#include <LigandMotifSearch.hh>

Inheritance diagram for protocols::motifs::LigandMotifSearch:

Collaboration diagram for protocols::motifs::LigandMotifSearch:

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef utility::vector1< Size >	Sizes

typedef core::pose::Pose	Pose

typedef protocols::dna::DnaDesignDefOP	DnaDesignDefOP

typedef protocols::dna::DnaDesignDefOPs	DnaDesignDefOPs

typedef core::pack::task::PackerTask	PackerTask

Public Member Functions
	LigandMotifSearch ()

virtual	~LigandMotifSearch ()

	LigandMotifSearch (LigandMotifSearch const &src)

LigandMotifSearch const &	operator= (LigandMotifSearch const &src)

void	run (Pose const &pose, utility::vector1< Size > &input_BPs)

void	run (Pose const &pose, PackerTask &task)

void	run (Pose const &pose, core::Real &ligand_motif_sphere)

void	initialize (Pose const &pose)

void	initialize (Pose const &pose, utility::vector1< Size > &input_BPs)

void	incorporate_motifs (Pose const &pose)

core::pack::rotamer_set::Rotamers	bp_rotamers (Size const seqpos)

core::pack::rotamer_set::Rotamers	get_rotamers ()

bool	protein_dna_motif ()

void	position_vector_setup (Pose const &pose)

void	identify_motif_build_positions (Pose const &pose, Sizes &build_positions)

utility::vector1< Size >	get_sphere_aa (Pose const &pose, core::Real cut1)

void	identify_motif_BuildPositions (Pose const &pose)

void	BuildPosition_from_Size (Pose const &pose, Size const input_BP)

void	defs2BuildPositions (Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs)

void	defs2BuildPositions_findts (Pose const &pose, protocols::dna::DnaDesignDefOPs const &defs)

utility::vector1< Size >	map2keyvector (std::map< Size, std::set< std::string > > mappositions)

utility::vector1< Size >	shorten_target_list (Pose const &pose, Size const bp, Sizes &full_tl)

void	protein_DNA_motif_build_positions_JA (Pose const &pose, Sizes &build_positions, Sizes &target_positions)

void	protein_DNA_motif_target_positions_JA (Pose const &pose, Sizes &build_positions, Sizes &target_positions, Sizes &short_tl)

void	override_option_input (Real const &r1, Real const &z1, Real const &r2, Real const &z2, Real const &d1, Size const &rlevel)

void	reset_option_input ()

void	set_motif_library (MotifLibrary &motiflibrary)

MotifCOPs const &	motif_library () const

Sizes const &	dna_positions () const

Sizes const &	protein_positions () const

std::map< Size, std::set < std::string > > const &	target_positions () const

BuildPositionOPs const &	build_positionOPs () const

std::map< std::string, core::conformation::ResidueOPs > const &	target_conformers_map () const

Real const &	ztest_cutoff_1 () const

Real const &	ztest_cutoff_2 () const

Real const &	rmsd_cutoff_1 () const

Real const &	rmsd_cutoff_2 () const

Real const &	dtest_cutoff () const

Size const &	rot_level () const

bool const &	minimize () const

Private Member Functions
void	init_options ()

Private Attributes
MotifCOPs	motif_library_

Sizes	dna_positions_

Sizes	protein_positions_

std::map< Size, std::set < std::string > >	target_positions_

BuildPositionOPs	build_positionOPs_

std::map< std::string, core::conformation::ResidueOPs >	target_conformers_map_

Real	ztest_cutoff_1_

Real	ztest_cutoff_2_

Real	rmsd_cutoff_1_

Real	rmsd_cutoff_2_

Real	dtest_cutoff_

Size	rot_level_

bool	minimize_

bool	bpdata_

std::string	bpdata_filename_

bool	output_

std::string	output_filename_

bool	data_

std::string	data_filename_

bool	quick_and_dirty_

bool	dump_motifs_

bool	clear_bprots_

Size	rots2add_

Detailed Description

Definition at line 50 of file LigandMotifSearch.hh.

Member Typedef Documentation

typedef protocols::dna::DnaDesignDefOP protocols::motifs::LigandMotifSearch::DnaDesignDefOP

Definition at line 59 of file LigandMotifSearch.hh.

typedef protocols::dna::DnaDesignDefOPs protocols::motifs::LigandMotifSearch::DnaDesignDefOPs

Definition at line 60 of file LigandMotifSearch.hh.

typedef core::pack::task::PackerTask protocols::motifs::LigandMotifSearch::PackerTask

Definition at line 61 of file LigandMotifSearch.hh.

typedef core::pose::Pose protocols::motifs::LigandMotifSearch::Pose

Definition at line 58 of file LigandMotifSearch.hh.

typedef core::Real protocols::motifs::LigandMotifSearch::Real

Definition at line 55 of file LigandMotifSearch.hh.

typedef core::Size protocols::motifs::LigandMotifSearch::Size

Definition at line 56 of file LigandMotifSearch.hh.

typedef utility::vector1< Size > protocols::motifs::LigandMotifSearch::Sizes

Definition at line 57 of file LigandMotifSearch.hh.

Constructor & Destructor Documentation

protocols::motifs::LigandMotifSearch::LigandMotifSearch ( )

Definition at line 92 of file LigandMotifSearch.cc.

References init_options().

protocols::motifs::LigandMotifSearch::~LigandMotifSearch ( )

virtual

Definition at line 89 of file LigandMotifSearch.cc.

protocols::motifs::LigandMotifSearch::LigandMotifSearch ( LigandMotifSearch const & src)

Definition at line 109 of file LigandMotifSearch.cc.

Member Function Documentation

core::pack::rotamer_set::Rotamers protocols::motifs::LigandMotifSearch::bp_rotamers ( Size const seqpos)

Definition at line 1122 of file LigandMotifSearch.cc.

References build_positionOPs_, and protocols::motifs::ms_tr().

Referenced by run().

BuildPositionOPs const& protocols::motifs::LigandMotifSearch::build_positionOPs ( ) const

inline

Definition at line 216 of file LigandMotifSearch.hh.

References build_positionOPs_.

void protocols::motifs::LigandMotifSearch::BuildPosition_from_Size	(	Pose const &	pose,
		Size const	input_BP
	)

Definition at line 1336 of file LigandMotifSearch.cc.

References build_positionOPs_, map2keyvector(), shorten_target_list(), target_positions(), and target_positions_.

Referenced by initialize().

void protocols::motifs::LigandMotifSearch::defs2BuildPositions	(	Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	defs
	)

Definition at line 1351 of file LigandMotifSearch.cc.

References build_positionOPs_, protocols::motifs::defs2map(), core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), and target_positions_.

void protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts	(	Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	defs
	)

Definition at line 1370 of file LigandMotifSearch.cc.

References build_positionOPs_, protocols::motifs::defs2map(), core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), shorten_target_list(), and target_positions_.

Sizes const& protocols::motifs::LigandMotifSearch::dna_positions ( ) const

inline

Definition at line 213 of file LigandMotifSearch.hh.

References dna_positions_.

Real const& protocols::motifs::LigandMotifSearch::dtest_cutoff ( ) const

inline

Definition at line 222 of file LigandMotifSearch.hh.

References dtest_cutoff_.

Referenced by incorporate_motifs().

core::pack::rotamer_set::Rotamers protocols::motifs::LigandMotifSearch::get_rotamers ( )

Definition at line 1110 of file LigandMotifSearch.cc.

References build_positionOPs_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::get_sphere_aa	(	Pose const &	pose,
		core::Real	cut1
	)

Definition at line 1194 of file LigandMotifSearch.cc.

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), protocols::motifs::ms_tr(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by run().

void protocols::motifs::LigandMotifSearch::identify_motif_build_positions	(	Pose const &	pose,
		Sizes &	build_positions
	)

Definition at line 1180 of file LigandMotifSearch.cc.

References dna_positions_, protocols::motifs::ms_tr(), protein_dna_motif(), and protein_DNA_motif_build_positions_JA().

void protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions ( Pose const & pose)

Definition at line 1313 of file LigandMotifSearch.cc.

References build_positionOPs_, core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), protein_DNA_motif_build_positions_JA(), shorten_target_list(), target_positions(), and target_positions_.

void protocols::motifs::LigandMotifSearch::incorporate_motifs ( Pose const & pose)

Definition at line 352 of file LigandMotifSearch.cc.

References core::chemical::aa_from_name(), protocols::motifs::add_motif_sc_constraints(), core::pose::Pose::append_residue_by_jump(), protocols::motifs::atom_specific_rms(), core::chemical::ChemicalManager::atom_type_set(), build_positionOPs_, protocols::motifs::build_rotamers_lite(), core::io::serialization::clone(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::scoring::ScoreFunctionFactory::create_score_function(), data_, data_filename_, protocols::dna::dna_full_name3(), dtest_cutoff(), dtest_cutoff_, dump_motifs_, core::io::pdb::dump_pdb(), core::sequence::end, core::pose::Pose::energies(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), protocols::motifs::make_base_pair_mutation(), minimize_, motif_library(), motif_library_, protocols::motifs::ms_tr(), core::conformation::Residue::name3(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, output_, output_filename_, core::pose::Pose::pdb_info(), quick_and_dirty_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rmsd_cutoff_1(), rmsd_cutoff_1_, rmsd_cutoff_2(), rmsd_cutoff_2_, rot_level_, rots2add_, target_conformers_map_, target_positions(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by run().

void protocols::motifs::LigandMotifSearch::init_options ( )

private

Definition at line 1506 of file LigandMotifSearch.cc.

References bpdata_, bpdata_filename_, clear_bprots_, data_, data_filename_, dump_motifs_, output_, output_filename_, quick_and_dirty_, and rots2add_.

Referenced by LigandMotifSearch().

void protocols::motifs::LigandMotifSearch::initialize ( Pose const & pose)

Definition at line 302 of file LigandMotifSearch.cc.

References protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

Referenced by run().

void protocols::motifs::LigandMotifSearch::initialize	(	Pose const &	pose,
		utility::vector1< Size > &	input_BPs
	)

Definition at line 320 of file LigandMotifSearch.cc.

References BuildPosition_from_Size(), protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, protocols::motifs::ms_tr(), position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::map2keyvector ( std::map< Size, std::set< std::string > > mappositions)

Definition at line 1391 of file LigandMotifSearch.cc.

References core::sequence::end.

Referenced by BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), and identify_motif_BuildPositions().

bool const& protocols::motifs::LigandMotifSearch::minimize ( ) const

inline

Definition at line 224 of file LigandMotifSearch.hh.

References minimize_.

MotifCOPs const& protocols::motifs::LigandMotifSearch::motif_library ( ) const

inline

Definition at line 212 of file LigandMotifSearch.hh.

References motif_library_.

Referenced by incorporate_motifs().

LigandMotifSearch const & protocols::motifs::LigandMotifSearch::operator= ( LigandMotifSearch const & src)

Definition at line 116 of file LigandMotifSearch.cc.

References bpdata_, bpdata_filename_, build_positionOPs_, clear_bprots_, data_, data_filename_, dtest_cutoff_, dump_motifs_, minimize_, motif_library_, output_, output_filename_, quick_and_dirty_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, rots2add_, target_conformers_map_, target_positions_, ztest_cutoff_1_, and ztest_cutoff_2_.

void protocols::motifs::LigandMotifSearch::override_option_input	(	Real const &	r1,
		Real const &	z1,
		Real const &	r2,
		Real const &	z2,
		Real const &	d1,
		Size const &	rlevel
	)

Definition at line 1464 of file LigandMotifSearch.cc.

References dtest_cutoff_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

void protocols::motifs::LigandMotifSearch::position_vector_setup ( Pose const & pose)

Definition at line 1165 of file LigandMotifSearch.cc.

References dna_positions_, core::sequence::end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), protein_positions_, core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by initialize().

bool protocols::motifs::LigandMotifSearch::protein_dna_motif ( )

Definition at line 1141 of file LigandMotifSearch.cc.

References core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_full_name3(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), motif_library_, and protocols::motifs::ms_tr().

Referenced by defs2BuildPositions(), defs2BuildPositions_findts(), identify_motif_build_positions(), and identify_motif_BuildPositions().

void protocols::motifs::LigandMotifSearch::protein_DNA_motif_build_positions_JA	(	Pose const &	pose,
		Sizes &	build_positions,
		Sizes &	target_positions
	)

Definition at line 1418 of file LigandMotifSearch.cc.

References protocols::dna::DnaInterfaceFinder::determine_protein_interface(), core::sequence::end, protocols::motifs::ms_tr(), and protein_positions_.

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

void protocols::motifs::LigandMotifSearch::protein_DNA_motif_target_positions_JA	(	Pose const &	pose,
		Sizes &	build_positions,
		Sizes &	target_positions,
		Sizes &	short_tl
	)