#include <FragmentExtension.hh>

Public Member Functions
	LoopComparator ()

void	apply (core::pose::Pose &pose)

void	push (LoopPartialSolutionStore const solutionset)

void	fill_pose (core::pose::Pose &pose)

void	set_scores (core::pose::Pose &pose)

void	set_density_sf (core::scoring::ScoreFunctionOP sf_dens)

void	set_vdw_sf (core::scoring::ScoreFunctionOP sf_vdw)

void	set_sequence (core::sequence::SequenceOP fullength_seq)

void	set_loops (utility::vector1< protocols::loops::Loop > loops)

void	set_read_from_file (bool read_from_file)

void	set_assign_incomplete (bool assign_incomplete)

core::Real	get_one_body_score ()

void	read_from_file ()

Private Attributes
utility::vector1< LoopPartialSolutionStore >	solutionsets_

core::scoring::ScoreFunctionOP	sf_dens_

core::scoring::ScoreFunctionOP	sf_vdw_

utility::vector1< utility::vector1< core::Real > >	one_body_energies_

std::map< std::pair< core::Size, core::Size >, utility::vector1< utility::vector1< core::Real > > >	two_body_energies_map_

core::sequence::SequenceOP	fullength_seq_

utility::vector1< protocols::loops::Loop >	loops_

core::Real	one_body_score_

bool	read_from_file_

bool	assign_incomplete_

Constructor & Destructor Documentation

◆ LoopComparator()

protocols::loop_grower::LoopComparator::LoopComparator ( )

inline

Member Function Documentation

◆ apply()

void protocols::loop_grower::LoopComparator::apply ( core::pose::Pose & pose )

References protocols::hotspot_hashing::accept, core::pose::Pose::delete_residue_range_slow(), core::sequence::end, protocols::simple_moves::bb_sampler::probability, core::scoring::rg, protocols::loop_grower::LoopPartialSolution::set_coordinates(), protocols::loops::start, and protocols::loop_grower::TR().

◆ fill_pose()

void protocols::loop_grower::LoopComparator::fill_pose ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::kinematics::FoldTree::cutpoint_by_jump(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), core::pose::Pose::fold_tree(), protocols::loop_grower::LoopPartialSolutionStore::get_cutpoint(), protocols::loop_grower::LoopPartialSolutionStore::get_lower_pose(), protocols::loop_grower::LoopPartialSolutionStore::get_upper_fasta(), protocols::loop_grower::LoopPartialSolutionStore::get_upper_pose(), core::pose::Pose::is_centroid(), core::kinematics::FoldTree::num_jump(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::residue_types_from_sequence(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), and protocols::loop_grower::TR().

◆ get_one_body_score()

core::Real protocols::loop_grower::LoopComparator::get_one_body_score ( )

inline

References one_body_score_.

◆ push()

void protocols::loop_grower::LoopComparator::push ( LoopPartialSolutionStore const solutionset )

inline

References solutionsets_.

◆ read_from_file()

void protocols::loop_grower::LoopComparator::read_from_file ( )

References protocols::loops::cut_point, protocols::hybridization::score, protocols::loop_grower::LoopPartialSolutionStore::set_cutpoint(), protocols::loop_grower::LoopPartialSolutionStore::set_fastas(), protocols::loop_grower::LoopPartialSolution::set_ids(), protocols::loop_grower::LoopPartialSolutionStore::set_poses(), protocols::loop_grower::LoopPartialSolution::set_positions(), protocols::loop_grower::LoopPartialSolution::set_score(), and protocols::loop_grower::LoopPartialSolutionStore::store().

Referenced by set_read_from_file().

◆ set_assign_incomplete()

void protocols::loop_grower::LoopComparator::set_assign_incomplete ( bool assign_incomplete )

inline

References assign_incomplete_.

◆ set_density_sf()

void protocols::loop_grower::LoopComparator::set_density_sf ( core::scoring::ScoreFunctionOP sf_dens )

inline

References sf_dens_.

◆ set_loops()

void protocols::loop_grower::LoopComparator::set_loops ( utility::vector1< protocols::loops::Loop > loops )

inline

References loops_.

◆ set_read_from_file()

void protocols::loop_grower::LoopComparator::set_read_from_file ( bool read_from_file )

inline

References read_from_file(), and read_from_file_.

◆ set_scores()

void protocols::loop_grower::LoopComparator::set_scores ( core::pose::Pose & pose )

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::loop_grower::LoopPartialSolutionStore::get_lower_fasta(), protocols::loop_grower::LoopPartialSolution::get_score(), protocols::loop_grower::LoopPartialSolutionStore::get_upper_fasta(), protocols::hybridization::score, protocols::loop_grower::LoopPartialSolution::set_coordinates(), protocols::loop_grower::LoopPartialSolutionStore::size(), protocols::loop_grower::TR(), and core::scoring::vdw.

◆ set_sequence()

void protocols::loop_grower::LoopComparator::set_sequence ( core::sequence::SequenceOP fullength_seq )

inline

References fullength_seq_.

◆ set_vdw_sf()

void protocols::loop_grower::LoopComparator::set_vdw_sf ( core::scoring::ScoreFunctionOP sf_vdw )

inline

References sf_vdw_.

Member Data Documentation

◆ assign_incomplete_

bool protocols::loop_grower::LoopComparator::assign_incomplete_

private

Referenced by set_assign_incomplete().

◆ fullength_seq_

core::sequence::SequenceOP protocols::loop_grower::LoopComparator::fullength_seq_

private

Referenced by set_sequence().

◆ loops_

utility::vector1< protocols::loops::Loop > protocols::loop_grower::LoopComparator::loops_

private

Referenced by set_loops().

◆ one_body_energies_

utility::vector1< utility::vector1<core::Real> > protocols::loop_grower::LoopComparator::one_body_energies_

private

◆ one_body_score_

core::Real protocols::loop_grower::LoopComparator::one_body_score_

private

Referenced by get_one_body_score().

◆ read_from_file_

bool protocols::loop_grower::LoopComparator::read_from_file_

private

Referenced by set_read_from_file().

◆ sf_dens_

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopComparator::sf_dens_

private

Referenced by set_density_sf().

◆ sf_vdw_

core::scoring::ScoreFunctionOP protocols::loop_grower::LoopComparator::sf_vdw_

private

Referenced by set_vdw_sf().

◆ solutionsets_

utility::vector1<LoopPartialSolutionStore> protocols::loop_grower::LoopComparator::solutionsets_

private

Referenced by push().

◆ two_body_energies_map_

std::map< std::pair< core::Size,core::Size >,utility::vector1< utility::vector1< core::Real> > > protocols::loop_grower::LoopComparator::two_body_energies_map_

private

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

src/protocols/loop_grower/FragmentExtension.hh
src/protocols/loop_grower/FragmentExtension.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ LoopComparator()

Member Function Documentation

◆ apply()

◆ fill_pose()

◆ get_one_body_score()

◆ push()

◆ read_from_file()

◆ set_assign_incomplete()

◆ set_density_sf()

◆ set_loops()

◆ set_read_from_file()

◆ set_scores()

◆ set_sequence()

◆ set_vdw_sf()

Member Data Documentation

◆ assign_incomplete_

◆ fullength_seq_

◆ loops_

◆ one_body_energies_

◆ one_body_score_

◆ read_from_file_

◆ sf_dens_

◆ sf_vdw_

◆ solutionsets_

◆ two_body_energies_map_