Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::motifs::LigandMotifSearch Class Reference

#include <LigandMotifSearch.hh>

Inheritance diagram for protocols::motifs::LigandMotifSearch:
Inheritance graph
[legend]

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)
 
LigandMotifSearchoperator= (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::Sizeget_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::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)
 
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

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 
)
void protocols::motifs::LigandMotifSearch::defs2BuildPositions ( Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  defs 
)
void protocols::motifs::LigandMotifSearch::defs2BuildPositions_findts ( Pose const &  pose,
protocols::dna::DnaDesignDefOPs const &  defs 
)
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 
)
void protocols::motifs::LigandMotifSearch::identify_motif_build_positions ( Pose const &  pose,
Sizes build_positions 
)
void protocols::motifs::LigandMotifSearch::identify_motif_BuildPositions ( Pose const &  pose)
void protocols::motifs::LigandMotifSearch::incorporate_motifs ( Pose const &  pose)
void protocols::motifs::LigandMotifSearch::init_options ( )
private
void protocols::motifs::LigandMotifSearch::initialize ( Pose const &  pose)
void protocols::motifs::LigandMotifSearch::initialize ( Pose const &  pose,
utility::vector1< core::Size > &  input_BPs 
)
utility::vector1< core::Size > protocols::motifs::LigandMotifSearch::map2keyvector ( std::map< core::Size, std::set< std::string > >  mappositions)
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)
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 
)
void protocols::motifs::LigandMotifSearch::position_vector_setup ( Pose const &  pose)
bool protocols::motifs::LigandMotifSearch::protein_dna_motif ( )
void protocols::motifs::LigandMotifSearch::protein_DNA_motif_build_positions_JA ( Pose const &  pose,
Sizes build_positions,
Sizes target_positions 
)
void protocols::motifs::LigandMotifSearch::protein_DNA_motif_target_positions_JA ( Pose const &  pose,
Sizes build_positions,
Sizes target_positions,
Sizes short_tl 
)
Sizes const& protocols::motifs::LigandMotifSearch::protein_positions ( ) const
inline

References protein_positions_.

void protocols::motifs::LigandMotifSearch::reset_option_input ( )
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 
)
void protocols::motifs::LigandMotifSearch::run ( Pose const &  pose,
PackerTask task 
)
void protocols::motifs::LigandMotifSearch::run ( Pose const &  pose,
core::Real ligand_motif_sphere 
)
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 
)
std::map< std::string, core::conformation::ResidueOPs > const& protocols::motifs::LigandMotifSearch::target_conformers_map ( ) const
inline
std::map< core::Size, std::set< std::string > > const& protocols::motifs::LigandMotifSearch::target_positions ( ) const
inline
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
bool protocols::motifs::LigandMotifSearch::clear_bprots_
private

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

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

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