Rosetta 3.4
Public Member Functions
protocols::loophash::LoopHashLibrary Class Reference

#include <LoopHashLibrary.hh>

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List of all members.

Public Member Functions

 LoopHashLibrary (const utility::vector1< core::Size > &init_sizes=utility::vector1< core::Size >(), const core::Size num_partitions=1, const core::Size assigned_num=0)
void extract_data_from_pose (core::pose::Pose &pose, core::Size nres, protocols::frag_picker::VallChunkOP chunk=NULL)
void extract_data_from_pose (core::pose::Pose &pose)
void test_loop_sample (core::pose::Pose &pose, core::Size nres)
void apply_random (core::pose::Pose &pose, core::Size &fir, core::Size &fjr, core::Real min_rms, core::Real max_rms)
void get_all (core::pose::Pose &pose, std::vector< core::io::silent::SilentStructOP > &lib_structs, core::Size start_res=1, core::Size stop_res=0, core::Real min_bbrms=0.0, core::Real max_bbrms=100000.0, core::Real min_rms=0.0, core::Real max_rms=100.0)
virtual void apply (core::pose::Pose &pose)
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
void setup_hash_maps ()
LoopHashMapgethash (core::Size size)
const std::vector< core::Size > & hash_sizes () const
const BackboneDBbackbone_database () const
const std::pair< core::Size,
core::Size
loopdb_range ()
void save_db ()
void load_db ()
void load_mergeddb ()
void delete_db ()
void merge (LoopHashLibraryOP second_lib, utility::vector1< core::Real > rms_cutoffs)
bool merge_bbdb (const BackboneDB &second_bbdb, core::Size &index_offset)
void sort ()
void create_db ()
void set_create_db (bool setting=true)
void set_db_path (std::string setting)
void graft_loop (const core::pose::Pose &src_pose, core::pose::Pose &tgt_pose, protocols::loops::Loop myloop)
void set_default_score_functions ()
void mem_foot_print ()
bool get_extra () const

Constructor & Destructor Documentation

protocols::loophash::LoopHashLibrary::LoopHashLibrary ( const utility::vector1< core::Size > &  init_sizes = utility::vector1core::Size >(),
const core::Size  num_partitions = 1,
const core::Size  assigned_num = 0 
)

Member Function Documentation

void protocols::loophash::LoopHashLibrary::apply ( core::pose::Pose pose) [virtual]
void protocols::loophash::LoopHashLibrary::apply_random ( core::pose::Pose pose,
core::Size fir,
core::Size fjr,
core::Real  min_rms,
core::Real  max_rms 
)
const BackboneDB& protocols::loophash::LoopHashLibrary::backbone_database ( ) const [inline]
virtual protocols::moves::MoverOP protocols::loophash::LoopHashLibrary::clone ( ) const [inline, virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::create_db ( )
void protocols::loophash::LoopHashLibrary::delete_db ( )
void protocols::loophash::LoopHashLibrary::extract_data_from_pose ( core::pose::Pose pose,
core::Size  nres,
protocols::frag_picker::VallChunkOP  chunk = NULL 
)
void protocols::loophash::LoopHashLibrary::extract_data_from_pose ( core::pose::Pose pose)
virtual protocols::moves::MoverOP protocols::loophash::LoopHashLibrary::fresh_instance ( ) const [inline, virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::get_all ( core::pose::Pose pose,
std::vector< core::io::silent::SilentStructOP > &  lib_structs,
core::Size  start_res = 1,
core::Size  stop_res = 0,
core::Real  min_bbrms = 0.0,
core::Real  max_bbrms = 100000.0,
core::Real  min_rms = 0.0,
core::Real  max_rms = 100.0 
)
bool protocols::loophash::LoopHashLibrary::get_extra ( ) const [inline]
virtual std::string protocols::loophash::LoopHashLibrary::get_name ( ) const [inline, virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

LoopHashMap & protocols::loophash::LoopHashLibrary::gethash ( core::Size  size)
void protocols::loophash::LoopHashLibrary::graft_loop ( const core::pose::Pose src_pose,
core::pose::Pose tgt_pose,
protocols::loops::Loop  myloop 
)
const std::vector< core::Size >& protocols::loophash::LoopHashLibrary::hash_sizes ( ) const [inline]
void protocols::loophash::LoopHashLibrary::load_db ( )
void protocols::loophash::LoopHashLibrary::load_mergeddb ( )
const std::pair< core::Size, core::Size > protocols::loophash::LoopHashLibrary::loopdb_range ( ) [inline]
void protocols::loophash::LoopHashLibrary::mem_foot_print ( )
void protocols::loophash::LoopHashLibrary::merge ( LoopHashLibraryOP  second_lib,
utility::vector1< core::Real rms_cutoffs 
)
bool protocols::loophash::LoopHashLibrary::merge_bbdb ( const BackboneDB second_bbdb,
core::Size index_offset 
)
void protocols::loophash::LoopHashLibrary::save_db ( )
void protocols::loophash::LoopHashLibrary::set_create_db ( bool  setting = true) [inline]
void protocols::loophash::LoopHashLibrary::set_db_path ( std::string  setting) [inline]
void protocols::loophash::LoopHashLibrary::set_default_score_functions ( )
void protocols::loophash::LoopHashLibrary::setup_hash_maps ( )

References protocols::loophash::TR().

Referenced by LoopHashLibrary().

void protocols::loophash::LoopHashLibrary::sort ( )
void protocols::loophash::LoopHashLibrary::test_loop_sample ( core::pose::Pose pose,
core::Size  nres 
)

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