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core::io::serialization Namespace Reference

Classes

struct  BUFFER
 

Typedefs

typedef std::vector
< core::pose::PoseSP
Pipe
 
typedef boost::shared_ptr< PipePipeSP
 
typedef std::map< std::string,
PipeSP
PipeMap
 
typedef boost::shared_ptr
< PipeMap
PipeMapSP
 
typedef boost::weak_ptr< PipeMapPipeMapWP
 

Functions

Pipeeach (PipeSP p)
 
core::pose::PoseSP at (PipeSP p, int idx)
 
PipeSP clone (PipeSP p)
 
int size (PipeSP p)
 
void insert (PipeMapSP p, std::string const &pipename, core::pose::PoseSP pose)
 
PipeSP at (PipeMapSP p, std::string const &pipename)
 
PipeMapSP clone (PipeMapSP p)
 
PipeMapSP inputPipeMap (core::pose::PoseSP p)
 
bool is_pseudoresidue (const conformation::Residue &residue)
 
static void swap_bytes (char *, unsigned int)
 
void write_bytes (char *x, unsigned int n, BUFFER &buf)
 Helper functions to read/write raw memory. More...
 
void read_bytes (char *x, unsigned int n, BUFFER &buf)
 
template<typename T >
static void write_bytes (T x, BUFFER &buf)
 Helper functions to read/write any single primitive type. More...
 
template<typename T >
static void read_bytes (T &x, BUFFER &buf)
 
void write_binary (char x, BUFFER &buf)
 Read/write a single primitive type to a buf. More...
 
void read_binary (char &x, BUFFER &buf)
 
void write_binary (bool x, BUFFER &buf)
 
void read_binary (bool &x, BUFFER &buf)
 
void write_binary (unsigned int x, BUFFER &buf)
 
void read_binary (unsigned int &x, BUFFER &buf)
 
void write_binary (float x, BUFFER &buf)
 
void read_binary (float &x, BUFFER &buf)
 
void write_binary (double x, BUFFER &buf)
 
void read_binary (double &x, BUFFER &buf)
 
void write_binary (const utility::vector1_bool &x, BUFFER &buf)
 Read/write simple structure to a buf. More...
 
void read_binary (utility::vector1_bool &x, BUFFER &buf)
 
void write_binary (const std::vector< std::string > &x, BUFFER &buf)
 
void read_binary (std::vector< std::string > &x, BUFFER &buf)
 
void write_binary (const std::string &x, BUFFER &buf)
 
void read_binary (std::string &x, BUFFER &buf)
 
void write_binary (const core::Vector &x, BUFFER &buf)
 
void read_binary (core::Vector &x, BUFFER &buf)
 
void check_binary_unsigned_int (unsigned int x, BUFFER &buf)
 Utility read/write. More...
 
void write_binary_chars (const char *x, BUFFER &buf)
 
void check_binary_chars (const char *x, BUFFER &buf)
 
void write_binary (const core::pose::Pose &pose, BUFFER &buf)
 Read/Write a pose to a file. More...
 
void read_binary (core::pose::Pose &pose, BUFFER &buf)
 

Typedef Documentation

typedef std::map< std::string, PipeSP > core::io::serialization::PipeMap
typedef boost::shared_ptr< PipeMap > core::io::serialization::PipeMapSP
typedef boost::weak_ptr< PipeMap > core::io::serialization::PipeMapWP
typedef boost::shared_ptr< Pipe > core::io::serialization::PipeSP

Function Documentation

core::pose::PoseSP core::io::serialization::at ( PipeSP  p,
int  idx 
)

Referenced by core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pose::Pose::center(), core::scoring::packing::compute_dec15_score(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_rosettaholes_score(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::hackelec::HackElecEnergy::create_rotamer_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie(), protocols::flexpep_docking::FlexPepDockingFlags::FlexPepDockingFlags(), protocols::swa::rna::get_atom_coordinates(), protocols::swa::rna::get_binary_rna_silent_struct_safe(), protocols::ligand_docking::ligand_options::Interface::get_interface_residues(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), protocols::ligand_docking::ligand_options::Interface::get_near_interface_residues(), protocols::swa::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2star(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer::moving_res_contact_filter(), core::pack::task::parse_resfile(), protocols::swa::rna::print_atom_info(), core::scoring::packing::HolesParams::read_data_file(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::scoring::packing::HolesParams::sep_ss(), protocols::swa::rna::set_to_origin(), protocols::swa::rna::translate_then_rotate_pose(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), and protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen().

PipeSP core::io::serialization::at ( PipeMapSP  p,
std::string const &  pipename 
)
void core::io::serialization::check_binary_chars ( const char *  x,
BUFFER &  buf 
)

References read_binary(), and THROW_EXCEPTION.

Referenced by read_binary().

void core::io::serialization::check_binary_unsigned_int ( unsigned int  x,
BUFFER &  buf 
)

Utility read/write.

References read_binary(), and THROW_EXCEPTION.

Referenced by read_binary().

PipeSP core::io::serialization::clone ( PipeSP  p)
PipeMapSP core::io::serialization::clone ( PipeMapSP  p)
Pipe& core::io::serialization::each ( PipeSP  p)
PipeMapSP core::io::serialization::inputPipeMap ( core::pose::PoseSP  p)
void core::io::serialization::insert ( PipeMapSP  p,
std::string const &  pipename,
core::pose::PoseSP  pose 
)
bool core::io::serialization::is_pseudoresidue ( const conformation::Residue &  residue)
void core::io::serialization::read_binary ( char &  x,
BUFFER &  buf 
)
void core::io::serialization::read_binary ( bool x,
BUFFER &  buf 
)

References read_bytes().

void core::io::serialization::read_binary ( unsigned int x,
BUFFER &  buf 
)

References read_bytes().

void core::io::serialization::read_binary ( float &  x,
BUFFER &  buf 
)

References read_bytes().

void core::io::serialization::read_binary ( double &  x,
BUFFER &  buf 
)

References read_bytes().

void core::io::serialization::read_binary ( utility::vector1_bool &  x,
BUFFER &  buf 
)

References read_binary(), and size().

void core::io::serialization::read_binary ( std::vector< std::string > &  x,
BUFFER &  buf 
)

References read_binary(), and size().

void core::io::serialization::read_binary ( std::string &  x,
BUFFER &  buf 
)

References read_binary(), and size().

void core::io::serialization::read_binary ( core::Vector x,
BUFFER &  buf 
)

References read_binary().

void core::io::serialization::read_binary ( core::pose::Pose pose,
BUFFER &  buf 
)
void core::io::serialization::read_bytes ( char *  x,
unsigned int  n,
BUFFER &  buf 
)
template<typename T >
static void core::io::serialization::read_bytes ( T &  x,
BUFFER &  buf 
)
static
int core::io::serialization::size ( PipeSP  p)

Referenced by core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_substitution(), protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::jd2::archive::VarianceStatisticsArchive::add_evaluated_structure(), protocols::jd2::archive::EvaluatedArchive::add_evaluated_structure(), protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::genetic_algorithm::GeneticAlgorithm::add_parents_from_current_generation(), core::sequence::PairScoringScheme::add_scored_pair(), protocols::abinitio::IterativeBase::add_structure(), protocols::jd2::archive::DebugArchive::add_structure(), protocols::rna::FragmentLibrary::add_torsion(), protocols::sparta::GDB::addVAR(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::enzdes::ApplyRandomStoredRBConf::apply(), protocols::enzdes::MinimizeStoredRBConfs::apply(), protocols::enzdes::DiversifyStoredRBConfs::apply(), protocols::viewer::triangleIterator::aquireNextQueue(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), core::chemical::ResidueType::assign_internal_coordinates(), core::pose::datacache::ObserverCache::attach(), protocols::motifs::MotifSearch::bp_motifhits(), protocols::motifs::MotifSearch::bp_rotamers(), protocols::match::downstream::SecondaryMatcherToDownstreamResidue::build(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), protocols::design_opt::calc_pareto_front(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::scoring::methods::LK_hack::calculate_orientation_vectors_and_pseudo_base_atoms(), protocols::jd2::archive::ArchiveManager::cancel_batch(), protocols::hybridization::CartesianHybridize::CartesianHybridize(), protocols::loops::loop_closure::ccd::ccd_moves(), protocols::match::Matcher::check_downstream_hit_incompatibility(), protocols::loops::loop_closure::ccd::check_overlap_pos(), core::pose::PDBInfo::check_residue_records_size(), protocols::loops::loop_closure::ccd::check_torsions(), core::io::silent::ProteinSilentStruct_Template< T >::chi(), protocols::hybridization::ChunkTrialMover::ChunkTrialMover(), protocols::scoring::ImplicitFastClashCheck::clash_count(), protocols::jd2::SingleFileBuffer::close(), protocols::abinitio::HedgeArchive::collect(), protocols::toolbox::match_enzdes_util::InvrotTarget::collect_all_inverse_rotamers(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), protocols::noesy_assign::StructureDependentPeakCalibrator::collect_upperbound_statistics(), protocols::noesy_assign::Resonance::combine(), core::conformation::symmetry::comma_strings_to_vector_map(), protocols::protein_interface_design::filters::BoltzmannFilter::compute(), protocols::simple_filters::Operator::compute(), protocols::abinitio::IterativeBase::compute_cores(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::etable::etrie::CountPairDataGeneric::conn_dist(), protocols::rna::RNA_Fragments::convert_based_on_match_type(), protocols::rna::convert_based_on_match_type(), core::conformation::Residue::copy_residue_connections(), protocols::frag_picker::GrabAllCollector::count_candidates(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::count_candidates(), core::pack::interaction_graph::HPatchEdge< V, E, G >::count_dynamic_memory(), protocols::cluster::ClusterBase::create_constraints(), core::scoring::electron_density::ElectronDensity::dCCdx_aacen(), core::scoring::electron_density::ElectronDensity::dCCdx_pat(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::kinematics::FoldTree::delete_segment(), protocols::frags::TorsionFragmentLibrary::derive_from_src_lib(), core::pose::datacache::ObserverCache::detach(), core::pack::rotamer_set::ContinuousRotamerSet::determine_rotcounts_for_restype(), protocols::frag_picker::scores::ProfileScoreStructL1::do_caching(), protocols::frag_picker::scores::ProfileScoreL1::do_caching(), protocols::frag_picker::scores::TalosSSSimilarity::do_caching(), protocols::frag_picker::scores::SecondarySimilarity::do_caching(), protocols::frag_picker::scores::do_one_line(), protocols::cluster::ClusterPhilStyle::do_redistribution(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::noesy_assign::CrossPeak::eliminated(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), protocols::multistate_design::MultiStateFitnessFunction::evaluate(), protocols::jd2::JobOutputter::evaluate(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomAngleSecMatchRPE::evaluate_residues(), protocols::match::downstream::AtomDihedralSecMatchRPE::evaluate_residues(), protocols::hybridization::HybridizeProtocol::expand_domains_to_full_length(), protocols::motifs::MotifDnaPacker::expand_motifs(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::genetic_algorithm::GeneticAlgorithm::fill_by_crossover(), protocols::genetic_algorithm::GeneticAlgorithm::fill_by_mutation(), core::io::silent::BinaryRNASilentStruct::fill_pose(), protocols::genetic_algorithm::GeneticAlgorithm::fill_with_random_entities(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), protocols::rna::RNA_ChunkLibrary::find_res_maps(), protocols::coarse_rna::CoarseRNA_Fragments::find_source_positions(), protocols::match::Matcher::finish_hit_generation_for_constraint(), protocols::jd2::SingleFileBuffer::flush(), core::fragment::picking_old::vall::VallLibrarian::fragments(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::jd2::archive::DebugArchive::generate_batch(), protocols::noesy_assign::StructureDependentPeakCalibrator::generate_constraints(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::fragment::FragSet::generate_insert_map(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::frag_picker::scores::AtomBasedConstraintsScore::get_atom_coordinates(), protocols::frag_picker::JCouplingIO::get_data(), protocols::frags::VallData::get_frags(), protocols::frags::RMSVallData::get_frags(), protocols::ligand_docking::ligand_options::Interface::get_interface_residues(), protocols::ligand_docking::ligand_options::Interface::get_near_interface_residues(), protocols::loops::loop_closure::ccd::get_overlap_pos(), protocols::toolbox::pose_metric_calculators::RotamerRecovery::get_rotamer_recovery(), protocols::loops::loop_closure::ccd::get_torsion_axis(), core::pack::interaction_graph::SymmLinearMemEdge::get_two_body_table_size(), core::pack::interaction_graph::LinearMemEdge::get_two_body_table_size(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), protocols::frag_picker::scores::AtomBasedConstraintsScore::has_atom(), core::id::SequenceMapping::identity(), protocols::abinitio::IterativeBase::idle(), core::init(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::scoring::Ramachandran::init_rama_sampling_table(), core::scoring::Ramachandran2B::init_rama_sampling_table_left(), core::scoring::Ramachandran2B::init_rama_sampling_table_right(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_extra_rotamer_perturbations(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), protocols::match::Matcher::initialize_from_file(), protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), protocols::simple_moves::GreenPacker::initialize_internal_correspondence_data(), protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line(), protocols::swa::rna::StepWiseRNA_RotamerGenerator::initialize_rotamers(), protocols::match::Matcher::initialize_scaffold_build_points(), protocols::frags::TorsionFragment::insert(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::rna::FullAtomRNA_Fragments::insert_fragment(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::features::HBondFeatures::insert_site_environment_row(), protocols::genetic_algorithm::DiscreteRandomizer::library_size(), protocols::genetic_algorithm::PositionSpecificRandomizer::library_size(), protocols::cluster::ClusterBase::limit_groups(), protocols::cluster::ClusterBase::limit_total_structures(), protocols::jd2::archive::MPIArchiveJobDistributor::load_new_batch(), protocols::toolbox::KClusterData::load_silent_files(), core::pack::dunbrack::load_unboundrot(), protocols::comparative_modeling::loops_are_closed(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::memory_use(), protocols::evaluation::MetaPoseEvaluator::name(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::jd2::archive::MPIArchiveJobDistributor::notify_archive(), core::optimization::SimpleDerivCheckResult::nsteps(), protocols::canonical_sampling::ParallelTempering::operator=(), protocols::toolbox::operator>>(), protocols::frag_picker::FragmentPicker::output_fragments(), core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag(), core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), protocols::frag_picker::FragmentPicker::pick_candidates(), protocols::rna::RNA_Fragments::pick_fragment_library(), protocols::rna::FullAtomRNA_Fragments::pick_fragment_library(), protocols::abinitio::Template::pick_large_frags(), protocols::hybridization::ChunkTrialMover::pick_random_template(), protocols::antibody::Antibody::populate_all_cdrs(), protocols::match::Matcher::predict_n_matches_for_hit_subsets(), protocols::match::Matcher::prepare_for_hit_generation_for_constraint(), core::scoring::NeighborList::prepare_for_scoring(), protocols::frags::TorsionFragmentLibrary::print(), protocols::cluster::ClusterBase::print_cluster_assignment(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), core::io::raw_data::DecoyStruct::print_conformation(), core::io::silent::BinaryRNASilentStruct::print_conformation(), core::io::silent::BinaryProteinSilentStruct::print_conformation(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), protocols::cluster::ClusterBase::print_raw_numbers(), protocols::frag_picker::GrabAllCollector::print_report(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::print_report(), protocols::cluster::ClusterBase::print_summary(), protocols::wum::MPI_WorkUnitManager_Slave::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Emperor::process_inbound_wus(), protocols::wum::DatabaseQueryWorkUnitManager< T >::process_inbound_wus(), protocols::wum::MPI_Relax::process_inbound_wus_master(), protocols::wum::MPI_WorkUnitManager::process_incoming_msgs(), protocols::simple_filters::SymmetricMotifFilter::process_motifs(), protocols::wum::MPI_WorkUnitManager_Slave::process_outbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_outbound_wus(), protocols::frag_picker::scores::ProfileScoreL1::ProfileScoreL1(), protocols::frag_picker::scores::ProfileScoreStructL1::ProfileScoreStructL1(), protocols::jd2::archive::ArchiveManager::queue_batch(), protocols::wum::WorkUnitBase::raw_data_dump(), read_binary(), core::scoring::packing::HolesParamsRes::read_data_file(), protocols::noesy_assign::NoesyModule::read_input_files(), protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs(), protocols::anchored_design::AnchorMoversData::read_options(), protocols::enzdes::enzutil::read_pose_from_pdb(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::jd2::archive::MPIArchiveJobDistributor::receive_batch(), protocols::frag_picker::nonlocal::NonlocalFrags::recover_checkpoint(), protocols::loops::loop_closure::ccd::refold_loop_torsion(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint(), core::chemical::ResidueType::reorder_primary_data(), protocols::match::downstream::AtomDistanceSecMatchRPE::require_candidate_residue_atoms_to_lie_near_target_atom(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::chemical::ResidueType::residue_connection_id_for_atom(), protocols::cluster::ClusterBase::return_lowest_poses_in_clusters(), protocols::cluster::ClusterBase::return_top_poses_in_clusters(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::jd2::MpiFileBuffer::run(), protocols::wum::WorkUnit_MoverWrapper::run(), protocols::toolbox::KClusterData::save_all_in_one(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::archive::ArchiveBase::save_to_file(), core::fragment::SecondaryStructure::SecondaryStructure(), protocols::loops::select_loop_frags(), protocols::loops::loop_mover::IndependentLoopMover::select_loops(), core::chemical::ResidueType::select_orient_atoms(), protocols::wum::MPI_WorkUnitManager::send_next_WU_on_request(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::sequence_space(), core::grid::CartGrid< core::Real >::serialize(), core::graph::ArrayPool< Real >::set_array_size(), core::graph::ArrayPool< Real >::set_block_size(), protocols::abinitio::FoldConstraints::set_default_options(), protocols::abinitio::ConstraintFragmentSampler::set_defaults(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::set_frames(), core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue(), protocols::match::downstream::TargetRotamerCoords::set_num_target_rotamers(), protocols::enzdes::ModifyStoredRBConfs::set_rigid_body_confs(), protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style(), core::io::sequence_comparation::DesignContrast::setPdbCodes(), protocols::swa::rna::SlicedPoseJobParameters::setup(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::scoring::NeighborList::setup(), protocols::sparta::GDB::setVAR(), core::scoring::constraints::SequenceProfileConstraint::show(), protocols::scoring::Interface::show(), core::pack::dunbrack::RotamerConstraint::show(), protocols::rotamer_recovery::PerNativeRRReporterHuman::show(), protocols::topology_broker::DofClaim::show(), core::sequence::simple_mapping_from_file(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), core::io::pdb::split(), core::scoring::methods::SuckerEnergy::SuckerEnergy(), protocols::jd2::archive::MPIArchiveJobDistributor::sync_batches(), protocols::rna::RNA_ChunkLibrary::test_matches(), protocols::rna::TorsionSet::TorsionSet(), protocols::viewer::triangleIterator::triangleIterator(), core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::trim(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::update_calc_chem_shift_list(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::update_offset_data(), core::pack::interaction_graph::HPatchEdge< V, E, G >::update_state_at_neighbor(), protocols::frag_picker::VallProvider::vallChunksFromLibrary(), core::sequence::MatrixScoringScheme::values_for_aa(), protocols::noesy_assign::PeakFileFormat::write_header(), protocols::simple_moves::DOFHistogramRecorder::write_mse_summary(), protocols::optimize_weights::PNatAAOptEPositionData::write_to_binary_file(), core::pack::scmin::CartSCMinMinimizerMap::zero_atom_derivative_vectors(), core::pack::scmin::AtomTreeSCMinMinimizerMap::zero_atom_derivative_vectors(), and core::optimization::symmetry::SymMinimizerMap::zero_torsion_vectors().

static void core::io::serialization::swap_bytes ( char *  ,
unsigned  int 
)
static

Helper function to write all binary files as little endian. If the current architecture is big endian, swap the bytes.

Referenced by read_bytes(), and write_bytes().

void core::io::serialization::write_binary ( char  x,
BUFFER &  buf 
)

Read/write a single primitive type to a buf.

Referenced by write_binary(), and write_binary_chars().

void core::io::serialization::write_binary ( bool  x,
BUFFER &  buf 
)

References write_bytes().

void core::io::serialization::write_binary ( unsigned int  x,
BUFFER &  buf 
)

References write_bytes().

void core::io::serialization::write_binary ( float  x,
BUFFER &  buf 
)

References write_bytes().

void core::io::serialization::write_binary ( double  x,
BUFFER &  buf 
)

References write_bytes().

void core::io::serialization::write_binary ( const utility::vector1_bool &  x,
BUFFER &  buf 
)

Read/write simple structure to a buf.

Read/write simple structure to a file.

References write_binary().

void core::io::serialization::write_binary ( const std::vector< std::string > &  x,
BUFFER &  buf 
)

References write_binary().

void core::io::serialization::write_binary ( const std::string &  x,
BUFFER &  buf 
)

References write_binary().

void core::io::serialization::write_binary ( const core::Vector x,
BUFFER &  buf 
)

References write_binary().

void core::io::serialization::write_binary ( const core::pose::Pose pose,
BUFFER &  buf 
)
void core::io::serialization::write_binary_chars ( const char *  x,
BUFFER &  buf 
)

References write_binary().

Referenced by write_binary().

void core::io::serialization::write_bytes ( char *  x,
unsigned int  n,
BUFFER &  buf 
)

Helper functions to read/write raw memory.

References swap_bytes(), THROW_EXCEPTION, and core::io::serialization::BUFFER::write().

Referenced by write_binary(), and write_bytes().

template<typename T >
static void core::io::serialization::write_bytes ( x,
BUFFER &  buf 
)
static

Helper functions to read/write any single primitive type.

References core::pack::interaction_graph::T(), and write_bytes().