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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
< 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< MotifOPMotifOPs
 
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)
 
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::Sizeget_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::Sizedefs2vector (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::Sizeget_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< boolbools_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 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

typedef utility::pointer::shared_ptr< BuildPosition const > protocols::motifs::BuildPositionCOP
typedef utility::pointer::shared_ptr< BuildPosition > protocols::motifs::BuildPositionOP
typedef utility::pointer::shared_ptr< IRCollection const > protocols::motifs::IRCollectionCOP
typedef utility::pointer::shared_ptr< IRCollection > protocols::motifs::IRCollectionOP
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::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 
)
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 
)
core::Real protocols::motifs::atom_specific_rms ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
utility::vector1< core::Size > const &  atoms 
)
core::Real protocols::motifs::atom_specific_rms ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
utility::vector1< std::string > const &  atoms 
)
core::Real protocols::motifs::backbone_stub_match ( core::conformation::Residue const &  r1,
core::conformation::Residue const &  r2 
)
utility::vector1< bool > protocols::motifs::bools_from_sizes ( core::Size const  nres,
utility::vector1< core::Size > const &  v 
)
std::map< core::Size, std::set< std::string > > protocols::motifs::bpdefs2map ( core::pose::Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  targets 
)
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 
)
utility::vector1< std::pair< core::Size, utility::vector1< std::string > > > protocols::motifs::defs2allowedtypes ( core::pose::Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  targets 
)
std::map< core::Size, std::set< std::string > > protocols::motifs::defs2map ( core::pose::Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  targets 
)
utility::vector1< core::Size > protocols::motifs::defs2vector ( core::pose::Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  targets 
)
utility::vector1< utility::file::FileName > protocols::motifs::get_filenames ( utility::vector1< utility::file::FileName > const &  listnames)
MotifLibrary const protocols::motifs::get_LigandMotifLibrary_user ( )
protocols::dna::DnaDesignDefOPs protocols::motifs::get_motif_build_position_defs_user ( )
utility::vector1< core::Size > protocols::motifs::get_motif_build_positions_user ( core::pose::Pose const &  pose)
MotifLibrary const protocols::motifs::get_MotifLibrary_user ( )
std::map< core::Size, std::set< std::string > > protocols::motifs::get_target_position_map_make_dna_mutations ( core::pose::Pose pose)
utility::vector1< core::Size > protocols::motifs::get_target_positions_make_dna_mutations ( core::pose::Pose pose)
utility::vector1< core::conformation::ResidueOP > const protocols::motifs::get_targetconformers_user ( )
static basic::Tracer protocols::motifs::irt ( "protocols.motifs.IRCollection"  ,
basic::t_info   
)
static
void protocols::motifs::load_build_position_data ( BuildPosition &  bp,
std::string const &  filename,
core::pose::Pose pose,
core::Size const  ligand_marker 
)
void protocols::motifs::make_base_pair_mutation ( core::pose::Pose pose,
core::Size const  seqpos,
core::chemical::AA const &  na 
)
void protocols::motifs::make_dna_mutations ( core::pose::Pose pose)
void protocols::motifs::make_dna_mutations ( core::pose::Pose pose,
protocols::dna::DnaDesignDefOPs const &  target 
)
static basic::Tracer protocols::motifs::ms_tr ( "protocols.motifs.MotifSearch"  ,
basic::t_info   
)
static
static basic::Tracer protocols::motifs::ms_tr ( "protocols.motifs.LigandMotifSearch"  ,
basic::t_info   
)
static
static basic::Tracer protocols::motifs::mt ( "protocols.motifs.Motif"  ,
basic::t_info   
)
static
static basic::Tracer protocols::motifs::mt ( "protocols.motifs.Motif"  ,
basic::t_info   
)
static
static basic::Tracer protocols::motifs::mu_tr ( "protocols.motifs.motif_utils"  ,
basic::t_info   
)
static
void protocols::motifs::mutate_loops_for_search ( core::pose::Pose pose,
protocols::loops::Loops flex_regions 
)
void protocols::motifs::mutate_position_vector_for_search ( core::pose::Pose pose,
utility::vector1< core::Size > &  trim_positions 
)
std::string protocols::motifs::name3_from_oneletter ( std::string const &  oneletter)

Referenced by bpdefs2map().

std::ostream& protocols::motifs::operator<< ( std::ostream &  os,
MotifLibrary const &  mlib 
)
std::ostream& protocols::motifs::operator<< ( std::ostream &  os,
const SingleMotif &  motif 
)
std::ostream& protocols::motifs::operator<< ( std::ostream &  os,
Motif const &  motif 
)
core::Real protocols::motifs::parallel_base_test ( core::conformation::Residue const &  pose_dna,
core::conformation::Residue const &  motif_dna 
)
std::map< std::string, utility::vector1< core::conformation::ResidueOP > > const protocols::motifs::setup_conformer_map ( utility::vector1< core::conformation::ResidueOP > const &  conformerOPs)
SingleMotifOP protocols::motifs::single_ligand_motif_from_stream ( std::istream &  motif_info)
SingleMotifOP protocols::motifs::single_motif_from_filename ( utility::file::FileName const &  motif_filename)
SingleMotifOP protocols::motifs::single_motif_from_stream ( utility::io::izstream &  motif_info)
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)
static basic::Tracer protocols::motifs::TR ( "devel.motifs.MotifDnaPacker"  )
static

Variable Documentation

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