protocols::motifs Namespace Reference

Classes
class	BuildPosition
class	IRCollection
class	LigandMotifSearch
class	Motif
class	MotifDnaPacker
class	MotifDnaPackerCreator
class	MotifHit
class	MotifLibrary
class	MotifSearch
class	SingleMotif

Typedefs
typedef utility::pointer::shared_ptr < BuildPosition >	BuildPositionOP
typedef utility::pointer::shared_ptr < BuildPosition const >	BuildPositionCOP
typedef utility::vector1 < BuildPositionOP >	BuildPositionOPs
typedef utility::vector1 < BuildPositionCOP >	BuildPositionCOPs
typedef utility::pointer::shared_ptr < IRCollection >	IRCollectionOP
typedef utility::pointer::shared_ptr < IRCollection const >	IRCollectionCOP
typedef utility::vector1 < IRCollectionOP >	IRCollectionOPs
typedef utility::pointer::shared_ptr < LigandMotifSearch >	LigandMotifSearchOP
typedef utility::pointer::shared_ptr < LigandMotifSearch const >	LigandMotifSearchCOP
typedef utility::pointer::shared_ptr < Motif >	MotifOP
typedef utility::pointer::shared_ptr < Motif const >	MotifCOP
typedef utility::vector1< MotifOP >	MotifOPs
typedef utility::vector1 < MotifCOP >	MotifCOPs
typedef utility::pointer::shared_ptr < MotifDnaPacker >	MotifDnaPackerOP
typedef utility::pointer::shared_ptr < MotifDnaPacker const >	MotifDnaPackerCOP
typedef utility::pointer::shared_ptr < MotifHit >	MotifHitOP
typedef utility::pointer::shared_ptr < MotifHit const >	MotifHitCOP
typedef utility::vector1 < MotifHitOP >	MotifHitOPs
typedef utility::vector1 < MotifHitCOP >	MotifHitCOPs
typedef utility::pointer::shared_ptr < MotifLibrary >	MotifLibraryOP
typedef utility::pointer::shared_ptr < MotifLibrary const >	MotifLibraryCOP
typedef utility::pointer::shared_ptr < MotifSearch >	MotifSearchOP
typedef utility::pointer::shared_ptr < MotifSearch const >	MotifSearchCOP
typedef utility::pointer::shared_ptr < SingleMotif >	SingleMotifOP
typedef utility::pointer::shared_ptr < SingleMotif const >	SingleMotifCOP
typedef utility::vector1 < SingleMotifOP >	SingleMotifOPs
typedef utility::vector1 < SingleMotifCOP >	SingleMotifCOPs

Functions
static thread_local basic::Tracer	irt ("protocols.motifs.IRCollection", basic::t_info)
static thread_local basic::Tracer	ms_tr ("protocols.motifs.LigandMotifSearch", basic::t_info)
static thread_local basic::Tracer	mt ("protocols.motifs.Motif", basic::t_info)
std::ostream &	operator<< (std::ostream &os, Motif const &motif)
static thread_local basic::Tracer	mu_tr ("protocols.motifs.motif_utils", basic::t_info)
SingleMotifOP	single_motif_from_filename (utility::file::FileName const &motif_filename)
SingleMotifOP	single_motif_from_stream (utility::io::izstream &motif_info)
SingleMotifOP	single_motif_from_stream (std::istream &motif_info)
SingleMotifOP	single_ligand_motif_from_stream (std::istream &motif_info)
core::Real	parallel_base_test (core::conformation::Residue const &pose_dna, core::conformation::Residue const &motif_dna)
core::Real	backbone_stub_match (core::conformation::Residue const &r1, core::conformation::Residue const &r2)
void	add_motif_bb_constraints (core::scoring::constraints::ConstraintSetOP cst_set, core::pose::Pose &pose, core::Size this_pos, core::conformation::Residue const &inv_rotamer)
void	add_motif_sc_constraints (core::scoring::constraints::ConstraintSetOP cst_set, core::pose::Pose &pose, core::Size this_pos, core::conformation::Residue const &inv_rotamer, MotifCOP this_motif, bool const is_it_forward)
void	mutate_position_vector_for_search (core::pose::Pose &pose, utility::vector1< core::Size > &trim_positions)
void	mutate_loops_for_search (core::pose::Pose &pose, protocols::loops::Loops &flex_regions)
MotifLibrary const	get_MotifLibrary_user ()
MotifLibrary const	get_LigandMotifLibrary_user ()
utility::vector1 < core::conformation::ResidueOP > const	get_targetconformers_user ()
std::map< std::string, utility::vector1 < core::conformation::ResidueOP > > const	setup_conformer_map (utility::vector1< core::conformation::ResidueOP > const &conformerOPs)
utility::vector1< core::Size >	get_target_positions_make_dna_mutations (core::pose::Pose &pose)
std::map< core::Size, std::set < std::string > >	get_target_position_map_make_dna_mutations (core::pose::Pose &pose)
void	make_dna_mutations (core::pose::Pose &pose)
void	make_dna_mutations (core::pose::Pose &pose, protocols::dna::DnaDesignDefOPs const &target)
utility::vector1< core::Size >	defs2vector (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
utility::vector1< std::pair < core::Size, utility::vector1 < std::string > > >	defs2allowedtypes (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::map< core::Size, std::set < std::string > >	defs2map (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::map< core::Size, std::set < std::string > >	bpdefs2map (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::string	name3_from_oneletter (std::string const &oneletter)
utility::vector1< core::Size >	get_motif_build_positions_user (core::pose::Pose const &pose)
utility::vector1 < protocols::dna::DnaDesignDefOP >	get_motif_build_position_defs_user ()
void	load_build_position_data (BuildPosition &bp, std::string const &filename, core::pose::Pose &pose, core::Size const )
void	load_build_position_data (BuildPosition &bp, std::string const &filename, core::pose::Pose &pose)
utility::vector1 < utility::file::FileName >	get_filenames (utility::vector1< utility::file::FileName > const &listnames)
core::conformation::ResidueOP	single_residue_from_stream (utility::io::izstream &residue_info)
utility::vector1< bool >	bools_from_sizes (core::Size const nres, utility::vector1< core::Size > const &v)
void	make_base_pair_mutation (core::pose::Pose &pose, core::Size const seqpos, core::chemical::AA const &na)
core::Real	atom_specific_rms (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atoms)
core::Real	atom_specific_rms (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< std::string > const &atoms)
core::pack::rotamer_set::RotamerSetOP	build_rotamers_lite (core::pose::Pose &pose, core::Size const rotamer_build_position, utility::vector1< bool > aa_info, core::Size const ex_, bool bump_check)
static thread_local basic::Tracer	TR ("devel.motifs.MotifDnaPacker")
std::ostream &	operator<< (std::ostream &os, MotifLibrary const &mlib)
static thread_local basic::Tracer	ms_tr ("protocols.motifs.MotifSearch", basic::t_info)
static thread_local basic::Tracer	mt ("protocols.motifs.Motif", basic::t_info)
std::ostream &	operator<< (std::ostream &os, const SingleMotif &motif)

Typedef Documentation

typedef utility::pointer::shared_ptr< BuildPosition const > protocols::motifs::BuildPositionCOP

typedef utility::vector1< BuildPositionCOP > protocols::motifs::BuildPositionCOPs

typedef utility::pointer::shared_ptr< BuildPosition > protocols::motifs::BuildPositionOP

typedef utility::vector1< BuildPositionOP > protocols::motifs::BuildPositionOPs

typedef utility::pointer::shared_ptr< IRCollection const > protocols::motifs::IRCollectionCOP

typedef utility::pointer::shared_ptr< IRCollection > protocols::motifs::IRCollectionOP

typedef utility::vector1< IRCollectionOP > protocols::motifs::IRCollectionOPs

typedef utility::pointer::shared_ptr< LigandMotifSearch const > protocols::motifs::LigandMotifSearchCOP

typedef utility::pointer::shared_ptr< LigandMotifSearch > protocols::motifs::LigandMotifSearchOP

typedef utility::pointer::shared_ptr< Motif const > protocols::motifs::MotifCOP

typedef utility::vector1< MotifCOP > protocols::motifs::MotifCOPs

typedef utility::pointer::shared_ptr< MotifDnaPacker const > protocols::motifs::MotifDnaPackerCOP

typedef utility::pointer::shared_ptr< MotifDnaPacker > protocols::motifs::MotifDnaPackerOP

typedef utility::pointer::shared_ptr< MotifHit const > protocols::motifs::MotifHitCOP

typedef utility::vector1< MotifHitCOP > protocols::motifs::MotifHitCOPs

typedef utility::pointer::shared_ptr< MotifHit > protocols::motifs::MotifHitOP

typedef utility::vector1< MotifHitOP > protocols::motifs::MotifHitOPs

typedef utility::pointer::shared_ptr< MotifLibrary const > protocols::motifs::MotifLibraryCOP

typedef utility::pointer::shared_ptr< MotifLibrary > protocols::motifs::MotifLibraryOP

typedef utility::pointer::shared_ptr< Motif > protocols::motifs::MotifOP

typedef utility::vector1< MotifOP > protocols::motifs::MotifOPs

typedef utility::pointer::shared_ptr< MotifSearch const > protocols::motifs::MotifSearchCOP

typedef utility::pointer::shared_ptr< MotifSearch > protocols::motifs::MotifSearchOP

typedef utility::pointer::shared_ptr< SingleMotif const > protocols::motifs::SingleMotifCOP

typedef utility::vector1< SingleMotifCOP > protocols::motifs::SingleMotifCOPs

typedef utility::pointer::shared_ptr< SingleMotif > protocols::motifs::SingleMotifOP

typedef utility::vector1< SingleMotifOP > protocols::motifs::SingleMotifOPs

Function Documentation

void protocols::motifs::add_motif_bb_constraints	(	core::scoring::constraints::ConstraintSetOP	cst_set,
		core::pose::Pose &	pose,
		core::Size	this_pos,
		core::conformation::Residue const &	inv_rotamer
	)

References core::chemical::ResidueType::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_index(), core::pose::Pose::residue(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::motifs::IRCollection::successful_loop_closure().

void protocols::motifs::add_motif_sc_constraints	(	core::scoring::constraints::ConstraintSetOP	cst_set,
		core::pose::Pose &	pose,
		core::Size	this_pos,
		core::conformation::Residue const &	inv_rotamer,
		MotifCOP	this_motif,
		bool const	is_it_forward
	)

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), and protocols::motifs::IRCollection::successful_loop_closure().

core::Real protocols::motifs::atom_specific_rms	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		utility::vector1< core::Size > const &	atoms
	)

References numeric::xyzVector< class >::length_squared(), and core::conformation::Residue::xyz().

Referenced by protocols::motifs::MotifSearch::incorporate_motifs(), and protocols::motifs::LigandMotifSearch::incorporate_motifs().

core::Real protocols::motifs::atom_specific_rms	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		utility::vector1< std::string > const &	atoms
	)

References numeric::xyzVector< class >::length_squared(), and core::conformation::Residue::xyz().

core::Real protocols::motifs::backbone_stub_match	(	core::conformation::Residue const &	r1,
		core::conformation::Residue const &	r2
	)

References core::chemical::ResidueType::aa(), core::chemical::aa_gly, core::conformation::Residue::atom_index(), numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by protocols::motifs::IRCollection::find_closest_backbone().

utility::vector1< bool > protocols::motifs::bools_from_sizes	(	core::Size const	nres,
		utility::vector1< core::Size > const &	v
	)

References protocols::match::upstream::b.

std::map< core::Size, std::set< std::string > > protocols::motifs::bpdefs2map	(	core::pose::Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	targets
	)

References c, utility::tools::make_vector1(), mu_tr(), name3_from_oneletter(), core::pose::Pose::pdb_info(), and x().

Referenced by protocols::motifs::MotifSearch::defs2BuildPositions(), and protocols::motifs::MotifSearch::defs2BuildPositions_findts().

core::pack::rotamer_set::RotamerSetOP protocols::motifs::build_rotamers_lite	(	core::pose::Pose &	pose,
		core::Size const	rotamer_build_position,
		utility::vector1< bool >	aa_info,
		core::Size const	ex_,
		bool	bump_check
	)

References create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, fa_atr, fa_rep, and core::pose::Pose::residue().

Referenced by protocols::motifs::MotifSearch::incorporate_motifs(), and protocols::motifs::LigandMotifSearch::incorporate_motifs().

utility::vector1< std::pair< core::Size, utility::vector1< std::string > > > protocols::motifs::defs2allowedtypes	(	core::pose::Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	targets
	)

References utility::tools::make_map(), utility::tools::make_vector1(), mu_tr(), and core::pose::Pose::pdb_info().

std::map< core::Size, std::set< std::string > > protocols::motifs::defs2map	(	core::pose::Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	targets
	)

References utility::tools::make_map(), utility::tools::make_vector1(), mu_tr(), and core::pose::Pose::pdb_info().

Referenced by protocols::motifs::LigandMotifSearch::defs2BuildPositions(), protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts(), and get_target_position_map_make_dna_mutations().

utility::vector1< core::Size > protocols::motifs::defs2vector	(	core::pose::Pose const &	pose,
		protocols::dna::DnaDesignDefOPs const &	targets
	)

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

Referenced by protocols::motifs::MotifDnaPacker::apply(), get_motif_build_positions_user(), and get_target_positions_make_dna_mutations().

utility::vector1< utility::file::FileName > protocols::motifs::get_filenames

(

utility::vector1< utility::file::FileName > const &

listnames

)

References filename().

Referenced by get_LigandMotifLibrary_user(), get_MotifLibrary_user(), and get_targetconformers_user().

MotifLibrary const protocols::motifs::get_LigandMotifLibrary_user

(

)

References protocols::motifs::MotifLibrary::add_ligand_from_file(), get_filenames(), mu_tr(), option, and user.

Referenced by protocols::motifs::LigandMotifSearch::initialize().

protocols::dna::DnaDesignDefOPs protocols::motifs::get_motif_build_position_defs_user

(

)

References protocols::dna::load_dna_design_defs_from_strings(), mu_tr(), option, and user.

Referenced by protocols::motifs::MotifSearch::initialize().

utility::vector1< core::Size > protocols::motifs::get_motif_build_positions_user

(

core::pose::Pose const &

pose

)

References defs2vector(), protocols::dna::load_dna_design_defs_from_strings(), mu_tr(), option, and user.

MotifLibrary const protocols::motifs::get_MotifLibrary_user

(

)

References protocols::motifs::MotifLibrary::add_from_file(), get_filenames(), mu_tr(), option, and user.

Referenced by protocols::motifs::MotifSearch::initialize().

std::map< core::Size, std::set< std::string > > protocols::motifs::get_target_position_map_make_dna_mutations

(

core::pose::Pose &

pose

)

References defs2map(), protocols::dna::load_dna_design_defs_from_options(), protocols::dna::load_dna_design_defs_from_strings(), make_dna_mutations(), mu_tr(), option, and user.

Referenced by protocols::motifs::MotifSearch::initialize().

utility::vector1< core::Size > protocols::motifs::get_target_positions_make_dna_mutations

(

core::pose::Pose &

pose

)

References defs2vector(), protocols::dna::load_dna_design_defs_from_options(), protocols::dna::load_dna_design_defs_from_strings(), make_dna_mutations(), mu_tr(), option, and user.

utility::vector1< core::conformation::ResidueOP > const protocols::motifs::get_targetconformers_user

(

)

References utility::file::file_exists(), filename(), get_filenames(), option, core::import_pose::pose_from_pdb(), and user.

Referenced by protocols::motifs::MotifSearch::initialize(), and protocols::motifs::LigandMotifSearch::initialize().

static thread_local basic::Tracer protocols::motifs::irt ( "protocols.motifs.IRCollection"  , basic::t_info    )

static

Referenced by protocols::motifs::IRCollection::successful_loop_closure(), and protocols::motifs::IRCollection::try_for_more().

void protocols::motifs::load_build_position_data	(	BuildPosition &	bp,
		std::string const &	filename,
		core::pose::Pose &	pose,
		core::Size	const
	)

References end, protocols::motifs::BuildPosition::keep_motif(), protocols::motifs::BuildPosition::keep_rotamer(), mu_tr(), core::pose::Pose::residue(), protocols::motifs::BuildPosition::seqpos(), set_chi_according_to_coordinates(), single_ligand_motif_from_stream(), and single_residue_from_stream().

Referenced by protocols::motifs::MotifSearch::initialize(), and protocols::motifs::LigandMotifSearch::run().

void protocols::motifs::load_build_position_data	(	BuildPosition &	bp,
		std::string const &	filename,
		core::pose::Pose &	pose
	)

References end, protocols::motifs::BuildPosition::keep_motif(), protocols::motifs::BuildPosition::keep_rotamer(), mu_tr(), core::pose::Pose::residue(), protocols::motifs::BuildPosition::seqpos(), set_chi_according_to_coordinates(), single_motif_from_stream(), and single_residue_from_stream().

void protocols::motifs::make_base_pair_mutation	(	core::pose::Pose &	pose,
		core::Size const	seqpos,
		core::chemical::AA const &	na
	)

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_base_partner(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), retrieve_base_partner_from_pose(), and utility_exit_with_message.

Referenced by protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), and make_dna_mutations().

void protocols::motifs::make_dna_mutations

(

core::pose::Pose &

pose

)

References protocols::dna::load_dna_design_defs_from_options(), protocols::dna::load_dna_design_defs_from_strings(), mu_tr(), option, and user.

Referenced by get_target_position_map_make_dna_mutations(), and get_target_positions_make_dna_mutations().

void protocols::motifs::make_dna_mutations	(	core::pose::Pose &	pose,
		protocols::dna::DnaDesignDefOPs const &	target
	)

References core::chemical::aa_from_name(), protocols::dna::dna_full_name3(), make_base_pair_mutation(), mu_tr(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::scoring::dna::set_base_partner().

static thread_local basic::Tracer protocols::motifs::ms_tr ( "protocols.motifs.MotifSearch"  , basic::t_info    )

static

static thread_local basic::Tracer protocols::motifs::ms_tr ( "protocols.motifs.LigandMotifSearch"  , basic::t_info    )

static

Referenced by protocols::motifs::MotifSearch::bp_motifhits(), protocols::motifs::MotifSearch::bp_rotamers(), protocols::motifs::LigandMotifSearch::bp_rotamers(), protocols::motifs::MotifSearch::defs2BuildPositions(), protocols::motifs::LigandMotifSearch::defs2BuildPositions(), protocols::motifs::MotifSearch::defs2BuildPositions_findts(), protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts(), protocols::motifs::LigandMotifSearch::get_sphere_aa(), protocols::motifs::MotifSearch::identify_motif_build_positions(), protocols::motifs::LigandMotifSearch::identify_motif_build_positions(), protocols::motifs::MotifSearch::identify_motif_BuildPositions(), protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::initialize(), protocols::motifs::LigandMotifSearch::initialize(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::motifs::MotifSearch::protein_DNA_motif_build_positions_JA(), protocols::motifs::LigandMotifSearch::protein_DNA_motif_build_positions_JA(), protocols::motifs::MotifSearch::protein_DNA_motif_target_positions_JA(), protocols::motifs::LigandMotifSearch::protein_DNA_motif_target_positions_JA(), and protocols::motifs::LigandMotifSearch::run().

static thread_local basic::Tracer protocols::motifs::mt ( "protocols.motifs.Motif"  , basic::t_info    )

static

static thread_local basic::Tracer protocols::motifs::mt ( "protocols.motifs.Motif"  , basic::t_info    )

static

Referenced by protocols::motifs::Motif::build_inverted_rotamers(), protocols::moves::FilterMover::max_tries(), protocols::motifs::Motif::Motif(), protocols::motifs::Motif::place_atoms(), protocols::motifs::Motif::place_residue(), protocols::backrub::BackrubSidechainMover::update_type(), protocols::simple_moves::sidechain_moves::SidechainMover::update_type(), and protocols::backrub::BackrubMover::update_type().

static thread_local basic::Tracer protocols::motifs::mu_tr ( "protocols.motifs.motif_utils"  , basic::t_info    )

static

Referenced by bpdefs2map(), defs2allowedtypes(), defs2map(), get_LigandMotifLibrary_user(), get_motif_build_position_defs_user(), get_motif_build_positions_user(), get_MotifLibrary_user(), get_target_position_map_make_dna_mutations(), get_target_positions_make_dna_mutations(), load_build_position_data(), and make_dna_mutations().

void protocols::motifs::mutate_loops_for_search	(	core::pose::Pose &	pose,
		protocols::loops::Loops &	flex_regions
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::pack::task::TaskFactory::create_packer_task(), core::scoring::get_score_function_legacy(), protocols::loops::Loops::is_loop_residue(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::motifs::IRCollection::incorporate_motifs().

void protocols::motifs::mutate_position_vector_for_search	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > &	trim_positions
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::pack::task::TaskFactory::create_packer_task(), core::scoring::get_score_function_legacy(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::motifs::IRCollection::incorporate_motifs().

std::string protocols::motifs::name3_from_oneletter

(

std::string const &

oneletter

)

References utility::tools::make_map().

Referenced by bpdefs2map().

std::ostream& protocols::motifs::operator<<	(	std::ostream &	os,
		MotifLibrary const &	mlib
	)

References protocols::motifs::MotifLibrary::begin(), and protocols::motifs::MotifLibrary::end().

std::ostream& protocols::motifs::operator<<	(	std::ostream &	os,
		const SingleMotif &	motif
	)

References protocols::motifs::Motif::print().

std::ostream& protocols::motifs::operator<<	(	std::ostream &	os,
		Motif const &	motif
	)

References protocols::motifs::Motif::print().

core::Real protocols::motifs::parallel_base_test	(	core::conformation::Residue const &	pose_dna,
		core::conformation::Residue const &	motif_dna
	)

References numeric::xyzVector< class >::dot(), core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), and q.

Referenced by protocols::motifs::MotifSearch::incorporate_motifs().

std::map< std::string, utility::vector1< core::conformation::ResidueOP > > const protocols::motifs::setup_conformer_map

(

utility::vector1< core::conformation::ResidueOP > const &

conformerOPs

)

Referenced by protocols::motifs::MotifSearch::initialize(), and protocols::motifs::LigandMotifSearch::initialize().

SingleMotifOP protocols::motifs::single_ligand_motif_from_stream

(

std::istream &

motif_info

)

Referenced by load_build_position_data(), and protocols::motifs::MotifLibrary::MotifLibrary().

SingleMotifOP protocols::motifs::single_motif_from_filename

(

utility::file::FileName const &

motif_filename

)

References utility::file::FileName::base(), utility::file::FileName::path(), and core::import_pose::pose_from_pdb().

Referenced by protocols::motifs::MotifLibrary::MotifLibrary().

SingleMotifOP protocols::motifs::single_motif_from_stream

(

utility::io::izstream &

motif_info

)

References utility::io::izstream::getline().

Referenced by load_build_position_data(), and protocols::motifs::MotifLibrary::MotifLibrary().

SingleMotifOP protocols::motifs::single_motif_from_stream

(

std::istream &

motif_info

)

core::conformation::ResidueOP protocols::motifs::single_residue_from_stream

(

utility::io::izstream &

residue_info

)

References core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, getline(), skip(), utility::string2float(), utility::string_split(), x(), y(), and z().

Referenced by load_build_position_data().

static thread_local basic::Tracer protocols::motifs::TR ( "devel.motifs.MotifDnaPacker"  )

static