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protocols::loophash::LoopHashLibrary Class Reference

#include <LoopHashLibrary.hh>

Inheritance diagram for protocols::loophash::LoopHashLibrary:
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Collaboration diagram for protocols::loophash::LoopHashLibrary:
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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)
 
bool test_saving_library (core::pose::Pose, core::Size ir, bool deposit)
 
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. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
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). More...
 
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
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void type (const std::string &type_in)
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Attributes

BackboneDB bbdb_
 
std::map< core::Size, LoopHashMaphash_
 
std::vector< core::Sizehash_sizes_
 
std::string db_path_
 
core::Size num_partitions_
 
core::Size assigned_num_
 
std::string assigned_string_
 
bool extra_
 
std::pair< core::Size, core::Sizeloopdb_range_
 
bool do_sanity_check_
 
bool create_db_
 
core::scoring::ScoreFunction scorefxn_rama_cst
 
core::scoring::ScoreFunction scorefxn_cen_cst
 
core::optimization::MinimizerOptions options
 
core::optimization::MinimizerOptions options2
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

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

References bbdb_.

Referenced by test_saving_library().

virtual protocols::moves::MoverOP protocols::loophash::LoopHashLibrary::clone ( ) const
inlinevirtual

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
inlinevirtual

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

References extra_.

virtual std::string protocols::loophash::LoopHashLibrary::get_name ( ) const
inlinevirtual

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

References hash_sizes_.

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

References loopdb_range_.

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

References create_db_.

void protocols::loophash::LoopHashLibrary::set_db_path ( std::string  setting)
inline

References db_path_.

void protocols::loophash::LoopHashLibrary::set_default_score_functions ( )
void protocols::loophash::LoopHashLibrary::setup_hash_maps ( )
void protocols::loophash::LoopHashLibrary::sort ( )

References hash_, and hash_sizes_.

void protocols::loophash::LoopHashLibrary::test_loop_sample ( core::pose::Pose pose,
core::Size  nres 
)
bool protocols::loophash::LoopHashLibrary::test_saving_library ( core::pose::Pose  pose,
core::Size  ir,
bool  deposit 
)

Member Data Documentation

core::Size protocols::loophash::LoopHashLibrary::assigned_num_
private
std::string protocols::loophash::LoopHashLibrary::assigned_string_
private
BackboneDB protocols::loophash::LoopHashLibrary::bbdb_
private
bool protocols::loophash::LoopHashLibrary::create_db_
private

Referenced by set_create_db().

std::string protocols::loophash::LoopHashLibrary::db_path_
private
bool protocols::loophash::LoopHashLibrary::do_sanity_check_
private
bool protocols::loophash::LoopHashLibrary::extra_
private
std::map< core::Size, LoopHashMap > protocols::loophash::LoopHashLibrary::hash_
private
std::vector< core::Size > protocols::loophash::LoopHashLibrary::hash_sizes_
private
std::pair< core::Size, core::Size > protocols::loophash::LoopHashLibrary::loopdb_range_
private
core::Size protocols::loophash::LoopHashLibrary::num_partitions_
private
core::optimization::MinimizerOptions protocols::loophash::LoopHashLibrary::options
private

Referenced by get_all(), and graft_loop().

core::optimization::MinimizerOptions protocols::loophash::LoopHashLibrary::options2
private

Referenced by get_all(), and graft_loop().

core::scoring::ScoreFunction protocols::loophash::LoopHashLibrary::scorefxn_cen_cst
private
core::scoring::ScoreFunction protocols::loophash::LoopHashLibrary::scorefxn_rama_cst
private

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