protocols::residue_optimization::MetapatchEnumeration Class Reference

#include <MetapatchEnumeration.hh>

Public Member Functions
	MetapatchEnumeration (core::pose::Pose pose, core::kinematics::MoveMapOP mm, core::scoring::ScoreFunctionOP score_fxn, core::Size mode, bool pack, core::Real threshold, utility::vector1< std::string > metapatch_names, core::Real taboo=5)
utility::vector1< core::Real >	final_scores ()
utility::vector1< std::string >	summary_lines ()
void	generate_metapatched_variants (core::Size resi)
core::Real	score ()

Private Member Functions
void	generate_derived_types (core::Size resi, core::Size tp, utility::vector1< std::string > &types_considered)
core::Real	binding (core::pose::Pose pose)
void	initial_sampling (core::pose::Pose &pose)
void	final_sampling (core::pose::Pose &mut_pose, core::Size resi)
bool	tabooed (utility::vector1< std::string > const &patch_names)
	OPPORTUNITIES FOR IMPROVEMENT. More...

Private Attributes
utility::vector1< core::Real >	final_scores_
utility::vector1< std::string >	summary_lines_
core::pose::Pose	pose_
core::kinematics::MoveMapOP	mm_
core::scoring::ScoreFunctionOP	sampling_score_fxn_
core::scoring::ScoreFunctionOP	evaluation_score_fxn_
core::Size	mode_
bool	pack_
core::Real	threshold_
utility::vector1< std::string >	metapatch_names_
core::Real	score_
core::Real	taboo_
utility::vector1< utility::vector1< std::string > >	tabooed_

Constructor & Destructor Documentation

MetapatchEnumeration()

protocols::residue_optimization::MetapatchEnumeration::MetapatchEnumeration ( core::pose::Pose  pose, core::kinematics::MoveMapOP  mm, core::scoring::ScoreFunctionOP  score_fxn, core::Size  mode, bool  pack, core::Real  threshold, utility::vector1< std::string >  metapatch_names, core::Real  taboo = 5  )

inline

Member Function Documentation

binding()

Real protocols::residue_optimization::MetapatchEnumeration::binding ( core::pose::Pose  pose )

private

final_sampling()

void protocols::residue_optimization::MetapatchEnumeration::final_sampling ( core::pose::Pose &  mut_pose, core::Size  resi  )

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), protocols::relax::AtomCoordinateCstMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::delete_virtual_residues(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pose::Pose::fold_tree(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::hybridization::score, protocols::relax::RelaxProtocolBase::set_movemap(), and core::pose::Pose::size().

final_scores()

utility::vector1< core::Real > protocols::residue_optimization::MetapatchEnumeration::final_scores ( )

inline

References final_scores_.

generate_derived_types()

void protocols::residue_optimization::MetapatchEnumeration::generate_derived_types ( core::Size  resi, core::Size  tp, utility::vector1< std::string > &  types_considered  )

private

References protocols::vip::base_name(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::dump_scored_pdb(), core::pose::Pose::energies(), core::chemical::FA_STANDARD, core::chemical::get_patch_names(), core::scoring::mm_twist, core::chemical::ResidueTypeBase::name(), core::scoring::Energies::onebody_energies(), core::conformation::Conformation::replace_residue(), core::pose::Pose::residue(), core::chemical::residue_type_base_name(), and core::conformation::TR().

generate_metapatched_variants()

void protocols::residue_optimization::MetapatchEnumeration::generate_metapatched_variants

(

core::Size

resi

)

References core::chemical::ResidueTypeBase::name(), and core::conformation::TR().

initial_sampling()

void protocols::residue_optimization::MetapatchEnumeration::initial_sampling ( core::pose::Pose &  pose )

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::addVirtualResAsRoot(), protocols::relax::AtomCoordinateCstMover::apply(), protocols::relax::FastRelax::apply(), protocols::relax::delete_virtual_residues(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pose::Pose::fold_tree(), protocols::mean_field::min(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::hybridization::score, protocols::relax::RelaxProtocolBase::set_movemap(), and core::pose::Pose::size().

score()

core::Real protocols::residue_optimization::MetapatchEnumeration::score ( )

inline

References score_.

summary_lines()

utility::vector1< std::string > protocols::residue_optimization::MetapatchEnumeration::summary_lines ( )

inline

References summary_lines_.

tabooed()

bool protocols::residue_optimization::MetapatchEnumeration::tabooed ( utility::vector1< std::string > const &  patch_names )

private

OPPORTUNITIES FOR IMPROVEMENT.

References core::conformation::TR().

Member Data Documentation

evaluation_score_fxn_

core::scoring::ScoreFunctionOP protocols::residue_optimization::MetapatchEnumeration::evaluation_score_fxn_

private

final_scores_

utility::vector1< core::Real > protocols::residue_optimization::MetapatchEnumeration::final_scores_

private

Referenced by final_scores().

metapatch_names_

utility::vector1< std::string > protocols::residue_optimization::MetapatchEnumeration::metapatch_names_

private

mm_

core::kinematics::MoveMapOP protocols::residue_optimization::MetapatchEnumeration::mm_

private

mode_

core::Size protocols::residue_optimization::MetapatchEnumeration::mode_

private

pack_

bool protocols::residue_optimization::MetapatchEnumeration::pack_

private

pose_

core::pose::Pose protocols::residue_optimization::MetapatchEnumeration::pose_

private

sampling_score_fxn_

core::scoring::ScoreFunctionOP protocols::residue_optimization::MetapatchEnumeration::sampling_score_fxn_

private

score_

core::Real protocols::residue_optimization::MetapatchEnumeration::score_

private

Referenced by score().

summary_lines_

utility::vector1< std::string > protocols::residue_optimization::MetapatchEnumeration::summary_lines_

private

Referenced by summary_lines().

taboo_

core::Real protocols::residue_optimization::MetapatchEnumeration::taboo_

private

tabooed_

utility::vector1< utility::vector1< std::string > > protocols::residue_optimization::MetapatchEnumeration::tabooed_

private

threshold_

core::Real protocols::residue_optimization::MetapatchEnumeration::threshold_

private

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

• src/protocols/residue_optimization/MetapatchEnumeration.hh
• src/protocols/residue_optimization/MetapatchEnumeration.cc