Classes
struct	BUFFER

Typedefs
typedef std::vector < core::pose::PoseSP >	Pipe

typedef boost::shared_ptr< Pipe >	PipeSP

typedef std::map< std::string, PipeSP >	PipeMap

typedef boost::shared_ptr < PipeMap >	PipeMapSP

typedef boost::weak_ptr< PipeMap >	PipeMapWP

Functions
Pipe &	each (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::vector< core::pose::PoseSP > core::io::serialization::Pipe

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::scoring::sasa::LeGrandSasa::calculate(), 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::vdwaals::VDW_Energy::create_rotamer_trie(), core::scoring::methods::MMLJEnergyInter::create_rotamer_trie(), core::scoring::elec::FA_ElecEnergy::create_rotamer_trie(), core::scoring::etable::BaseEtableEnergy< Derived >::create_rotamer_trie(), core::fragment::picking_old::vall::eval::ABEGOEval::eval_impl(), core::pose::symmetry::get_intracomponent_and_interneighbor_subs(), core::pose::symmetry::get_intracomponent_and_intraneighbor_subs(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), core::pack::task::parse_resfile(), core::scoring::packing::HolesParams::read_data_file(), core::scoring::packing::HolesParams::sep_ss(), core::scoring::methods::LKB_ResidueInfo::setup_atom_weights(), and core::chemical::ResidueTypeKinWriter::write_restype().

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 )

References core::conformation::Residue::aa(), and core::chemical::aa_vrt.

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

Referenced by check_binary_chars(), check_binary_unsigned_int(), and read_binary().

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(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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
	)

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

Referenced by read_binary(), and read_bytes().

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::chemical::ResidueType::assign_internal_coordinates(), 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::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::RotamericSingleResidueDunbrackLibrary< T >::enumerate_chi_sets(), core::scoring::methods::ResidualDipolarCouplingEnergy::eval_dipolar(), 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::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::scoring::Ramachandran::init_rama_sampling_table(), core::scoring::Ramachandran2B::init_rama_sampling_table_left(), core::scoring::Ramachandran2B::init_rama_sampling_table_right(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), core::pack::dunbrack::load_unboundrot(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::optimization::SimpleDerivCheckResult::nsteps(), core::pack::dunbrack::SingleResidueDunbrackLibrary::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::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_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
	)

References write_binary(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void core::io::serialization::write_binary	(	const core::pose::Pose &	pose,
		BUFFER &	buf
	)

Read/Write a pose to a file.

References core::conformation::Residue::atoms(), core::conformation::Residue::chain(), core::pose::Pose::fold_tree(), j, core::pose::Pose::jump(), core::chemical::ResidueTypeSet::name(), core::chemical::ResidueType::name(), core::pose::Pose::num_jump(), residue, core::pose::Pose::residue(), core::chemical::ResidueType::residue_type_set(), core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), write_binary(), and write_binary_chars().

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().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation