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protocols::motifs::MotifSearch Class Reference

#include <MotifSearch.hh>

Inheritance diagram for protocols::motifs::MotifSearch:
Inheritance graph
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef utility::vector1
< core::Size
Sizes
 
typedef core::pose::Pose Pose
 
typedef
protocols::dna::DnaDesignDefOP 
DnaDesignDefOP
 
typedef
protocols::dna::DnaDesignDefOPs 
DnaDesignDefOPs
 

Public Member Functions

 MotifSearch ()
 
 ~MotifSearch () override
 
 MotifSearch (MotifSearch const &src)
 
MotifSearchoperator= (MotifSearch const &src)
 
void run (Pose &pose, Sizes &input_BPs)
 
void initialize (Pose &pose, Sizes &input_BPs)
 
void incorporate_motifs (Pose const &pose)
 
core::pack::rotamer_set::Rotamers bp_rotamers (core::Size const seqpos)
 
protocols::motifs::MotifHitCOPs bp_motifhits (core::Size const seqpos)
 
bool protein_dna_motif ()
 
void position_vector_setup (Pose const &pose)
 
void identify_motif_build_positions (Pose const &pose, Sizes &build_positions)
 
void identify_motif_BuildPositions (Pose const &pose)
 
void BuildPosition_from_Size (Pose const &pose, core::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< core::Sizemap2keyvector (std::map< core::Size, std::set< std::string > > mappositions)
 
utility::vector1< core::Sizeshorten_target_list (Pose const &pose, core::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, core::Size const &rlevel, bool const bpdata, bool const bump_check)
 
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< core::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
 
core::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< core::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_
 
core::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_
 
core::Size rots2add_
 
bool restrict_to_wt_
 
bool rerun_motifsearch_
 
bool bump_check_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::motifs::MotifSearch::MotifSearch ( )

References init_options().

protocols::motifs::MotifSearch::~MotifSearch ( )
overridedefault
protocols::motifs::MotifSearch::MotifSearch ( MotifSearch const &  src)

Member Function Documentation

protocols::motifs::MotifHitCOPs protocols::motifs::MotifSearch::bp_motifhits ( core::Size const  seqpos)
core::pack::rotamer_set::Rotamers protocols::motifs::MotifSearch::bp_rotamers ( core::Size const  seqpos)
BuildPositionOPs const& protocols::motifs::MotifSearch::build_positionOPs ( ) const
inline

References build_positionOPs_.

void protocols::motifs::MotifSearch::BuildPosition_from_Size ( Pose const &  pose,
core::Size const  input_BP 
)
void protocols::motifs::MotifSearch::defs2BuildPositions ( Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  defs 
)
void protocols::motifs::MotifSearch::defs2BuildPositions_findts ( Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  defs 
)
Sizes const& protocols::motifs::MotifSearch::dna_positions ( ) const
inline

References dna_positions_.

Real const& protocols::motifs::MotifSearch::dtest_cutoff ( ) const
inline

References dtest_cutoff_.

Referenced by incorporate_motifs().

void protocols::motifs::MotifSearch::identify_motif_build_positions ( Pose const &  pose,
Sizes build_positions 
)
void protocols::motifs::MotifSearch::identify_motif_BuildPositions ( Pose const &  pose)
void protocols::motifs::MotifSearch::incorporate_motifs ( Pose const &  pose)

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::scoring::automorphic_rmsd(), build_positionOPs_, protocols::motifs::build_rotamers_lite(), bump_check_, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), 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::scoring::get_score_function_legacy(), 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_, protocols::motifs::parallel_base_test(), core::pose::Pose::pdb_info(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, quick_and_dirty_, core::pose::Pose::replace_residue(), rerun_motifsearch_, core::pose::Pose::residue(), rmsd_cutoff_1(), rmsd_cutoff_1_, rmsd_cutoff_2(), rmsd_cutoff_2_, rot_level_, rots2add_, target_conformers_map_, target_positions(), target_positions_, core::scoring::Energies::total_energies(), core::conformation::Residue::xyz(), ztest_cutoff_1(), ztest_cutoff_1_, ztest_cutoff_2(), and ztest_cutoff_2_.

Referenced by run().

void protocols::motifs::MotifSearch::init_options ( )
private
void protocols::motifs::MotifSearch::initialize ( Pose pose,
Sizes input_BPs 
)
utility::vector1< core::Size > protocols::motifs::MotifSearch::map2keyvector ( std::map< core::Size, std::set< std::string > >  mappositions)
bool const& protocols::motifs::MotifSearch::minimize ( ) const
inline

References minimize_.

MotifCOPs const& protocols::motifs::MotifSearch::motif_library ( ) const
inline

References motif_library_.

Referenced by incorporate_motifs().

MotifSearch & protocols::motifs::MotifSearch::operator= ( MotifSearch const &  src)
void protocols::motifs::MotifSearch::override_option_input ( Real const &  r1,
Real const &  z1,
Real const &  r2,
Real const &  z2,
Real const &  d1,
core::Size const &  rlevel,
bool const  bpdata,
bool const  bump_check 
)
void protocols::motifs::MotifSearch::position_vector_setup ( Pose const &  pose)
bool protocols::motifs::MotifSearch::protein_dna_motif ( )
void protocols::motifs::MotifSearch::protein_DNA_motif_build_positions_JA ( Pose const &  pose,
Sizes build_positions,
Sizes target_positions 
)
void protocols::motifs::MotifSearch::protein_DNA_motif_target_positions_JA ( Pose const &  pose,
Sizes build_positions,
Sizes target_positions,
Sizes short_tl 
)
Sizes const& protocols::motifs::MotifSearch::protein_positions ( ) const
inline

References protein_positions_.

void protocols::motifs::MotifSearch::reset_option_input ( )
Real const& protocols::motifs::MotifSearch::rmsd_cutoff_1 ( ) const
inline

References rmsd_cutoff_1_.

Referenced by incorporate_motifs().

Real const& protocols::motifs::MotifSearch::rmsd_cutoff_2 ( ) const
inline

References rmsd_cutoff_2_.

Referenced by incorporate_motifs().

core::Size const& protocols::motifs::MotifSearch::rot_level ( ) const
inline

References rot_level_.

void protocols::motifs::MotifSearch::run ( Pose pose,
Sizes input_BPs 
)
void protocols::motifs::MotifSearch::set_motif_library ( MotifLibrary motiflibrary)

References motif_library_.

utility::vector1< core::Size > protocols::motifs::MotifSearch::shorten_target_list ( Pose const &  pose,
core::Size const  bp,
Sizes full_tl 
)
std::map< std::string, core::conformation::ResidueOPs > const& protocols::motifs::MotifSearch::target_conformers_map ( ) const
inline
std::map< core::Size, std::set< std::string > > const& protocols::motifs::MotifSearch::target_positions ( ) const
inline
Real const& protocols::motifs::MotifSearch::ztest_cutoff_1 ( ) const
inline

References ztest_cutoff_1_.

Referenced by incorporate_motifs().

Real const& protocols::motifs::MotifSearch::ztest_cutoff_2 ( ) const
inline

References ztest_cutoff_2_.

Referenced by incorporate_motifs().

Member Data Documentation

bool protocols::motifs::MotifSearch::bpdata_
private
std::string protocols::motifs::MotifSearch::bpdata_filename_
private

Referenced by init_options(), initialize(), and operator=().

BuildPositionOPs protocols::motifs::MotifSearch::build_positionOPs_
private
bool protocols::motifs::MotifSearch::bump_check_
private
bool protocols::motifs::MotifSearch::clear_bprots_
private

Referenced by init_options(), initialize(), and operator=().

bool protocols::motifs::MotifSearch::data_
private
std::string protocols::motifs::MotifSearch::data_filename_
private
Sizes protocols::motifs::MotifSearch::dna_positions_
private
Real protocols::motifs::MotifSearch::dtest_cutoff_
private
bool protocols::motifs::MotifSearch::dump_motifs_
private
bool protocols::motifs::MotifSearch::minimize_
private
MotifCOPs protocols::motifs::MotifSearch::motif_library_
private
bool protocols::motifs::MotifSearch::output_
private
std::string protocols::motifs::MotifSearch::output_filename_
private
Sizes protocols::motifs::MotifSearch::protein_positions_
private
bool protocols::motifs::MotifSearch::quick_and_dirty_
private
bool protocols::motifs::MotifSearch::rerun_motifsearch_
private
bool protocols::motifs::MotifSearch::restrict_to_wt_
private
Real protocols::motifs::MotifSearch::rmsd_cutoff_1_
private
Real protocols::motifs::MotifSearch::rmsd_cutoff_2_
private
core::Size protocols::motifs::MotifSearch::rot_level_
private
core::Size protocols::motifs::MotifSearch::rots2add_
private
std::map< std::string, core::conformation::ResidueOPs > protocols::motifs::MotifSearch::target_conformers_map_
private
std::map< core::Size, std::set< std::string > > protocols::motifs::MotifSearch::target_positions_
private
Real protocols::motifs::MotifSearch::ztest_cutoff_1_
private
Real protocols::motifs::MotifSearch::ztest_cutoff_2_
private

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