Rosetta 3.4
Public Types | Public Member Functions
protocols::motifs::MotifSearch Class Reference

#include <MotifSearch.hh>

Inheritance diagram for protocols::motifs::MotifSearch:
Inheritance graph
Collaboration diagram for protocols::motifs::MotifSearch:
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List of all members.

Public Types

typedef core::Real Real
typedef core::Size Size
typedef utility::vector1< SizeSizes
typedef core::pose::Pose Pose

Public Member Functions

 MotifSearch ()
 ~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< Sizemap2keyvector (std::map< Size, std::set< std::string > > mappositions)
utility::vector1< Sizeshorten_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)
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

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

protocols::motifs::MotifHitCOPs protocols::motifs::MotifSearch::bp_motifhits ( Size const  seqpos)
core::pack::rotamer_set::Rotamers protocols::motifs::MotifSearch::bp_rotamers ( Size const  seqpos)
BuildPositionOPs const& protocols::motifs::MotifSearch::build_positionOPs ( ) const [inline]
void protocols::motifs::MotifSearch::BuildPosition_from_Size ( Pose const &  pose,
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]
Real const& protocols::motifs::MotifSearch::dtest_cutoff ( ) const [inline]

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

Referenced by incorporate_motifs().

MotifSearch const & 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,
Size const &  rlevel,
bool const  bpdata 
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]
void protocols::motifs::MotifSearch::reset_option_input ( )
Real const& protocols::motifs::MotifSearch::rmsd_cutoff_1 ( ) const [inline]

Referenced by incorporate_motifs().

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

Referenced by incorporate_motifs().

Size const& protocols::motifs::MotifSearch::rot_level ( ) const [inline]
void protocols::motifs::MotifSearch::run ( Pose pose,
Sizes input_BPs 
void protocols::motifs::MotifSearch::set_motif_library ( MotifLibrary motiflibrary)
utility::vector1< core::Size > protocols::motifs::MotifSearch::shorten_target_list ( Pose const &  pose,
Size const  bp,
Sizes full_tl 
std::map< std::string, core::conformation::ResidueOPs > const& protocols::motifs::MotifSearch::target_conformers_map ( ) const [inline]
std::map< Size, std::set< std::string > > const& protocols::motifs::MotifSearch::target_positions ( ) const [inline]
Real const& protocols::motifs::MotifSearch::ztest_cutoff_1 ( ) const [inline]

Referenced by incorporate_motifs().

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

Referenced by incorporate_motifs().

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