Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::motifs::MotifSearch Class Reference

#include <MotifSearch.hh>

Public Types

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

Public Member Functions

 MotifSearch ()
 
virtual ~MotifSearch ()
 
 MotifSearch (MotifSearch const &src)
 
MotifSearch const & 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 (Size const seqpos)
 
protocols::motifs::MotifHitCOPs bp_motifhits (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, 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< Size > map2keyvector (std::map< Size, std::set< std::string > > mappositions)
 
utility::vector1< Size > shorten_target_list (Pose const &pose, 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, 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< 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
 
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< 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_
 
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_
 
Size rots2add_
 
bool restrict_to_wt_
 
bool rerun_motifsearch_
 
bool bump_check_
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

References dtest, init_options(), motifs, option, options, r1, r2, rotlevel, z1, and z2.

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

Member Function Documentation

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

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

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

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

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

References build_positionOPs_.

void protocols::motifs::MotifSearch::BuildPosition_from_Size ( Pose const &  pose,
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().

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

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

Referenced by initialize().

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

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

Referenced by initialize().

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 
)

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

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

References build_positionOPs_, 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().

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_, clone(), utility::io::ozstream::close(), core::pose::Pose::constraint_set(), 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(), empty, end, core::pose::Pose::energies(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), get_score_function_legacy(), protocols::motifs::make_base_pair_mutation(), minimize_, motif_filename, motif_library(), motif_library_, movemap, protocols::motifs::ms_tr, core::conformation::Residue::name3(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, utility::io::ozstream::open_append(), options, 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(), residue_type_set, 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(), type, 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

References basic::options::OptionKeys::motifs::BPData, bpdata_, bpdata_filename_, bump_check_, basic::options::OptionKeys::motifs::clear_bprots, clear_bprots_, data_, basic::options::OptionKeys::motifs::data_file, data_filename_, basic::options::OptionKeys::motifs::dump_motifs, dump_motifs_, basic::options::OptionKeys::motifs::no_rotamer_bump, basic::options::option, output_, basic::options::OptionKeys::motifs::output_file, output_filename_, basic::options::OptionKeys::motifs::quick_and_dirty, quick_and_dirty_, basic::options::OptionKeys::motifs::rerun_motifsearch, rerun_motifsearch_, basic::options::OptionKeys::motifs::restrict_to_wt, restrict_to_wt_, basic::options::OptionKeys::motifs::rots2add, rots2add_, and user.

Referenced by MotifSearch().

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_, 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_, motifs, 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().

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

References end.

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

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 const & 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_.

void protocols::motifs::MotifSearch::override_option_input ( Real const &  r1,
Real const &  z1,
Real const &  r2,
Real const &  z2,
Real const &  d1,
Size const &  rlevel,
bool const  bpdata,
bool const  bump_check 
)

References bpdata_, bump_check_, dtest_cutoff_, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, ztest_cutoff_1_, and ztest_cutoff_2_.

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

References dna_positions_, end, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), protein_positions_, core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by initialize().

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

References core::conformation::ResidueFactory::create_residue(), protocols::dna::dna_full_name3(), FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), motif_library_, protocols::motifs::ms_tr, and residue_type_set.

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

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

References protocols::dna::DnaInterfaceFinder::determine_protein_interface(), end, protocols::motifs::ms_tr, and protein_positions_.

Referenced by identify_motif_build_positions(), and identify_motif_BuildPositions().

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

References protocols::dna::DnaInterfaceFinder::determine_dna_interface(), end, and protocols::motifs::ms_tr.

Referenced by shorten_target_list().

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

References protein_positions_.

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

References basic::options::OptionKeys::motifs::dtest, dtest_cutoff_, basic::options::option, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, rmsd_cutoff_1_, rmsd_cutoff_2_, rot_level_, basic::options::OptionKeys::motifs::rotlevel, basic::options::OptionKeys::motifs::z1, basic::options::OptionKeys::motifs::z2, ztest_cutoff_1_, and ztest_cutoff_2_.

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().

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

References rot_level_.

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

References incorporate_motifs(), and initialize().

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

References protocols::motifs::MotifLibrary::begin(), protocols::motifs::MotifLibrary::end(), and motif_library_.

utility::vector1< core::Size > protocols::motifs::MotifSearch::shorten_target_list ( Pose const &  pose,
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::MotifSearch::target_conformers_map ( ) const
inline

References target_conformers_map_.

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

References target_positions_.

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

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

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

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

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

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=().

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

std::map< 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().

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

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

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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