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Rosetta
2020.50
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#include <LoopHashLibrary.hh>
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=nullptr) |
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) |
void | apply (core::pose::Pose &pose) override |
Main Method. More... | |
protocols::moves::MoverOP | clone () const override |
Return a clone of the Mover object. More... | |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Generates a new Mover object freshly created with the default ctor. More... | |
void | setup_hash_maps () |
LoopHashMap const & | gethash (core::Size size) const |
LoopHashMap & | gethash (core::Size size) |
std::vector< core::Size > const & | hash_sizes () const |
Return a list of the loop lengths present in the library. More... | |
BackboneDB const & | backbone_database () const |
std::pair< core::Size, core::Size > | loopdb_range () const |
void | save_db () const |
void | load_db () |
void | load_mergeddb () |
void | delete_db () |
void | merge (LoopHashLibraryOP second_lib, utility::vector1< core::Real > rms_cutoffs) |
Take two LoopHash libraries and merge them. More... | |
bool | merge_bbdb (const BackboneDB &second_bbdb, core::Size &index_offset) |
Take two backbone databases and merge them. More... | |
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 () const |
bool | get_extra () const |
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Mover () | |
virtual MoverOP | create () |
MoverCOP | get_self_ptr () const |
MoverOP | get_self_ptr () |
MoverCAP | get_self_weak_ptr () const |
MoverAP | get_self_weak_ptr () |
Mover (std::string const &type_name) | |
sets the type for a mover; name_ has been removed (2010/05/14) More... | |
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... | |
virtual bool | reinitialize_for_each_job () const |
Inform 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 |
Inform 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... | |
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... | |
void | set_type (std::string const &setting) |
Set the 'type' string. More... | |
std::string | get_type () const |
void | type (const std::string &type_in) |
Set the 'type' string. More... | |
std::string const & | type () const |
Get the set 'type' string. More... | |
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 | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
virtual void | set_current_tag (std::string const &new_tag) |
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... | |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
virtual core::Real | last_proposal_density_ratio () |
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 Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Private Attributes | |
BackboneDB | bbdb_ |
The backbone library for this HashLibrary (the actual data) More... | |
std::map< core::Size, LoopHashMap > | hash_ |
A map of Hashmaps, each for a different loop size. More... | |
std::vector< core::Size > | hash_sizes_ |
Kind-of a redundant store of sizes (remove this?) More... | |
std::string | db_path_ |
Path to database. More... | |
core::Size | num_partitions_ |
The number of partitions the database is split into. More... | |
core::Size | assigned_num_ |
Which partition slice is assigned to this library. More... | |
std::string | assigned_string_ |
Need so we can set the database string once. More... | |
bool | extra_ |
Whether this database holds extra data in the backbone database or not. More... | |
std::pair< core::Size, core::Size > | loopdb_range_ |
The proteins of the backbone database that are loaded (when loading a merged database, otherwise (0,0)) More... | |
bool | do_sanity_check_ |
bool | create_db_ |
core::scoring::ScoreFunctionOP | scorefxn_rama_cst_ |
core::scoring::ScoreFunctionOP | scorefxn_cen_cst_ |
core::optimization::MinimizerOptions | options_ |
core::optimization::MinimizerOptions | options2_ |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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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... | |
protocols::loophash::LoopHashLibrary::LoopHashLibrary | ( | const utility::vector1< core::Size > & | init_sizes = utility::vector1< core::Size >() , |
const core::Size | num_partitions = 1 , |
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const core::Size | assigned_num = 0 |
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::scoring::CA_rmsd(), core::chemical::CENTROID_t, get_all(), core::scoring::get_score_function(), protocols::loophash::MAXIMAL_FLOAT, core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::antibody::design::relax, core::scoring::rg, core::scoring::rms, protocols::noesy_assign::round(), protocols::hybridization::score, core::pose::set_ss_from_phipsi(), core::util::switch_to_residue_type_set(), protocols::loophash::TR(), and core::io::silent::SilentFileData::write_silent_struct().
void protocols::loophash::LoopHashLibrary::apply_random | ( | core::pose::Pose & | pose, |
core::Size & | fir, | ||
core::Size & | fjr, | ||
core::Real | min_rms, | ||
core::Real | max_rms | ||
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References protocols::loophash::BackboneSegment::apply_to_pose(), bbdb_, protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::LoopHashMap::get_loop_size(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), protocols::loophash::get_rt_over_leap(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LoopHashMap::lookup(), protocols::loophash::LeapIndex::offset, protocols::loophash::BackboneSegment::print(), protocols::loophash::BackboneSegment::read_from_pose(), core::pose::Pose::size(), protocols::hybridization::t, and protocols::loophash::TR().
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inline |
References bbdb_.
Referenced by test_saving_library().
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inlineoverridevirtual |
Return a clone of the Mover object.
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.
void protocols::loophash::LoopHashLibrary::create_db | ( | ) |
void protocols::loophash::LoopHashLibrary::delete_db | ( | ) |
References assigned_string_, db_path_, hash_sizes_, core::id::to_string(), and protocols::loophash::TR().
void protocols::loophash::LoopHashLibrary::extract_data_from_pose | ( | core::pose::Pose & | pose, |
core::Size | nres, | ||
protocols::frag_picker::VallChunkOP | chunk = nullptr |
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) |
References core::kinematics::FoldTree::add_edge(), protocols::loophash::LoopHashMap::add_leap(), protocols::loophash::BackboneDB::add_pose(), bbdb_, core::pose::Pose::fold_tree(), protocols::loophash::get_rt_over_leap_fast(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::offset, protocols::make_rot_lib::PEPTIDE, protocols::loophash::BackboneSegment::read_from_pose(), core::pose::Pose::size(), protocols::hybridization::t, and protocols::loophash::TR().
Referenced by create_db(), and extract_data_from_pose().
void protocols::loophash::LoopHashLibrary::extract_data_from_pose | ( | core::pose::Pose & | pose | ) |
References extract_data_from_pose(), and core::pose::Pose::size().
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inlineoverridevirtual |
Generates a new Mover object freshly created with the default ctor.
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.
void protocols::loophash::LoopHashLibrary::get_all | ( | core::pose::Pose & | pose, |
std::vector< core::io::silent::SilentStructOP > & | lib_structs, | ||
core::Size | start_res = 1 , |
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core::Size | stop_res = 0 , |
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core::Real | min_bbrms = 0.0 , |
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core::Real | max_bbrms = 100000.0 , |
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core::Real | min_rms = 0.0 , |
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core::Real | max_rms = 100.0 |
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References protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::Loops::add_loop(), protocols::loophash::BackboneSegment::apply_to_pose(), bbdb_, core::scoring::CA_rmsd(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::LoopHashMap::get_loop_size(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), protocols::loophash::get_rt_over_leap(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LoopHashMap::lookup(), protocols::loophash::LeapIndex::offset, options2_, options_, protocols::loophash::BackboneSegment::read_from_pose(), core::scoring::rg, scorefxn_cen_cst_, scorefxn_rama_cst_, core::kinematics::MoveMap::set_bb(), core::pose::Pose::size(), protocols::hybridization::t, protocols::loophash::TR(), and core::pose::transfer_phi_psi().
Referenced by apply().
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inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
LoopHashMap const & protocols::loophash::LoopHashLibrary::gethash | ( | core::Size | size | ) | const |
References hash_.
Referenced by apply_random(), extract_data_from_pose(), get_all(), merge(), test_loop_sample(), and test_saving_library().
LoopHashMap & protocols::loophash::LoopHashLibrary::gethash | ( | core::Size | size | ) |
References hash_.
void protocols::loophash::LoopHashLibrary::graft_loop | ( | const core::pose::Pose & | src_pose, |
core::pose::Pose & | tgt_pose, | ||
protocols::loops::Loop | myloop | ||
) |
References protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::Loops::add_loop(), core::scoring::CA_rmsd(), core::optimization::AtomTreeMinimizer::run(), scorefxn_cen_cst_, scorefxn_rama_cst_, core::kinematics::MoveMap::set_bb(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loophash::TR(), and core::pose::transfer_phi_psi().
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inline |
Return a list of the loop lengths present in the library.
References hash_sizes_.
void protocols::loophash::LoopHashLibrary::load_db | ( | ) |
Only support reading from text, extra data is mandatory. Used when created merged text db.
References assigned_string_, bbdb_, db_path_, extra_, hash_, hash_sizes_, protocols::loophash::BackboneDB::read_db(), core::id::to_string(), and protocols::loophash::TR().
void protocols::loophash::LoopHashLibrary::load_mergeddb | ( | ) |
Only support reading from merged text. Extra data is optional and handled by extra_.
References assigned_num_, assigned_string_, bbdb_, db_path_, extra_, hash_, hash_sizes_, loopdb_range_, num_partitions_, protocols::loophash::BackboneDB::read_db(), core::id::to_string(), and protocols::loophash::TR().
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References loopdb_range_.
void protocols::loophash::LoopHashLibrary::mem_foot_print | ( | ) | const |
void protocols::loophash::LoopHashLibrary::merge | ( | LoopHashLibraryOP | second_lib, |
utility::vector1< core::Real > | rms_cutoffs | ||
) |
Take two LoopHash libraries and merge them.
Throws out non-unique fragments defined as follows: if a new fragment is in a bucket with a key also in the master library, and if the RMS between the new fragment and the members of the master bucket is lower than the rms_cutoff
, it is non-unique. Thus, an rms_cutoff
of zero will not throw away any fragments.
References protocols::loophash::LoopHashMap::add_leap(), bbdb_, protocols::loophash::LoopHashMap::bbdb_range(), extra_, protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::key, merge_bbdb(), protocols::loophash::LeapIndex::offset, protocols::loophash::LoopHashMap::radial_lookup_withkey(), protocols::sic_dock::range(), and protocols::loophash::TR().
bool protocols::loophash::LoopHashLibrary::merge_bbdb | ( | const BackboneDB & | second_bbdb, |
core::Size & | index_offset | ||
) |
Take two backbone databases and merge them.
Just takes Data structs from one and copies to the other
References protocols::loophash::BackboneDB::add_extra_data(), protocols::loophash::BackboneDB::add_protein(), bbdb_, extra_, protocols::loophash::BBData::extra_key, protocols::loophash::BackboneDB::extra_size(), protocols::loophash::BackboneDB::get_extra_data(), protocols::loophash::BackboneDB::get_protein(), and protocols::loophash::BackboneDB::size().
Referenced by merge().
void protocols::loophash::LoopHashLibrary::save_db | ( | ) | const |
Only support writing to text, always include extra data
References assigned_string_, bbdb_, db_path_, hash_, hash_sizes_, core::id::to_string(), protocols::loophash::TR(), and protocols::loophash::BackboneDB::write_db().
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References create_db_.
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inline |
References db_path_.
void protocols::loophash::LoopHashLibrary::set_default_score_functions | ( | ) |
References core::scoring::cbeta, core::scoring::cenpack, core::scoring::coordinate_constraint, core::scoring::env, core::scoring::hs_pair, core::scoring::pair, core::scoring::rama, core::scoring::rg, core::scoring::rsigma, scorefxn_cen_cst_, scorefxn_rama_cst_, core::scoring::sheet, core::scoring::ss_pair, and core::scoring::vdw.
Referenced by LoopHashLibrary().
void protocols::loophash::LoopHashLibrary::setup_hash_maps | ( | ) |
References hash_, hash_sizes_, and protocols::loophash::TR().
Referenced by LoopHashLibrary().
void protocols::loophash::LoopHashLibrary::sort | ( | ) |
This function destroys the backbone_index_map reference, so sorting is only done when the hash will not longer be used. Required after merging, before saving so that merged db can be loaded as slices.
References hash_, and hash_sizes_.
void protocols::loophash::LoopHashLibrary::test_loop_sample | ( | core::pose::Pose & | pose, |
core::Size | nres | ||
) |
References core::kinematics::FoldTree::add_edge(), protocols::loophash::LoopHashMap::add_leap(), protocols::loophash::BackboneDB::add_pose(), protocols::loophash::BackboneSegment::apply_to_pose(), bbdb_, do_sanity_check_, core::pose::Pose::fold_tree(), protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::LoopHashMap::get_loop_size(), protocols::loophash::LoopHashMap::get_peptide(), protocols::loophash::get_rmsd(), protocols::loophash::get_rt_over_leap(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::LeapIndex::key, protocols::loophash::LoopHashMap::lookup_withkey(), protocols::loophash::LeapIndex::offset, protocols::make_rot_lib::PEPTIDE, protocols::loophash::BackboneSegment::print(), protocols::loophash::BackboneSegment::read_from_pose(), core::pose::Pose::size(), protocols::hybridization::t, and protocols::loophash::TR().
bool protocols::loophash::LoopHashLibrary::test_saving_library | ( | core::pose::Pose | pose, |
core::Size | ir, | ||
bool | deposit | ||
) |
References protocols::loophash::BackboneDB::add_pose(), backbone_database(), bbdb_, protocols::loophash::BackboneDB::get_backbone_segment(), protocols::loophash::get_rt_over_leap_fast(), gethash(), hash_sizes_, protocols::loophash::LeapIndex::index, protocols::loophash::BackboneSegment::read_from_pose(), core::pose::Pose::size(), protocols::hybridization::t, and protocols::loophash::TR().
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Which partition slice is assigned to this library.
Referenced by create_db(), load_mergeddb(), and LoopHashLibrary().
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Need so we can set the database string once.
Referenced by create_db(), delete_db(), load_db(), load_mergeddb(), LoopHashLibrary(), and save_db().
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The backbone library for this HashLibrary (the actual data)
Referenced by apply_random(), backbone_database(), extract_data_from_pose(), get_all(), load_db(), load_mergeddb(), mem_foot_print(), merge(), merge_bbdb(), save_db(), test_loop_sample(), and test_saving_library().
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Referenced by set_create_db().
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Path to database.
Referenced by delete_db(), load_db(), load_mergeddb(), LoopHashLibrary(), save_db(), and set_db_path().
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Referenced by LoopHashLibrary(), and test_loop_sample().
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Whether this database holds extra data in the backbone database or not.
Referenced by create_db(), get_extra(), load_db(), load_mergeddb(), LoopHashLibrary(), merge(), and merge_bbdb().
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A map of Hashmaps, each for a different loop size.
Referenced by gethash(), load_db(), load_mergeddb(), mem_foot_print(), save_db(), setup_hash_maps(), and sort().
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Kind-of a redundant store of sizes (remove this?)
Referenced by apply_random(), delete_db(), extract_data_from_pose(), get_all(), hash_sizes(), load_db(), load_mergeddb(), LoopHashLibrary(), mem_foot_print(), merge(), save_db(), setup_hash_maps(), sort(), test_loop_sample(), and test_saving_library().
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The proteins of the backbone database that are loaded (when loading a merged database, otherwise (0,0))
Referenced by load_mergeddb(), loopdb_range(), and LoopHashLibrary().
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The number of partitions the database is split into.
Referenced by create_db(), load_mergeddb(), and LoopHashLibrary().
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Referenced by get_all().
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Referenced by get_all().
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Referenced by get_all(), graft_loop(), and set_default_score_functions().
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Referenced by get_all(), graft_loop(), and set_default_score_functions().