IdentifyLigandMotifs Class Reference

#include <IdentifyLigandMotifs.hh>

Public Member Functions
	IdentifyLigandMotifs ()
	~IdentifyLigandMotifs ()
void	process_file_list ()
void	get_atom_trios (utility::vector1< utility::vector1< core::Size > > &motif_indices_list, utility::vector1< utility::vector1< core::Size > > &all_motif_indices, core::conformation::Residue const &ligres)
protocols::motifs::MotifLibrary	get_motif_library ()
void	write_motifs_to_disk ()

Private Member Functions
core::Real	get_hbond_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
void	output_single_motif_to_MotifLibrary (core::pose::Pose &src_pose, protocols::motifs::MotifLibrary &motifs, std::string &pdb_name, core::Size prot_pos, core::Size lig_pos, utility::vector1< core::Size > &lig_atoms, core::Real pack_score, core::Real hb_score)
void	output_single_motif_to_pdb (core::pose::Pose &src_pose, std::string &pdb_name, core::Size prot_pos, core::Size lig_pos, utility::vector1< core::Size > &lig_atoms)
core::Real	get_packing_score (core::pose::Pose &pose, core::Size pos1, core::Size pos2, core::scoring::ScoreFunction &scorefxn)
void	process_for_motifs (core::pose::Pose &pose, std::string &pdb_name, protocols::motifs::MotifLibrary &motifs)
void	ligand_to_residue_analysis (core::Size lig_pos, core::Size prot_pos, core::pose::Pose &pose, std::string &pdb_name, protocols::motifs::MotifLibrary &motifs, core::scoring::ScoreFunctionOP scorefxn, utility::vector1< utility::vector1< core::Size > > &motif_indices_list)

Private Attributes
std::string	motif_pdb_output_path_
std::string	motif_file_output_
bool	output_motifs_
bool	output_motifs_as_pdb_
protocols::motifs::MotifLibrary	motif_library_

Constructor & Destructor Documentation

IdentifyLigandMotifs()

IdentifyLigandMotifs::IdentifyLigandMotifs

(

)

References TR().

~IdentifyLigandMotifs()

IdentifyLigandMotifs::~IdentifyLigandMotifs ( )

default

Member Function Documentation

get_atom_trios()

void IdentifyLigandMotifs::get_atom_trios	(	utility::vector1< utility::vector1< core::Size > > &	motif_indices_list,
		utility::vector1< utility::vector1< core::Size > > &	all_motif_indices,
		core::conformation::Residue const &	ligres
	)

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), core::conformation::Residue::bonded_neighbor(), core::chemical::AtomType::is_hydrogen(), core::conformation::Residue::natoms(), and TR().

get_hbond_score()

core::Real IdentifyLigandMotifs::get_hbond_score ( core::pose::Pose &  pose, core::Size  pos1, core::Size  pos2, core::scoring::ScoreFunction &  scorefxn  )

private

References core::scoring::ScoreFunction::eval_cd_2b_sc_sc(), core::scoring::ScoreFunction::eval_ci_2b_sc_sc(), core::scoring::hbond_sc, and core::pose::Pose::residue().

get_motif_library()

protocols::motifs::MotifLibrary IdentifyLigandMotifs::get_motif_library

(

)

get_packing_score()

core::Real IdentifyLigandMotifs::get_packing_score ( core::pose::Pose &  pose, core::Size  pos1, core::Size  pos2, core::scoring::ScoreFunction &  scorefxn  )

private

References core::scoring::ScoreFunction::eval_ci_2b_sc_sc(), core::scoring::fa_atr, and core::pose::Pose::residue().

ligand_to_residue_analysis()

void IdentifyLigandMotifs::ligand_to_residue_analysis ( core::Size  lig_pos, core::Size  prot_pos, core::pose::Pose &  pose, std::string &  pdb_name, protocols::motifs::MotifLibrary &  motifs, core::scoring::ScoreFunctionOP  scorefxn, utility::vector1< utility::vector1< core::Size > > &  motif_indices_list  )

private

References core::sequence::end, core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_protein(), protocols::mean_field::min(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::total_score, TR(), and core::conformation::Residue::xyz().

output_single_motif_to_MotifLibrary()

void IdentifyLigandMotifs::output_single_motif_to_MotifLibrary ( core::pose::Pose &  src_pose, protocols::motifs::MotifLibrary &  motifs, std::string &  pdb_name, core::Size  prot_pos, core::Size  lig_pos, utility::vector1< core::Size > &  lig_atoms, core::Real  pack_score, core::Real  hb_score  )

private

References protocols::motifs::MotifLibrary::add_to_library(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::motifs::Motif::store_remark(), and core::id::to_string().

output_single_motif_to_pdb()

void IdentifyLigandMotifs::output_single_motif_to_pdb ( core::pose::Pose &  src_pose, std::string &  pdb_name, core::Size  prot_pos, core::Size  lig_pos, utility::vector1< core::Size > &  lig_atoms  )

private

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::conformation(), core::io::pdb::dump_pdb(), core::conformation::Conformation::insert_chain_ending(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::conformation::Residue::natoms(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::set_xyz(), TR(), and core::conformation::Residue::xyz().

process_file_list()

void IdentifyLigandMotifs::process_file_list

(

)

References core::scoring::fa_atr, core::scoring::fa_dun, core::scoring::fa_pair, core::scoring::fa_rep, core::scoring::fa_sol, core::import_pose::pose_stream::MetaPoseInputStream::fill_pose(), core::import_pose::pose_stream::MetaPoseInputStream::get_last_pose_descriptor_string(), core::import_pose::pose_stream::MetaPoseInputStream::has_another_pose(), core::scoring::hbond_bb_sc, core::scoring::hbond_sc, core::scoring::p_aa_pp, core::scoring::ScoreFunction::set_weight(), and core::import_pose::pose_stream::streams_from_cmd_line().

process_for_motifs()

void IdentifyLigandMotifs::process_for_motifs ( core::pose::Pose &  pose, std::string &  pdb_name, protocols::motifs::MotifLibrary &  motifs  )

private

References core::chemical::ResidueType::is_ligand(), core::conformation::Residue::n_virtual_atoms(), core::conformation::Residue::name(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and TR().

write_motifs_to_disk()

void IdentifyLigandMotifs::write_motifs_to_disk

(

)

References protocols::motifs::write_motifs_to_disk().

Member Data Documentation

motif_file_output_

std::string IdentifyLigandMotifs::motif_file_output_

private

motif_library_

protocols::motifs::MotifLibrary IdentifyLigandMotifs::motif_library_

private

motif_pdb_output_path_

std::string IdentifyLigandMotifs::motif_pdb_output_path_

private

output_motifs_

bool IdentifyLigandMotifs::output_motifs_

private

output_motifs_as_pdb_

bool IdentifyLigandMotifs::output_motifs_as_pdb_

private

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

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