LigandDiscoverySearch Class Reference

#include <LigandDiscoverySearch.hh>

Public Member Functions
	~LigandDiscoverySearch ()
	LigandDiscoverySearch (core::pose::PoseOP pose_from_PDB, protocols::motifs::MotifCOPs motif_library, utility::vector1< core::conformation::ResidueOP > all_residues, 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_position (core::Size working_position)
core::Size	get_working_position ()
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)

Private Member Functions
	LigandDiscoverySearch ()
void	create_protein_representation_matrix (core::Size &x_shift, core::Size &y_shift, core::Size &z_shift, int &x_bound_int, int &y_bound_int, int &z_bound_int)
bool	ligand_clash_check (core::conformation::ResidueOP ligresOP, core::Size x_shift, core::Size y_shift, core::Size z_shift, int x_bound_int, int y_bound_int, int z_bound_int)

Private Attributes
core::pose::PoseOP	working_pose_
protocols::motifs::MotifCOPs	motif_library_
protocols::motifs::MotifCOPs	motif_library_for_select_residue_
utility::vector1< core::conformation::ResidueOP >	all_residues_
core::Size	working_position_
utility::vector1< utility::vector1< utility::vector1< bool > > >	protein_representation_matrix_

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,
		core::Size	working_position
	)

LigandDiscoverySearch() [2/2]

LigandDiscoverySearch::LigandDiscoverySearch ( )

private

Member Function Documentation

create_protein_representation_matrix()

void LigandDiscoverySearch::create_protein_representation_matrix ( core::Size &  x_shift, core::Size &  y_shift, core::Size &  z_shift, int &  x_bound_int, int &  y_bound_int, int &  z_bound_int  )

private

References protocols::motifs::ms_tr().

discover()

core::Size LigandDiscoverySearch::discover

(

std::string

output_prefix

)

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, core::chemical::DISULFIDE, core::io::pdb::dump_pdb(), core::scoring::fa_atr, core::scoring::fa_elec, core::scoring::fa_intra_rep, core::scoring::fa_rep, core::chemical::FA_STANDARD, core::chemical::FULL_ATOM_t, protocols::ligand_docking::get_interface_deltas(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, mergeSort(), protocols::motifs::ms_tr(), core::scoring::rama, core::scoring::res_type_constraint, 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 protocols::motifs::ms_tr().

get_working_pose()

core::pose::PoseOP LigandDiscoverySearch::get_working_pose

(

)

get_working_position()

core::Size LigandDiscoverySearch::get_working_position

(

)

ligand_clash_check()

bool LigandDiscoverySearch::ligand_clash_check ( core::conformation::ResidueOP  ligresOP, core::Size  x_shift, core::Size  y_shift, core::Size  z_shift, int  x_bound_int, int  y_bound_int, int  z_bound_int  )

private

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

)

set_working_pose() [2/2]

void LigandDiscoverySearch::set_working_pose

(

core::pose::PoseOP

pose_from_PDB

)

set_working_position()

void LigandDiscoverySearch::set_working_position

(

core::Size

working_position

)

Member Data Documentation

all_residues_

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

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

protein_representation_matrix_

utility::vector1<utility::vector1<utility::vector1<bool> > > LigandDiscoverySearch::protein_representation_matrix_

private

working_pose_

core::pose::PoseOP LigandDiscoverySearch::working_pose_

private

working_position_

core::Size LigandDiscoverySearch::working_position_

private

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

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