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protocols::motifs::LigandMotifSearch Class Reference

#include <LigandMotifSearch.hh>

Inheritance diagram for protocols::motifs::LigandMotifSearch:
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
 
typedef
core::pack::task::PackerTask 		PackerTask
 

Public Member Functions

 LigandMotifSearch ()
 
 ~LigandMotifSearch () override
 
 LigandMotifSearch (LigandMotifSearch const &src)
 
LigandMotifSearch & operator= (LigandMotifSearch const &src)
 
void run (Pose const &pose, utility::vector1< core::Size > &input_BPs)
 
void run (Pose const &pose, PackerTask &task)
 
void run (Pose const &pose, core::Real &ligand_motif_sphere)
 
void initialize (Pose const &pose)
 
void initialize (Pose const &pose, utility::vector1< core::Size > &input_BPs)
 
void incorporate_motifs (Pose const &pose)
 
core::pack::rotamer_set::Rotamers bp_rotamers (core::Size const seqpos)
 
core::pack::rotamer_set::Rotamers get_rotamers ()
 
bool protein_dna_motif ()
 
void position_vector_setup (Pose const &pose)
 
void identify_motif_build_positions (Pose const &pose, Sizes &build_positions)
 
utility::vector1< core::Size > get_sphere_aa (Pose const &pose, core::Real cut1)
 
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)
 
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_
 

Member Typedef Documentation

typedef protocols::dna::DnaDesignDefOP protocols::motifs::LigandMotifSearch::DnaDesignDefOP
typedef protocols::dna::DnaDesignDefOPs protocols::motifs::LigandMotifSearch::DnaDesignDefOPs
typedef core::pack::task::PackerTask protocols::motifs::LigandMotifSearch::PackerTask
typedef core::pose::Pose protocols::motifs::LigandMotifSearch::Pose
typedef core::Real protocols::motifs::LigandMotifSearch::Real
typedef core::Size protocols::motifs::LigandMotifSearch::Size
typedef utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::Sizes

Constructor & Destructor Documentation

protocols::motifs::LigandMotifSearch::LigandMotifSearch ( )

References init_options().

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

Member Function Documentation

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

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

Referenced by run().

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

References build_positionOPs_.

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

References build_positionOPs_, map2keyvector(), shorten_target_list(), target_positions(), and target_positions_.

Referenced by initialize().

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

References build_positionOPs_, protocols::motifs::defs2map(), core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), and target_positions_.

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

References build_positionOPs_, protocols::motifs::defs2map(), core::sequence::end, map2keyvector(), protocols::motifs::ms_tr(), protein_dna_motif(), shorten_target_list(), and target_positions_.

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

References dna_positions_.

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

References dtest_cutoff_.

Referenced by incorporate_motifs().

core::pack::rotamer_set::Rotamers protocols::motifs::LigandMotifSearch::get_rotamers ( )

References build_positionOPs_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::get_sphere_aa ( Pose const &  pose,
core::Real  cut1 
)

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), protocols::motifs::ms_tr(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by run().

void protocols::motifs::LigandMotifSearch::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().

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

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

void protocols::motifs::LigandMotifSearch::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(), build_positionOPs_, protocols::motifs::build_rotamers_lite(), 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_, core::pose::Pose::pdb_info(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, quick_and_dirty_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rmsd_cutoff_1(), rmsd_cutoff_1_, rmsd_cutoff_2(), rmsd_cutoff_2_, rot_level_, rots2add_, core::pose::Pose::size(), target_conformers_map_, target_positions(), core::scoring::Energies::total_energies(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by run().

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

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

Referenced by LigandMotifSearch().

void protocols::motifs::LigandMotifSearch::initialize ( Pose const &  pose)

References protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

Referenced by run().

void protocols::motifs::LigandMotifSearch::initialize ( Pose const &  pose,
utility::vector1< core::Size > &  input_BPs 
)

References BuildPosition_from_Size(), protocols::motifs::get_LigandMotifLibrary_user(), protocols::motifs::get_targetconformers_user(), protocols::motifs::MotifLibrary::library(), motif_library_, protocols::motifs::ms_tr(), position_vector_setup(), protocols::motifs::setup_conformer_map(), and target_conformers_map_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::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().

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

References minimize_.

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

References motif_library_.

Referenced by incorporate_motifs().

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

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

void protocols::motifs::LigandMotifSearch::override_option_input ( Real const &  r1,
Real const &  z1,
Real const &  r2,
Real const &  z2,
Real const &  d1,
core::Size const &  rlevel 
)

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

void protocols::motifs::LigandMotifSearch::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().

bool protocols::motifs::LigandMotifSearch::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().

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

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

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

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

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

Referenced by shorten_target_list().

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

References protein_positions_.

void protocols::motifs::LigandMotifSearch::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_.

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

References rmsd_cutoff_1_.

Referenced by incorporate_motifs().

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

References rmsd_cutoff_2_.

Referenced by incorporate_motifs().

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

References rot_level_.

void protocols::motifs::LigandMotifSearch::run ( Pose const &  pose,
utility::vector1< core::Size > &  input_BPs 
)

References incorporate_motifs(), initialize(), and protocols::motifs::ms_tr().

void protocols::motifs::LigandMotifSearch::run ( Pose const &  pose,
PackerTask &  task 
)

References core::pose::add_variant_type_to_residue(), core::pack::task::ResidueLevelTask::append_rotamerset_operation(), core::pack::task::PackerTask::being_designed(), bp_rotamers(), build_positionOPs_, clear_bprots_, incorporate_motifs(), initialize(), core::conformation::Residue::is_protein(), protocols::motifs::LIGAND, protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr(), core::pack::task::PackerTask::nonconst_residue_task(), output_, output_filename_, core::pose::Pose::residue(), rot(), core::pose::Pose::size(), core::chemical::SPECIAL_ROT, and target_positions().

void protocols::motifs::LigandMotifSearch::run ( Pose const &  pose,
core::Real &  ligand_motif_sphere 
)

References build_positionOPs_, clear_bprots_, get_sphere_aa(), incorporate_motifs(), initialize(), protocols::motifs::LIGAND, protocols::motifs::load_build_position_data(), motif_library_, protocols::motifs::ms_tr(), output_, and output_filename_.

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

References motif_library_.

utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::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().

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

References target_conformers_map_.

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

References target_positions_.

Referenced by BuildPosition_from_Size(), identify_motif_BuildPositions(), incorporate_motifs(), and run().

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

References ztest_cutoff_1_.

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

References ztest_cutoff_2_.

Member Data Documentation

bool protocols::motifs::LigandMotifSearch::bpdata_
private

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

std::string protocols::motifs::LigandMotifSearch::bpdata_filename_
private

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

BuildPositionOPs protocols::motifs::LigandMotifSearch::build_positionOPs_
private

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

bool protocols::motifs::LigandMotifSearch::clear_bprots_
private

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

bool protocols::motifs::LigandMotifSearch::data_
private

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

std::string protocols::motifs::LigandMotifSearch::data_filename_
private

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

Sizes protocols::motifs::LigandMotifSearch::dna_positions_
private

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

Real protocols::motifs::LigandMotifSearch::dtest_cutoff_
private

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

bool protocols::motifs::LigandMotifSearch::dump_motifs_
private

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

bool protocols::motifs::LigandMotifSearch::minimize_
private

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

MotifCOPs protocols::motifs::LigandMotifSearch::motif_library_
private

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

bool protocols::motifs::LigandMotifSearch::output_
private

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

std::string protocols::motifs::LigandMotifSearch::output_filename_
private

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

Sizes protocols::motifs::LigandMotifSearch::protein_positions_
private

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

bool protocols::motifs::LigandMotifSearch::quick_and_dirty_
private

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

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_1_
private

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

Real protocols::motifs::LigandMotifSearch::rmsd_cutoff_2_
private

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

core::Size protocols::motifs::LigandMotifSearch::rot_level_
private

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

core::Size protocols::motifs::LigandMotifSearch::rots2add_
private

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

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

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

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

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

Real protocols::motifs::LigandMotifSearch::ztest_cutoff_1_
private

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

Real protocols::motifs::LigandMotifSearch::ztest_cutoff_2_
private

Referenced by 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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