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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< IdentifyLigandMotifs > IdentifyLigandMotifsOP
 
typedef utility::pointer::shared_ptr< IdentifyLigandMotifs const > IdentifyLigandMotifsCOP
 
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< LigandDiscoverySearch > LigandDiscoverySearchOP
 
typedef utility::pointer::shared_ptr< LigandDiscoverySearch const > LigandDiscoverySearchCOP
 
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 basic::Tracer irt ("protocols.motifs.IRCollection", basic::t_info)
 
static basic::Tracer ms_tr ("protocols.motifs.LigandMotifSearch", basic::t_info)
 
static basic::Tracer mt ("protocols.motifs.Motif", basic::t_info)
 
std::ostream & operator<< (std::ostream &os, Motif const &motif)
 
static 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)
 
SingleMotifOP single_ligand_motif_from_stream (std::istream &motif_info, bool check_for_bad_motifs)
 
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 ()
 
MotifLibrary const get_LigandMotifLibrary_user (bool check_for_bad_motifs, utility::vector1< std::string > const &ligand_atom_names)
 
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 ligand_marker)
 
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)
 
std::istream & operator>> (std::istream &motif_info, SingleMotifOP &retval)
 
void write_motifs_to_disk (MotifLibrary ml, std::string filename)
 
void write_motifs_to_disk (MotifCOPs motifcops, std::string filename)
 
static basic::Tracer TR ("devel.motifs.MotifDnaPacker")
 
std::ostream & operator<< (std::ostream &os, MotifLibrary const &mlib)
 
static basic::Tracer ms_tr ("protocols.motifs.MotifSearch", basic::t_info)
 
static basic::Tracer mt ("protocols.motifs.Motif", basic::t_info)
 
std::ostream & operator<< (std::ostream &os, const SingleMotif &motif)
 

Variables

core::Size const NO_LIGAND = 0
 
core::Size const LIGAND = 1
 

Typedef Documentation

◆ BuildPositionCOP

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

◆ BuildPositionCOPs

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

◆ BuildPositionOP

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

◆ BuildPositionOPs

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

◆ IdentifyLigandMotifsCOP

typedef utility::pointer::shared_ptr< IdentifyLigandMotifs const > protocols::motifs::IdentifyLigandMotifsCOP

◆ IdentifyLigandMotifsOP

typedef utility::pointer::shared_ptr< IdentifyLigandMotifs > protocols::motifs::IdentifyLigandMotifsOP

◆ IRCollectionCOP

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

◆ IRCollectionOP

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

◆ IRCollectionOPs

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

◆ LigandDiscoverySearchCOP

typedef utility::pointer::shared_ptr< LigandDiscoverySearch const > protocols::motifs::LigandDiscoverySearchCOP

◆ LigandDiscoverySearchOP

typedef utility::pointer::shared_ptr< LigandDiscoverySearch > protocols::motifs::LigandDiscoverySearchOP

◆ LigandMotifSearchCOP

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

◆ LigandMotifSearchOP

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

◆ MotifCOP

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

◆ MotifCOPs

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

◆ MotifDnaPackerCOP

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

◆ MotifDnaPackerOP

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

◆ MotifHitCOP

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

◆ MotifHitCOPs

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

◆ MotifHitOP

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

◆ MotifHitOPs

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

◆ MotifLibraryCOP

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

◆ MotifLibraryOP

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

◆ MotifOP

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

◆ MotifOPs

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

◆ MotifSearchCOP

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

◆ MotifSearchOP

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

◆ SingleMotifCOP

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

◆ SingleMotifCOPs

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

◆ SingleMotifOP

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

◆ SingleMotifOPs

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

Function Documentation

◆ add_motif_bb_constraints()

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::ResidueTypeBase::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().

◆ add_motif_sc_constraints()

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::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

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

◆ atom_specific_rms() [1/2]

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

References core::conformation::Residue::xyz().

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

◆ atom_specific_rms() [2/2]

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

References core::conformation::Residue::xyz().

◆ backbone_stub_match()

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

References core::chemical::aa_gly, protocols::hybridization::r1, and protocols::hybridization::r2.

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

◆ bools_from_sizes()

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

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

◆ bpdefs2map()

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

References core::pose::PDBPoseMap::find(), mu_tr(), name3_from_oneletter(), and core::pose::Pose::pdb_info().

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

◆ build_rotamers_lite()

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 core::pack::rotamer_set::bump_check(), core::pack::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, core::scoring::fa_atr, core::scoring::fa_rep, and core::scoring::ScoreFunction::set_weight().

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

◆ defs2allowedtypes()

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

References core::pose::PDBPoseMap::find(), mu_tr(), and core::pose::Pose::pdb_info().

◆ defs2map()

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

References core::pose::PDBPoseMap::find(), 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().

◆ defs2vector()

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

References core::pose::PDBPoseMap::find(), and core::pose::Pose::pdb_info().

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

◆ get_filenames()

utility::vector1< utility::file::FileName > protocols::motifs::get_filenames ( utility::vector1< utility::file::FileName > const &  listnames)

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

◆ get_LigandMotifLibrary_user() [1/2]

MotifLibrary const protocols::motifs::get_LigandMotifLibrary_user ( )

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

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

◆ get_LigandMotifLibrary_user() [2/2]

MotifLibrary const protocols::motifs::get_LigandMotifLibrary_user ( bool  check_for_bad_motifs,
utility::vector1< std::string > const &  ligand_atom_names 
)

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

◆ get_motif_build_position_defs_user()

protocols::dna::DnaDesignDefOPs protocols::motifs::get_motif_build_position_defs_user ( )

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

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

◆ get_motif_build_positions_user()

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(), and mu_tr().

◆ get_MotifLibrary_user()

MotifLibrary const protocols::motifs::get_MotifLibrary_user ( )

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

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

◆ get_target_position_map_make_dna_mutations()

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(), and mu_tr().

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

◆ get_target_positions_make_dna_mutations()

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(), and mu_tr().

◆ get_targetconformers_user()

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

References protocols::abinitio::filename(), get_filenames(), core::import_pose::PDB_file, and core::import_pose::pose_from_file().

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

◆ irt()

static 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().

◆ load_build_position_data()

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

References protocols::abinitio::filename(), protocols::motifs::BuildPosition::keep_motif(), protocols::motifs::BuildPosition::keep_rotamer(), LIGAND, core::conformation::Residue::mainchain_torsions(), mu_tr(), core::pose::Pose::residue(), protocols::motifs::BuildPosition::seqpos(), core::conformation::set_chi_according_to_coordinates(), single_ligand_motif_from_stream(), single_motif_from_stream(), and single_residue_from_stream().

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

◆ make_base_pair_mutation()

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

References protocols::cluster::calibur::aa, core::conformation::Residue::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_base_partner(), core::conformation::Residue::is_DNA(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::scoring::dna::retrieve_base_partner_from_pose(), core::conformation::Residue::type(), and core::chemical::ResidueTypeBase::variant_types().

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

◆ make_dna_mutations() [1/2]

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(), and mu_tr().

Referenced by get_target_position_map_make_dna_mutations(), and get_target_positions_make_dna_mutations().

◆ make_dna_mutations() [2/2]

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(), core::pose::PDBPoseMap::find(), 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().

◆ ms_tr() [1/2]

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

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

◆ ms_tr() [2/2]

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

◆ mt() [1/2]

static 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::constel::SingResCnlCrea::strip_atoms(), protocols::backrub::BackrubMover::update_type(), protocols::backrub::BackrubSidechainMover::update_type(), and protocols::simple_moves::sidechain_moves::SidechainMover::update_type().

◆ mt() [2/2]

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

◆ mu_tr()

static 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(), make_dna_mutations(), operator>>(), and single_ligand_motif_from_stream().

◆ mutate_loops_for_search()

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::size().

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

◆ mutate_position_vector_for_search()

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::size().

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

◆ name3_from_oneletter()

std::string protocols::motifs::name3_from_oneletter ( std::string const &  oneletter)

Referenced by bpdefs2map().

◆ operator<<() [1/3]

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

◆ operator<<() [2/3]

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

◆ operator<<() [3/3]

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

◆ operator>>()

std::istream & protocols::motifs::operator>> ( std::istream &  motif_info,
SingleMotifOP &  retval 
)

References mu_tr().

◆ parallel_base_test()

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

References core::scoring::dna::get_y_axis(), core::scoring::dna::get_z_axis(), and core::chemical::rings::q.

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

◆ setup_conformer_map()

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().

◆ single_ligand_motif_from_stream() [1/2]

SingleMotifOP protocols::motifs::single_ligand_motif_from_stream ( std::istream &  motif_info)

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

◆ single_ligand_motif_from_stream() [2/2]

SingleMotifOP protocols::motifs::single_ligand_motif_from_stream ( std::istream &  motif_info,
bool  check_for_bad_motifs 
)

References mu_tr(), and single_ligand_motif_from_stream().

◆ single_motif_from_filename()

SingleMotifOP protocols::motifs::single_motif_from_filename ( utility::file::FileName const &  motif_filename)

References core::import_pose::PDB_file, and core::import_pose::pose_from_file().

◆ single_motif_from_stream() [1/2]

SingleMotifOP protocols::motifs::single_motif_from_stream ( std::istream &  motif_info)

◆ single_motif_from_stream() [2/2]

SingleMotifOP protocols::motifs::single_motif_from_stream ( utility::io::izstream &  motif_info)

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

◆ single_residue_from_stream()

core::conformation::ResidueOP protocols::motifs::single_residue_from_stream ( utility::io::izstream &  residue_info)

References core::conformation::ResidueFactory::create_residue(), and core::chemical::FA_STANDARD.

Referenced by load_build_position_data().

◆ TR()

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

◆ write_motifs_to_disk() [1/2]

void protocols::motifs::write_motifs_to_disk ( MotifCOPs  motifcops,
std::string  filename 
)

References protocols::abinitio::filename().

◆ write_motifs_to_disk() [2/2]

void protocols::motifs::write_motifs_to_disk ( MotifLibrary  ml,
std::string  filename 
)

References protocols::abinitio::filename(), and protocols::motifs::MotifLibrary::library().

Referenced by IdentifyLigandMotifs::write_motifs_to_disk().

Variable Documentation

◆ LIGAND

core::Size const protocols::motifs::LIGAND = 1

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

◆ NO_LIGAND

core::Size const protocols::motifs::NO_LIGAND = 0
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