiasAssigner Class Reference

#include <FragmentBiasAssigner.hh>

Inheritance diagram for protocols::hybridization::FragmentBiasAssigner:
Inheritance graph
[legend]

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

◆ FragmentBiasAssigner()

protocols::hybridization::FragmentBiasAssigner::FragmentBiasAssigner ( core::pose::Pose &  pose)

References core::init::init().

Member Function Documentation

◆ assign_fragprobs()

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

References protocols::hybridization::fragbias_tr().

◆ assign_prob_with_rsd_wdw()

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

References protocols::hybridization::fragbias_tr().

◆ automode()

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().

◆ automode_scores()

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.

◆ bfactors()

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().

◆ cal_perrsd_score()

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().

◆ chainbreak()

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().

◆ compute_frag_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().

◆ cumulate_probability()

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

References cumulative_.

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

◆ density()

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().

◆ density_nbr()

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().

◆ exclude_residues()

void protocols::hybridization::FragmentBiasAssigner::exclude_residues ( std::set< core::Size >  residues_to_exclude)

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

◆ fragbias_reporter()

void protocols::hybridization::FragmentBiasAssigner::fragbias_reporter ( core::pose::Pose &  pose)

References protocols::hybridization::fragbias_tr().

◆ geometry()

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().

◆ include_residues()

void protocols::hybridization::FragmentBiasAssigner::include_residues ( std::set< core::Size >  residues_to_include)

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

◆ init()

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().

◆ rama()

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().

◆ set_rsd_wdw_to_assign_prob()

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().

◆ set_score_threshold()

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

References score_threshold_.

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

◆ set_wdw_to_freeze()

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

References wdw_to_freeze_.

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

◆ uniform()

void protocols::hybridization::FragmentBiasAssigner::uniform ( )

References protocols::hybridization::fragbias_tr().

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

◆ user()

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

◆ cumulative_

bool protocols::hybridization::FragmentBiasAssigner::cumulative_
private

Referenced by cumulate_probability().

◆ fragmentProbs_

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

◆ fragProbs_assigned_

bool protocols::hybridization::FragmentBiasAssigner::fragProbs_assigned_
private

◆ n_symm_subunit_

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

◆ nres_

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

◆ perrsd_dens_

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

◆ perrsd_geometry_

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

◆ perrsd_nbrdens_

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

◆ perrsd_rama_

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

◆ rsd_wdw_size_

int protocols::hybridization::FragmentBiasAssigner::rsd_wdw_size_
private

Referenced by set_rsd_wdw_to_assign_prob().

◆ score_threshold_

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

Referenced by set_score_threshold().

◆ symminfo_

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

◆ wdw_to_freeze_

int protocols::hybridization::FragmentBiasAssigner::wdw_to_freeze_
private

Referenced by set_wdw_to_freeze().

The documentation for this class was generated from the following files:
Generated on Thu Sep 11 2025 21:32:37 for Rosetta by doxygen 1.9.1