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protocols::motifs::MotifSearch Class Reference

#include <MotifSearch.hh>

Inheritance diagram for protocols::motifs::MotifSearch:
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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)
 
MotifSearch & operator= (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::Size > map2keyvector (std::map< core::Size, std::set< std::string > > mappositions)
 
utility::vector1< core::Size > shorten_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

◆ DnaDesignDefOP

typedef protocols::dna::DnaDesignDefOP protocols::motifs::MotifSearch::DnaDesignDefOP

◆ DnaDesignDefOPs

typedef protocols::dna::DnaDesignDefOPs protocols::motifs::MotifSearch::DnaDesignDefOPs

◆ Pose

typedef core::pose::Pose protocols::motifs::MotifSearch::Pose

◆ Real

typedef core::Real protocols::motifs::MotifSearch::Real

◆ Size

typedef core::Size protocols::motifs::MotifSearch::Size

◆ Sizes

typedef utility::vector1< core::Size > protocols::motifs::MotifSearch::Sizes

Constructor & Destructor Documentation

◆ MotifSearch() [1/2]

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

References init_options().

◆ ~MotifSearch()

protocols::motifs::MotifSearch::~MotifSearch ( )
overridedefault

◆ MotifSearch() [2/2]

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

Member Function Documentation

◆ bp_motifhits()

protocols::motifs::MotifHitCOPs protocols::motifs::MotifSearch::bp_motifhits ( core::Size const  seqpos)

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

◆ bp_rotamers()

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

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

◆ build_positionOPs()

BuildPositionOPs const& protocols::motifs::MotifSearch::build_positionOPs ( ) const
inline

References build_positionOPs_.

◆ BuildPosition_from_Size()

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

References build_positionOPs_, map2keyvector(), core::conformation::Residue::name3(), core::pose::Pose::residue(), restrict_to_wt_, shorten_target_list(), target_positions(), and target_positions_.

Referenced by initialize().

◆ defs2BuildPositions()

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

References protocols::motifs::bpdefs2map(), build_positionOPs_, core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), and target_positions_.

Referenced by initialize().

◆ defs2BuildPositions_findts()

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

References protocols::motifs::bpdefs2map(), build_positionOPs_, core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), shorten_target_list(), and target_positions_.

Referenced by initialize().

◆ dna_positions()

Sizes const& protocols::motifs::MotifSearch::dna_positions ( ) const
inline

References dna_positions_.

◆ dtest_cutoff()

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

References dtest_cutoff_.

Referenced by incorporate_motifs().

◆ identify_motif_build_positions()

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

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

◆ identify_motif_BuildPositions()

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

References build_positionOPs_, core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), core::conformation::Residue::name3(), protein_dna_motif(), protein_DNA_motif_build_positions_JA(), core::pose::Pose::residue(), restrict_to_wt_, shorten_target_list(), target_positions(), and target_positions_.

Referenced by initialize().

◆ incorporate_motifs()

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::Atom::xyz(), core::conformation::Residue::xyz(), ztest_cutoff_1(), ztest_cutoff_1_, ztest_cutoff_2(), and ztest_cutoff_2_.

Referenced by run().

◆ init_options()

void protocols::motifs::MotifSearch::init_options ( )
private

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

Referenced by MotifSearch().

◆ initialize()

void protocols::motifs::MotifSearch::initialize ( Pose &  pose,
Sizes &  input_BPs 
)

References bpdata_, bpdata_filename_, build_positionOPs_, BuildPosition_from_Size(), clear_bprots_, defs2BuildPositions(), defs2BuildPositions_findts(), protocols::dna::dna_full_name3(), dna_positions_, core::sequence::end, protocols::motifs::get_motif_build_position_defs_user(), protocols::motifs::get_MotifLibrary_user(), protocols::motifs::get_target_position_map_make_dna_mutations(), protocols::motifs::get_targetconformers_user(), identify_motif_BuildPositions(), protocols::motifs::MotifLibrary::library(), protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr(), core::conformation::Residue::name3(), position_vector_setup(), core::pose::Pose::residue(), protocols::motifs::setup_conformer_map(), target_conformers_map_, and target_positions_.

Referenced by run().

◆ map2keyvector()

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

References core::sequence::end.

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

◆ minimize()

bool const& protocols::motifs::MotifSearch::minimize ( ) const
inline

References minimize_.

◆ motif_library()

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

References motif_library_.

Referenced by incorporate_motifs().

◆ operator=()

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

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

◆ override_option_input()

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 
)

References bpdata_, core::pack::rotamer_set::bump_check(), bump_check_, dtest_cutoff_, protocols::hybridization::r1, protocols::hybridization::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

◆ position_vector_setup()

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

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

Referenced by initialize().

◆ protein_dna_motif()

bool protocols::motifs::MotifSearch::protein_dna_motif ( )

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

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

◆ protein_DNA_motif_build_positions_JA()

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

References core::sequence::end, protocols::motifs::ms_tr(), protein_positions_, and target_positions().

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

◆ protein_DNA_motif_target_positions_JA()

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

References core::sequence::end, protocols::motifs::ms_tr(), and target_positions().

Referenced by shorten_target_list().

◆ protein_positions()

Sizes const& protocols::motifs::MotifSearch::protein_positions ( ) const
inline

References protein_positions_.

◆ reset_option_input()

void protocols::motifs::MotifSearch::reset_option_input ( )

References dtest_cutoff_, protocols::hybridization::r1, protocols::hybridization::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

◆ rmsd_cutoff_1()

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

References rmsd_cutoff_1_.

Referenced by incorporate_motifs().

◆ rmsd_cutoff_2()

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

References rmsd_cutoff_2_.

Referenced by incorporate_motifs().

◆ rot_level()

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

References rot_level_.

◆ run()

void protocols::motifs::MotifSearch::run ( Pose &  pose,
Sizes &  input_BPs 
)

References incorporate_motifs(), and initialize().

◆ set_motif_library()

void protocols::motifs::MotifSearch::set_motif_library ( MotifLibrary &  motiflibrary)

References motif_library_.

◆ shorten_target_list()

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

References protein_DNA_motif_target_positions_JA().

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

◆ target_conformers_map()

std::map< std::string, core::conformation::ResidueOPs > const& protocols::motifs::MotifSearch::target_conformers_map ( ) const
inline

References target_conformers_map_.

◆ target_positions()

std::map< core::Size, std::set< std::string > > const& protocols::motifs::MotifSearch::target_positions ( ) const
inline

References target_positions_.

Referenced by BuildPosition_from_Size(), identify_motif_BuildPositions(), incorporate_motifs(), protein_DNA_motif_build_positions_JA(), and protein_DNA_motif_target_positions_JA().

◆ ztest_cutoff_1()

Real const& protocols::motifs::MotifSearch::ztest_cutoff_1 ( ) const
inline

References ztest_cutoff_1_.

Referenced by incorporate_motifs().

◆ ztest_cutoff_2()

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

References ztest_cutoff_2_.

Referenced by incorporate_motifs().

Member Data Documentation

◆ bpdata_

bool protocols::motifs::MotifSearch::bpdata_
private

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

◆ bpdata_filename_

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

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

◆ build_positionOPs_

BuildPositionOPs protocols::motifs::MotifSearch::build_positionOPs_
private

Referenced by bp_motifhits(), bp_rotamers(), build_positionOPs(), BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), identify_motif_BuildPositions(), incorporate_motifs(), initialize(), and operator=().

◆ bump_check_

bool protocols::motifs::MotifSearch::bump_check_
private

Referenced by incorporate_motifs(), init_options(), operator=(), and override_option_input().

◆ clear_bprots_

bool protocols::motifs::MotifSearch::clear_bprots_
private

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

◆ data_

bool protocols::motifs::MotifSearch::data_
private

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

◆ data_filename_

std::string protocols::motifs::MotifSearch::data_filename_
private

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

◆ dna_positions_

Sizes protocols::motifs::MotifSearch::dna_positions_
private

Referenced by dna_positions(), identify_motif_build_positions(), initialize(), and position_vector_setup().

◆ dtest_cutoff_

Real protocols::motifs::MotifSearch::dtest_cutoff_
private

Referenced by dtest_cutoff(), incorporate_motifs(), operator=(), override_option_input(), and reset_option_input().

◆ dump_motifs_

bool protocols::motifs::MotifSearch::dump_motifs_
private

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

◆ minimize_

bool protocols::motifs::MotifSearch::minimize_
private

Referenced by incorporate_motifs(), minimize(), and operator=().

◆ motif_library_

MotifCOPs protocols::motifs::MotifSearch::motif_library_
private

Referenced by incorporate_motifs(), initialize(), motif_library(), operator=(), protein_dna_motif(), and set_motif_library().

◆ output_

bool protocols::motifs::MotifSearch::output_
private

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

◆ output_filename_

std::string protocols::motifs::MotifSearch::output_filename_
private

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

◆ protein_positions_

Sizes protocols::motifs::MotifSearch::protein_positions_
private

Referenced by position_vector_setup(), protein_DNA_motif_build_positions_JA(), and protein_positions().

◆ quick_and_dirty_

bool protocols::motifs::MotifSearch::quick_and_dirty_
private

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

◆ rerun_motifsearch_

bool protocols::motifs::MotifSearch::rerun_motifsearch_
private

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

◆ restrict_to_wt_

bool protocols::motifs::MotifSearch::restrict_to_wt_
private

Referenced by BuildPosition_from_Size(), identify_motif_BuildPositions(), init_options(), and operator=().

◆ rmsd_cutoff_1_

Real protocols::motifs::MotifSearch::rmsd_cutoff_1_
private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rmsd_cutoff_1().

◆ rmsd_cutoff_2_

Real protocols::motifs::MotifSearch::rmsd_cutoff_2_
private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rmsd_cutoff_2().

◆ rot_level_

core::Size protocols::motifs::MotifSearch::rot_level_
private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and rot_level().

◆ rots2add_

core::Size protocols::motifs::MotifSearch::rots2add_
private

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

◆ target_conformers_map_

std::map< std::string, core::conformation::ResidueOPs > protocols::motifs::MotifSearch::target_conformers_map_
private

Referenced by incorporate_motifs(), initialize(), operator=(), and target_conformers_map().

◆ target_positions_

std::map< core::Size, std::set< std::string > > protocols::motifs::MotifSearch::target_positions_
private

Referenced by BuildPosition_from_Size(), defs2BuildPositions(), defs2BuildPositions_findts(), identify_motif_BuildPositions(), incorporate_motifs(), initialize(), operator=(), and target_positions().

◆ ztest_cutoff_1_

Real protocols::motifs::MotifSearch::ztest_cutoff_1_
private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and ztest_cutoff_1().

◆ ztest_cutoff_2_

Real protocols::motifs::MotifSearch::ztest_cutoff_2_
private

Referenced by incorporate_motifs(), operator=(), override_option_input(), reset_option_input(), and ztest_cutoff_2().

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