Rosetta Core  2014.35
Classes | Typedefs | Functions
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

Function Documentation

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

References read_bytes().

int core::io::serialization::size ( PipeSP  p)

Referenced by core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_substitution(), core::sequence::PairScoringScheme::add_scored_pair(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), 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(), core::io::rna::RDAT::check_rdat(), core::pose::PDBInfo::check_residue_records_size(), core::io::silent::ProteinSilentStruct_Template< T >::chi(), core::conformation::symmetry::comma_strings_to_vector_map(), 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(), core::conformation::Residue::copy_residue_connections(), core::pack::interaction_graph::HPatchEdge< V, E, G >::count_dynamic_memory(), 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(), core::pack::rotamer_set::ContinuousRotamerSet::determine_rotcounts_for_restype(), core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::enumerate_chi_sets(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), core::io::rna::RDAT::fill_data_from_features(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), core::fragment::picking_old::vall::VallLibrarian::fragments(), core::fragment::FragSet::generate_insert_map(), core::io::rna::get_rna_data_info(), core::pack::interaction_graph::SymmLinearMemEdge::get_two_body_table_size(), core::pack::interaction_graph::LinearMemEdge::get_two_body_table_size(), core::id::SequenceMapping::identity(), core::init::init(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), core::pose::datacache::CacheableDataType::initialize_name_map(), core::pack::dunbrack::load_unboundrot(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::optimization::SimpleDerivCheckResult::nsteps(), core::io::rna::RDAT::output_data(), core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(), core::pack::dunbrack::SingleResiduePeptoidLibrary::packed_rotno_2_rotwell(), core::pack::annealer::RotamerAssigningAnnealer::pick_a_rotamer(), core::scoring::NeighborList::prepare_for_scoring(), core::io::silent::ScoreJumpFileSilentStruct::print_conformation(), core::io::raw_data::DecoyStruct::print_conformation(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), core::import_pose::read_additional_pdb_data(), read_binary(), core::scoring::packing::HolesParamsRes::read_data_file(), core::scoring::rna::data::RNA_DMS_Potential::read_DMS_stats_file(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(), core::io::rna::RDAT::read_rdat_file(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions(), core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::fragment::SecondaryStructure::SecondaryStructure(), core::chemical::ResidueType::select_orient_atoms(), core::grid::CartGrid< T >::serialize(), core::graph::ArrayPool< double >::set_array_size(), core::graph::ArrayPool< double >::set_block_size(), core::scoring::FACTSPotential::set_default(), core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue(), core::io::sequence_comparation::DesignContrast::setPdbCodes(), core::pack::scmin::CartSCMinMinimizerMap::setup(), core::scoring::NeighborList::setup(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), core::scoring::constraints::SequenceProfileConstraint::show(), core::pack::dunbrack::RotamerConstraint::show(), core::sequence::simple_mapping_from_file(), core::io::pdb::split(), core::scoring::methods::SuckerEnergy::SuckerEnergy(), core::scoring::etable::etrie::TrieCountPairGeneric::TrieCountPairGeneric(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::update_calc_chem_shift_list(), core::pack::interaction_graph::HPatchEdge< V, E, G >::update_state_at_neighbor(), core::sequence::MatrixScoringScheme::values_for_aa(), 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 
)
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 ( T  x,
BUFFER &  buf 
)
static

Helper functions to read/write any single primitive type.

References write_bytes().