#include <LigandDiscoverySearch.hh>

Public Types
typedef utility::vector1< utility::vector1< utility::vector1< core::Size > > >	atom_trios

Public Member Functions
	~LigandDiscoverySearch ()

	LigandDiscoverySearch (core::pose::PoseOP pose_from_PDB, protocols::motifs::MotifCOPs motif_library, utility::vector1< core::conformation::ResidueOP > all_residues, utility::vector1< core::Size > working_position)

void	set_motif_library (protocols::motifs::MotifCOPs motif_library)

void	set_motif_library (protocols::motifs::MotifLibrary motif_library)

protocols::motifs::MotifCOPs	get_motif_library ()

void	set_working_positions (utility::vector1< core::Size > working_position)

void	set_working_positions (core::Size working_position)

void	add_working_positions (utility::vector1< core::Size > working_positions)

void	add_working_positions (core::Size working_positions)

utility::vector1< core::Size >	get_working_positions ()

void	set_working_pose (core::pose::PoseOP pose_from_PDB)

void	set_working_pose (core::pose::Pose pose_from_PDB)

core::pose::PoseOP	get_working_pose ()

void	set_all_residues (utility::vector1< core::conformation::ResidueOP > all_residues)

utility::vector1< core::conformation::ResidueOP >	get_all_residues ()

core::Size	discover (std::string output_prefix)

protocols::motifs::MotifCOPs	get_motif_sublibrary_by_aa (std::string residue_name)

atom_trios	derive_adjacent_atoms_of_ligand (const core::conformation::ResidueOP ligresOP, const core::chemical::AtomTypeSetCOP atset)

core::Real	get_pose_ddg (core::scoring::ScoreFunctionOP score_fxn, core::pose::PoseOP &my_pose)

Private Member Functions
	LigandDiscoverySearch ()

void	seed_cutoff_values ()

void	setup_score_functions ()

bool	make_minipose (core::pose::PoseOP &minipose, const core::conformation::ResidueOP ligresOP)

bool	score_minipose (const core::pose::PoseOP &minipose, core::Real &fa_rep, core::Real &fa_atr, core::Real &fa_atr_rep_score_before)

void	add_constraints_to_working_pose (const core::Size trip_atom_1, const core::Size trip_atom_2, const core::Size trip_atom_3, const core::Size working_position, const core::conformation::ResidueOP ligresOP)

void	add_ligand_to_pose_residuetypeset (const core::chemical::MutableResidueTypeOP lig_mrt)

protocols::ligand_docking::HighResDockerOP	make_HighResDockOP_for_discovery (const core::scoring::ScoreFunctionOP my_fxn)

void	run_HighResDock_on_working_pose (const protocols::ligand_docking::HighResDockerOP my_HighResDocker)

void	reset_working_pose ()

Private Attributes
core::pose::PoseOP	working_pose_

core::pose::Pose	original_pose_

protocols::motifs::MotifCOPs	motif_library_

protocols::motifs::MotifCOPs	motif_library_for_select_residue_

utility::vector1< core::conformation::ResidueOP >	all_residues_

utility::vector1< core::Size >	working_positions_

core::Real	fa_rep_cutoff_

core::Real	fa_atr_cutoff_

core::Real	fa_atr_rep_cutoff_

core::Real	whole_fxn_cutoff_

core::Real	ddg_cutoff_

core::Size	min_motifs_cutoff_

core::Size	min_sig_motifs_cutoff_

core::Real	real_motif_ratio_cutoff_

core::scoring::ScoreFunctionOP	whole_score_fxn_

core::scoring::ScoreFunctionOP	fa_atr_fxn_

core::scoring::ScoreFunctionOP	fa_rep_fxn_

core::scoring::ScoreFunctionOP	fa_atr_rep_fxn_

core::scoring::ScoreFunctionOP	working_fxn_

protocols::protein_grid::ProteinGridOP	clash_pose_grid_

protocols::protein_grid::ProteinGridOP	sf_pose_grid_

Member Typedef Documentation

◆ atom_trios

typedef utility::vector1<utility::vector1<utility::vector1<core::Size> > > LigandDiscoverySearch::atom_trios

Constructor & Destructor Documentation

◆ ~LigandDiscoverySearch()

LigandDiscoverySearch::~LigandDiscoverySearch ( )

default

◆ LigandDiscoverySearch() [1/2]

LigandDiscoverySearch::LigandDiscoverySearch	(	core::pose::PoseOP	pose_from_PDB,
		protocols::motifs::MotifCOPs	motif_library,
		utility::vector1< core::conformation::ResidueOP >	all_residues,
		utility::vector1< core::Size >	working_position
	)

◆ LigandDiscoverySearch() [2/2]

LigandDiscoverySearch::LigandDiscoverySearch ( )

private

Member Function Documentation

◆ add_constraints_to_working_pose()

void LigandDiscoverySearch::add_constraints_to_working_pose	(	const core::Size	trip_atom_1,
		const core::Size	trip_atom_2,
		const core::Size	trip_atom_3,
		const core::Size	working_position,
		const core::conformation::ResidueOP	ligresOP
	)

private

◆ add_ligand_to_pose_residuetypeset()

void LigandDiscoverySearch::add_ligand_to_pose_residuetypeset ( const core::chemical::MutableResidueTypeOP lig_mrt )

private

References core::chemical::FULL_ATOM_t.

◆ add_working_positions() [1/2]

void LigandDiscoverySearch::add_working_positions ( core::Size working_positions )

◆ add_working_positions() [2/2]

void LigandDiscoverySearch::add_working_positions ( utility::vector1< core::Size > working_positions )

◆ derive_adjacent_atoms_of_ligand()

LigandDiscoverySearch::atom_trios LigandDiscoverySearch::derive_adjacent_atoms_of_ligand	(	const core::conformation::ResidueOP	ligresOP,
		const core::chemical::AtomTypeSetCOP	atset
	)

◆ discover()

core::Size LigandDiscoverySearch::discover ( std::string output_prefix )

References core::pose::add_comment(), core::io::pdb::dump_pdb(), IdentifyLigandMotifs::evaluate_motifs_of_pose(), core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::FA_STANDARD, protocols::motifs::hash_motif_library_into_map(), mergeSort(), ms_tr(), and core::id::to_string().

◆ get_all_residues()

utility::vector1< core::conformation::ResidueOP > LigandDiscoverySearch::get_all_residues ( )

◆ get_motif_library()

protocols::motifs::MotifCOPs LigandDiscoverySearch::get_motif_library ( )

◆ get_motif_sublibrary_by_aa()

protocols::motifs::MotifCOPs LigandDiscoverySearch::get_motif_sublibrary_by_aa ( std::string residue_name )

References ms_tr().

◆ get_pose_ddg()

core::Real LigandDiscoverySearch::get_pose_ddg	(	core::scoring::ScoreFunctionOP	score_fxn,
		core::pose::PoseOP &	my_pose
	)

References protocols::ligand_docking::get_interface_deltas().

◆ get_working_pose()

core::pose::PoseOP LigandDiscoverySearch::get_working_pose ( )

◆ get_working_positions()

utility::vector1< core::Size > LigandDiscoverySearch::get_working_positions ( )

◆ make_HighResDockOP_for_discovery()

protocols::ligand_docking::HighResDockerOP LigandDiscoverySearch::make_HighResDockOP_for_discovery ( const core::scoring::ScoreFunctionOP my_fxn )

private

◆ make_minipose()

bool LigandDiscoverySearch::make_minipose	(	core::pose::PoseOP &	minipose,
		const core::conformation::ResidueOP	ligresOP
	)

private

References core::chemical::DISULFIDE, core::io::pdb::dump_pdb(), and ms_tr().

◆ reset_working_pose()

void LigandDiscoverySearch::reset_working_pose ( )

private

◆ run_HighResDock_on_working_pose()

void LigandDiscoverySearch::run_HighResDock_on_working_pose ( const protocols::ligand_docking::HighResDockerOP my_HighResDocker )

private

◆ score_minipose()

bool LigandDiscoverySearch::score_minipose	(	const core::pose::PoseOP &	minipose,
		core::Real &	fa_rep,
		core::Real &	fa_atr,
		core::Real &	fa_atr_rep_score_before
	)

private

References core::scoring::fa_atr, core::scoring::fa_rep, and ms_tr().

◆ seed_cutoff_values()

void LigandDiscoverySearch::seed_cutoff_values ( )

private

References ms_tr().

◆ set_all_residues()

void LigandDiscoverySearch::set_all_residues ( utility::vector1< core::conformation::ResidueOP > all_residues )

◆ set_motif_library() [1/2]

void LigandDiscoverySearch::set_motif_library ( protocols::motifs::MotifCOPs motif_library )

◆ set_motif_library() [2/2]

void LigandDiscoverySearch::set_motif_library ( protocols::motifs::MotifLibrary motif_library )

References protocols::motifs::MotifLibrary::library().

◆ set_working_pose() [1/2]

void LigandDiscoverySearch::set_working_pose ( core::pose::Pose pose_from_PDB )

References core::pose::Pose::clone().

◆ set_working_pose() [2/2]

void LigandDiscoverySearch::set_working_pose ( core::pose::PoseOP pose_from_PDB )

◆ set_working_positions() [1/2]

void LigandDiscoverySearch::set_working_positions ( core::Size working_position )

◆ set_working_positions() [2/2]

void LigandDiscoverySearch::set_working_positions ( utility::vector1< core::Size > working_position )

◆ setup_score_functions()

void LigandDiscoverySearch::setup_score_functions ( )

private

References core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::fa_atr, and core::scoring::fa_rep.

Member Data Documentation

◆ all_residues_

utility::vector1<core::conformation::ResidueOP> LigandDiscoverySearch::all_residues_

private

◆ clash_pose_grid_

protocols::protein_grid::ProteinGridOP LigandDiscoverySearch::clash_pose_grid_

private

◆ ddg_cutoff_

core::Real LigandDiscoverySearch::ddg_cutoff_

private

◆ fa_atr_cutoff_

core::Real LigandDiscoverySearch::fa_atr_cutoff_

private

◆ fa_atr_fxn_

core::scoring::ScoreFunctionOP LigandDiscoverySearch::fa_atr_fxn_

private

◆ fa_atr_rep_cutoff_

core::Real LigandDiscoverySearch::fa_atr_rep_cutoff_

private

◆ fa_atr_rep_fxn_

core::scoring::ScoreFunctionOP LigandDiscoverySearch::fa_atr_rep_fxn_

private

◆ fa_rep_cutoff_

core::Real LigandDiscoverySearch::fa_rep_cutoff_

private

◆ fa_rep_fxn_

core::scoring::ScoreFunctionOP LigandDiscoverySearch::fa_rep_fxn_

private

◆ min_motifs_cutoff_

core::Size LigandDiscoverySearch::min_motifs_cutoff_

private

◆ min_sig_motifs_cutoff_

core::Size LigandDiscoverySearch::min_sig_motifs_cutoff_

private

◆ motif_library_

protocols::motifs::MotifCOPs LigandDiscoverySearch::motif_library_

private

◆ motif_library_for_select_residue_

protocols::motifs::MotifCOPs LigandDiscoverySearch::motif_library_for_select_residue_

private

◆ original_pose_

core::pose::Pose LigandDiscoverySearch::original_pose_

private

◆ real_motif_ratio_cutoff_

core::Real LigandDiscoverySearch::real_motif_ratio_cutoff_

private

◆ sf_pose_grid_

protocols::protein_grid::ProteinGridOP LigandDiscoverySearch::sf_pose_grid_

private

◆ whole_fxn_cutoff_

core::Real LigandDiscoverySearch::whole_fxn_cutoff_

private

◆ whole_score_fxn_

core::scoring::ScoreFunctionOP LigandDiscoverySearch::whole_score_fxn_

private

◆ working_fxn_

core::scoring::ScoreFunctionOP LigandDiscoverySearch::working_fxn_

private

◆ working_pose_

core::pose::PoseOP LigandDiscoverySearch::working_pose_

private

◆ working_positions_

utility::vector1<core::Size> LigandDiscoverySearch::working_positions_

private

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

src/protocols/motifs/LigandDiscoverySearch.hh
src/protocols/motifs/LigandDiscoverySearch.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ atom_trios

Constructor & Destructor Documentation

◆ ~LigandDiscoverySearch()

◆ LigandDiscoverySearch() [1/2]

◆ LigandDiscoverySearch() [2/2]

Member Function Documentation

◆ add_constraints_to_working_pose()

◆ add_ligand_to_pose_residuetypeset()

◆ add_working_positions() [1/2]

◆ add_working_positions() [2/2]

◆ derive_adjacent_atoms_of_ligand()

◆ discover()

◆ get_all_residues()

◆ get_motif_library()

◆ get_motif_sublibrary_by_aa()

◆ get_pose_ddg()

◆ get_working_pose()

◆ get_working_positions()

◆ make_HighResDockOP_for_discovery()

◆ make_minipose()

◆ reset_working_pose()

◆ run_HighResDock_on_working_pose()

◆ score_minipose()

◆ seed_cutoff_values()

◆ set_all_residues()

◆ set_motif_library() [1/2]

◆ set_motif_library() [2/2]

◆ set_working_pose() [1/2]

◆ set_working_pose() [2/2]

◆ set_working_positions() [1/2]

◆ set_working_positions() [2/2]

◆ setup_score_functions()

Member Data Documentation

◆ all_residues_

◆ clash_pose_grid_

◆ ddg_cutoff_

◆ fa_atr_cutoff_

◆ fa_atr_fxn_

◆ fa_atr_rep_cutoff_

◆ fa_atr_rep_fxn_

◆ fa_rep_cutoff_

◆ fa_rep_fxn_

◆ min_motifs_cutoff_

◆ min_sig_motifs_cutoff_

◆ motif_library_

◆ motif_library_for_select_residue_

◆ original_pose_

◆ real_motif_ratio_cutoff_

◆ sf_pose_grid_

◆ whole_fxn_cutoff_

◆ whole_score_fxn_

◆ working_fxn_

◆ working_pose_

◆ working_positions_