core::io::silent Namespace Reference

Classes
class	BinarySilentStruct
	why this inheritance pathway? this makes no sense! More...
class	BinarySilentStructCreator
	creator for the BinarySilentStruct class More...
class	EnergyNames
class	ProteinSilentStruct_SinglePrecCreator
	creator for the ProteinSilentStruct_SinglePrec class More...
class	ProteinSilentStruct_Template
class	ProteinSilentStructCreator
	creator for the ProteinSilentStruct class More...
class	RNA_SilentStruct
class	RNA_SilentStructCreator
	creator for the RNA_SilentStruct class More...
class	ScoreFileSilentStruct
class	ScoreFileSilentStructCreator
	creator for the ScoreFileSilentStruct class More...
class	ScoreJumpFileSilentStruct
class	ScoreJumpFileSilentStructCreator
	creator for the ScoreJumpFileSilentStruct class More...
class	SharedSilentData
class	SilentEnergy
	Helper class for silent-file classes to keep track of energy information. More...
class	SilentFileData
	Abstract base class for classes that read and write different types of silent-files. Silent-files can contain SilentStruct objects which are expected, to be uniquely identified by some sort of string-based tag inside the file. More...
class	SilentFileLoader
class	SilentFileLoaderCreator
	creator for the SilentFileLoader class More...
class	SilentFileOptions
class	SilentFileOptionsCreator
	creator for the SilentFileOptions class More...
class	SilentStruct
class	SilentStructCreator
	Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...
class	SilentStructFactory
class	SilentStructRegistrator
	This templated class will register an instance of an SilentStructCreator (class T) with the SilentStructFactory. It will ensure that no SilentStructCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	SimpleSequenceData

Typedefs
typedef utility::pointer::owning_ptr < EnergyNames >	EnergyNamesOP
typedef ProteinSilentStruct_Template < float >	ProteinSilentStruct_SinglePrec
typedef ProteinSilentStruct_Template < core::Real >	ProteinSilentStruct
typedef utility::pointer::owning_ptr < SharedSilentData >	SharedSilentDataOP
typedef utility::pointer::owning_ptr < SimpleSequenceData >	SimpleSequenceDataOP
typedef utility::pointer::owning_ptr < SilentStruct >	SilentStructOP
typedef utility::pointer::owning_ptr < SilentStruct const >	SilentStructCOP
typedef utility::pointer::owning_ptr < ProteinSilentStruct >	ProteinSilentStructOP
typedef utility::pointer::owning_ptr < BinarySilentStruct >	BinarySilentStructOP
typedef utility::pointer::owning_ptr < RNA_SilentStruct >	RNA_SilentStructOP
typedef std::map< std::string, SilentStructOP >	Structure_Map
typedef utility::vector1 < SilentStructOP >	SilentStructOPs
typedef utility::pointer::owning_ptr < SilentFileData >	SilentFileDataOP
typedef utility::pointer::owning_ptr < SilentFileLoader >	SilentFileLoaderOP
typedef utility::pointer::owning_ptr < SilentFileLoader const >	SilentFileLoaderCOP
typedef utility::pointer::owning_ptr < SilentFileOptions >	SilentFileOptionsOP
typedef utility::pointer::owning_ptr < SilentFileOptions const >	SilentFileOptionsCOP
typedef utility::pointer::owning_ptr < SilentStructCreator >	SilentStructCreatorOP
typedef utility::pointer::owning_ptr < SilentStructCreator const >	SilentStructCreatorCOP
typedef utility::pointer::owning_ptr < SilentStructFactory >	SilentStructFactoryOP
typedef utility::pointer::owning_ptr < SequenceFactory >	SequenceFactoryOP

Enumerations
enum	SharedSilentDataType { energynames = 1, simplesequencedata }

Functions
bool	SilentEnergy_sort_by_name (const SilentEnergy &score_energy1, const SilentEnergy &score_energy2)
void	gzip (void)
	gzip all of the files in -out::file::silent(). More...
std::map< std::string, bool >	initialize_tag_is_done (std::string const &silent_file)

Variables
static basic::Tracer	pss_tr ("core.io.silent")
static basic::Tracer	tr ("core.io.silent")
static basic::Tracer	tr ("core.io.silent.ScoreFileSilentStruct")
static basic::Tracer	tr ("core.io.silent.ScoreJumpFileSilentStruct")
static basic::Tracer	tr ("core.io.silent.SilentFileData")
static numeric::random::RandomGenerator	RG (21458)
static basic::Tracer	tr ("core.io.silent.SilentStruct")
static basic::Tracer	tr ("core.io.silent")
static basic::Tracer	tr ("core.io.silent")

Typedef Documentation

typedef utility::pointer::owning_ptr< BinarySilentStruct > core::io::silent::BinarySilentStructOP

typedef utility::pointer::owning_ptr< EnergyNames > core::io::silent::EnergyNamesOP

typedef ProteinSilentStruct_Template< core::Real > core::io::silent::ProteinSilentStruct

typedef ProteinSilentStruct_Template< float > core::io::silent::ProteinSilentStruct_SinglePrec

typedef utility::pointer::owning_ptr< ProteinSilentStruct > core::io::silent::ProteinSilentStructOP

typedef utility::pointer::owning_ptr< RNA_SilentStruct > core::io::silent::RNA_SilentStructOP

typedef utility::pointer::owning_ptr< SequenceFactory > core::io::silent::SequenceFactoryOP

typedef utility::pointer::owning_ptr< SharedSilentData > core::io::silent::SharedSilentDataOP

typedef utility::pointer::owning_ptr< SilentFileData > core::io::silent::SilentFileDataOP

typedef utility::pointer::owning_ptr< SilentFileLoader const > core::io::silent::SilentFileLoaderCOP

typedef utility::pointer::owning_ptr< SilentFileLoader > core::io::silent::SilentFileLoaderOP

typedef utility::pointer::owning_ptr< SilentFileOptions const > core::io::silent::SilentFileOptionsCOP

typedef utility::pointer::owning_ptr< SilentFileOptions > core::io::silent::SilentFileOptionsOP

typedef utility::pointer::owning_ptr< SilentStruct const > core::io::silent::SilentStructCOP

typedef utility::pointer::owning_ptr< SilentStructCreator const > core::io::silent::SilentStructCreatorCOP

typedef utility::pointer::owning_ptr< SilentStructCreator > core::io::silent::SilentStructCreatorOP

typedef utility::pointer::owning_ptr< SilentStructFactory > core::io::silent::SilentStructFactoryOP

typedef utility::pointer::owning_ptr< SilentStruct > core::io::silent::SilentStructOP

typedef utility::vector1< SilentStructOP > core::io::silent::SilentStructOPs

typedef utility::pointer::owning_ptr< SimpleSequenceData > core::io::silent::SimpleSequenceDataOP

typedef std::map< std::string, SilentStructOP > core::io::silent::Structure_Map

Enumeration Type Documentation

enum core::io::silent::SharedSilentDataType

Enumerator
energynames
simplesequencedata

Function Documentation

void core::io::silent::gzip

(

)

gzip all of the files in -out::file::silent().

References basename, utility::io::izstream::clear(), utility::io::izstream::close(), core::sequence::end, utility::file::gzip(), basic::options::option, option, out::file::silent, out::silent_gz, and tr.

std::map< std::string, bool > core::io::silent::initialize_tag_is_done

(

std::string const &

silent_file

)

References utility::file::file_exists(), and core::io::silent::SilentFileData::read_tags_fast().

bool core::io::silent::SilentEnergy_sort_by_name	(	const SilentEnergy &	score_energy1,
		const SilentEnergy &	score_energy2
	)

References core::io::silent::SilentEnergy::name().

Referenced by core::io::silent::SilentStruct::sort_silent_scores().

Variable Documentation

basic::Tracer core::io::silent::pss_tr("core.io.silent")

static

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::add_chain_ending(), core::io::silent::ProteinSilentStruct_Template< T >::chain_endings(), core::io::silent::ProteinSilentStruct_Template< T >::chi(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), and core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines().

numeric::random::RandomGenerator core::io::silent::RG(21458)

static

Referenced by core::io::silent::SilentFileData::_read_file().

basic::Tracer core::io::silent::tr("core.io.silent")

static

basic::Tracer core::io::silent::tr("core.io.silent")

static

basic::Tracer core::io::silent::tr("core.io.silent.ScoreFileSilentStruct")

static

basic::Tracer core::io::silent::tr("core.io.silent.ScoreJumpFileSilentStruct")

static

basic::Tracer core::io::silent::tr("core.io.silent.SilentFileData")

static

basic::Tracer core::io::silent::tr("core.io.silent")

static

Referenced by core::io::silent::SilentFileData::_read_file(), core::io::silent::BinarySilentStruct::add_chain_ending(), core::io::silent::SilentStruct::add_comment(), core::io::silent::SilentStruct::add_parent_remark(), core::io::silent::SilentFileData::add_structure(), core::io::silent::SilentFileData::add_structure_replace_tag_if_necessary(), core::io::silent::BinarySilentStruct::chain_endings(), core::io::silent::SilentStruct::comment_from_line(), core::io::silent::SilentStruct::detect_fullatom(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::energies_into_pose(), core::io::silent::SilentStruct::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::SilentStruct::fill_struct(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::SilentStruct::finish_pose(), core::io::silent::ScoreFileSilentStruct::get_CA_xyz(), core::io::silent::ScoreJumpFileSilentStruct::get_CA_xyz(), core::io::silent::ScoreFileSilentStruct::get_debug_rmsd(), core::io::silent::ScoreJumpFileSilentStruct::get_debug_rmsd(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), gzip(), core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::SilentFileData::matched_tags(), core::io::silent::SilentStruct::parse_energies(), core::io::silent::RNA_SilentStruct::print_conformation(), core::io::silent::SilentStruct::read_score_headers(), core::io::silent::SilentStruct::read_sequence(), core::io::silent::SilentFileData::read_silent_struct_type_from_remark(), core::io::silent::SilentFileData::read_stream(), core::io::silent::SilentFileData::reverse_score_filter(), and core::io::silent::SilentFileData::score_filter().

basic::Tracer core::io::silent::tr("core.io.silent.SilentStruct")

static