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Rosetta Protocols
2014.35
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#include <HierarchicalLevel.hh>
Private Member Functions | |
void | sort_pool (Pool_RMSD_OP &pool_ptr) |
core::Size | find_address (Address &query, utility::vector1< Address > &addresses) |
void | string_to_address (std::string &, Address &) |
void | address_to_string (std::string &, Address &) |
void | sort_addresses (utility::vector1< Address > &addresses) |
bool | less_than (Address &addr1, Address &addr2) |
void | max_level_index (Address &) |
void | reset (Address &addr, utility::vector1< core::Real > &rms) |
void | print_address (Address &address) |
core::Size | num_matching_levels (Address &address1, Address &address2) |
void | add_elem_to_cache (FArray2D_double &coords, std::string &tag, Address &input_addr) |
std::list< PoolData >::iterator | find (Address &address) |
PoolData | load_pool (Address &address) |
Additional Inherited Members | |
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core::Size | natom () const |
ObjexxFCL::FArray3D_double const & | coords () const |
std::string const & | tag (core::Size index) const |
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::HierarchicalLevel | ( | core::Size | nlevels, |
std::string | filename | ||
) |
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::HierarchicalLevel | ( | core::Size | nlevels | ) |
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::HierarchicalLevel | ( | core::Size | level, |
core::Size | max_levels | ||
) |
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References find(), basic::HIERARCHICAL_ADD_ELEM_TO_CACHE, max_cache_size_, pool_cache_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::Pool_RMSD(), PROF_START, PROF_STOP, runtime_assert, and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag().
Referenced by add_new().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new | ( | core::pose::Pose const & | pose, |
std::string & | tag, | ||
Address & | address, | ||
bool | write_to_file, | ||
core::Size | new_level | ||
) |
Referenced by add_new().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new | ( | core::io::silent::SilentStruct & | , |
std::string & | tag, | ||
Address & | address, | ||
bool | write_to_file, | ||
core::Size | new_level | ||
) |
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new | ( | FArray2D_double & | coord, |
std::string & | tag, | ||
Address & | address | ||
) |
References add_new().
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_new | ( | FArray2D_double & | coord, |
std::string & | tag, | ||
Address & | address, | ||
bool | resolve_remaining_levels | ||
) |
References add_elem_to_cache(), address(), address_exists_in_cache(), find(), has_next_level(), basic::HIERARCHICAL_ADD, level_, level_find(), next_level_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pool_, pool_cache_, pool_exists(), PROF_START, PROF_STOP, runtime_assert, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::tag(), protocols::canonical_sampling::mc_convergence_checks::TR, and utility_exit.
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::add_to_top_level | ( | FArray2D_double & | coords, |
std::string & | tag | ||
) |
utility::vector1< core::Size > & protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::address | ( | core::Size | index | ) |
References pool_cache_.
Referenced by add_new().
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::address_exists_in_cache | ( | Address & | addr | ) |
References find(), has_next_level(), level_, next_level_, and pool_cache_.
Referenced by add_new().
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References q.
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::clear | ( | ) |
References pool_cache_.
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::debug_print_addresses | ( | ) |
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::debug_print_hierarchy | ( | ) |
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::debug_print_size_per_level | ( | ) |
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::equal_addresses | ( | Address & | address1, |
Address & | address2 | ||
) |
Referenced by find(), and find_address().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::evaluate | ( | core::pose::Pose const & | pose, |
std::string & | best_decoy, | ||
utility::vector1< core::Real > & | best_rmsd, | ||
Address & | address | ||
) |
Referenced by evaluate().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::evaluate | ( | core::io::silent::SilentStruct const & | , |
std::string & | best_decoy, | ||
utility::vector1< core::Real > & | best_rmsd, | ||
Address & | address | ||
) |
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::evaluate | ( | FArray2D_double & | coords, |
std::string & | best_decoy, | ||
utility::vector1< core::Real > & | best_rmsd, | ||
Address & | address | ||
) |
References evaluate().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::evaluate | ( | FArray2D_double & | coords, |
std::string & | best_decoy, | ||
utility::vector1< core::Real > & | best_rmsd, | ||
Address & | address, | ||
bool | reset_all_levels, | ||
bool | load_if_missing | ||
) |
References find(), has_next_level(), basic::HIERARCHICAL_EVALUATE, level_, lib_full_path(), load_pool(), max_cache_size_, max_levels_, next_level_, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::pool_, pool_cache_, print_address(), PROF_START, PROF_STOP, radius_, reset(), round(), runtime_assert, and protocols::canonical_sampling::mc_convergence_checks::TR.
std::string & protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::filename | ( | ) |
References filename_.
Referenced by pool_exists(), and write_headers_to_hierarchy().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::fill_top_level | ( | Pool_RMSD_OP & | top_level_pool | ) |
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References equal_addresses(), basic::HIERARCHICAL_FIND, pool_cache_, PROF_START, and PROF_STOP.
Referenced by add_elem_to_cache(), add_new(), address_exists_in_cache(), evaluate(), and level_find().
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References equal_addresses(), basic::HIERARCHICAL_FIND_ADDRESS, PROF_START, and PROF_STOP.
Referenced by sort_pool().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::first_zero_pos | ( | Address & | address | ) |
Referenced by level_find().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::get_addresses_at_level | ( | utility::vector1< Address > & | addresses_at_level | ) |
References pool_cache_.
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::has_next_level | ( | ) |
References next_level_.
Referenced by add_new(), address_exists_in_cache(), debug_print_addresses(), debug_print_hierarchy(), debug_print_size_per_level(), evaluate(), level_find(), level_radius(), level_size(), max_cache_size(), and max_level_index().
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Referenced by sort_addresses().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::level | ( | ) |
References level_.
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::level_find | ( | Address & | address, |
core::Size const & | level, | ||
std::list< PoolData >::iterator & | itr | ||
) |
References find(), first_zero_pos(), has_next_level(), basic::HIERARCHICAL_FIND, level_, load_pool(), next_level_, pool_cache_, pool_exists(), PROF_START, PROF_STOP, runtime_assert, and protocols::canonical_sampling::mc_convergence_checks::TR.
Referenced by add_new(), and pool_size().
core::Real protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::level_radius | ( | core::Size | level | ) |
References has_next_level(), level_, next_level_, radius_, and runtime_assert.
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::level_size | ( | core::Size | level | ) |
References has_next_level(), level_, max_levels_, next_level_, runtime_assert, and size().
std::string protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::lib_full_path | ( | Address & | address | ) |
core::Size evaluate( FArray2D_double&, std::string & best_decoy, core::Real & best_rmsd, Address & best_indices, utility::vector1< Address > & prev_address, utility::vector1< core::Size > & prev_indices ); std::list<PoolData> & get_cache(); //for debugging
References utility::file::FileName::base(), mc::hierarchical_pool, cluster::K_n_sub, basic::LIB_FULL_PATH, option, utility::file::FileName::path(), PROF_START, PROF_STOP, runtime_assert, s, and protocols::canonical_sampling::mc_convergence_checks::TR.
Referenced by evaluate(), load_pool(), max_level_index(), pool_exists(), and write_headers_to_hierarchy().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::max_cache_size | ( | core::Size | max_size | ) |
References has_next_level(), max_cache_size_, and next_level_.
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::max_cache_size | ( | ) |
References max_cache_size_.
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References utility::file::file_exists(), has_next_level(), level_, lib_full_path(), max_levels_, next_free_address_index_, and next_level_.
Referenced by write_headers_to_hierarchy().
HierarchicalLevelOP protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::next_level | ( | ) |
References next_level_.
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::nlevels | ( | ) |
References max_levels_.
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References runtime_assert.
bool protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::pool_exists | ( | Address & | address | ) |
References utility::file::file_exists(), filename(), and lib_full_path().
Referenced by add_new(), and level_find().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::pool_size | ( | Address & | address, |
core::Size | level | ||
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References protocols::canonical_sampling::mc_convergence_checks::TR.
Referenced by debug_print_hierarchy(), evaluate(), and print_addresses_at_level().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::print_addresses_at_level | ( | ) |
References pool_cache_, and print_address().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::radius | ( | core::Real | radius | ) |
core::Real protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::radius | ( | ) |
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this function not used core::Size HierarchicalLevel::next_free_address( Address & query_address, core::Size level ) { runtime_assert( level != 1 ); core::Size next_index = 0; if( level_ != level && has_next_level() ) { next_index = next_level_->next_free_address( query_address, level ); } else { runtime_assert( level_ == level ); if ( next_free_address_index_ > 0 ) { next_free_address_index_++; next_index = next_free_address_index_; } else { runtime_assert( first_zero_pos( query_address ) == level ); //this level is unresolved Address address = query_address; address[ level_ ] = pool_cache_.size() + 1; for( core::Size ii = level_ + 1; ii <= address.size(); ii++ ) { address[ ii ] = 0; //just to be safe } std::string test_file = lib_full_path( address ); while( utility::file::file_exists( test_file ) ) { address[ level_ ] = address[ level_ ] + 1; test_file = lib_full_path( address ); } next_free_address_index_ = address[ level_ ]; next_index = next_free_address_index_; } } return next_index; }
Referenced by evaluate().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::round | ( | core::Real & | rmsd | ) |
References basic::HIERARCHICAL_ROUND, PROF_START, PROF_STOP, remainder(), t, and protocols::canonical_sampling::mc_convergence_checks::TR.
Referenced by evaluate(), and test_round().
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::size | ( | ) |
References pool_cache_.
Referenced by debug_print_hierarchy(), level_size(), and sort_pool().
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References basic::HIERARCHICAL_SORT_ADDRESSES, less_than(), protocols::ddg::min_index(), PROF_START, and PROF_STOP.
Referenced by sort_pool().
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References protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::coords(), find_address(), utility::pointer::owning_ptr< T >::get(), PROF_START, PROF_STOP, runtime_assert, size(), sort_addresses(), basic::SORT_POOL, string_to_address(), tags, and protocols::canonical_sampling::mc_convergence_checks::TR.
Referenced by fill_top_level(), and load_pool().
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References length.
Referenced by sort_pool().
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::test_round | ( | ) |
References exit, round(), t, and protocols::canonical_sampling::mc_convergence_checks::TR.
core::Size protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::top_level_pool_size | ( | ) |
void protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel::write_headers_to_hierarchy | ( | core::io::silent::SilentStructOP & | ss | ) |
References filename(), lib_full_path(), max_level_index(), and max_levels_.
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Referenced by filename().
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Referenced by add_new(), add_to_top_level(), address_exists_in_cache(), debug_print_addresses(), debug_print_hierarchy(), debug_print_size_per_level(), evaluate(), fill_top_level(), HierarchicalLevel(), level(), level_find(), level_radius(), level_size(), max_level_index(), and top_level_pool_size().
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Referenced by add_elem_to_cache(), evaluate(), and max_cache_size().
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Referenced by evaluate(), HierarchicalLevel(), level_size(), max_level_index(), nlevels(), and write_headers_to_hierarchy().
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Referenced by max_level_index().
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Referenced by HierarchicalLevel().
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std::string lib_full_path(std::string tag_origin );
Referenced by add_elem_to_cache(), add_new(), add_to_top_level(), address(), address_exists_in_cache(), clear(), debug_print_addresses(), debug_print_hierarchy(), debug_print_size_per_level(), evaluate(), fill_top_level(), find(), get_addresses_at_level(), HierarchicalLevel(), level_find(), print_addresses_at_level(), size(), and top_level_pool_size().
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Referenced by evaluate(), HierarchicalLevel(), level_radius(), and radius().