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	RigidBodySilentStruct
class	RigidBodySilentStructCreator
	creator for the RigidBodySilentStruct 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	SilentFileOptions
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::shared_ptr < BinarySilentStruct >	BinarySilentStructOP
typedef utility::pointer::shared_ptr < EnergyNames >	EnergyNamesOP
typedef utility::pointer::shared_ptr < ScoreJumpFileSilentStruct >	ScoreJumpFileSilentStructOP
typedef ProteinSilentStruct_Template < float >	ProteinSilentStruct_SinglePrec
typedef ProteinSilentStruct_Template < core::Real >	ProteinSilentStruct
typedef utility::pointer::shared_ptr < SharedSilentData >	SharedSilentDataOP
typedef utility::pointer::shared_ptr < SimpleSequenceData >	SimpleSequenceDataOP
typedef utility::pointer::shared_ptr < SilentStruct >	SilentStructOP
typedef utility::pointer::shared_ptr < SilentStruct const >	SilentStructCOP
typedef utility::pointer::shared_ptr < ProteinSilentStruct >	ProteinSilentStructOP
typedef utility::pointer::shared_ptr < RNA_SilentStruct >	RNA_SilentStructOP
typedef std::map< std::string, SilentStructOP >	Structure_Map
typedef utility::vector1 < SilentStructOP >	SilentStructOPs
typedef utility::pointer::shared_ptr < SilentFileData >	SilentFileDataOP
typedef utility::pointer::shared_ptr < SilentFileOptions >	SilentFileOptionsOP
typedef utility::pointer::shared_ptr < SilentFileOptions const >	SilentFileOptionsCOP
typedef utility::pointer::shared_ptr < SilentStructCreator >	SilentStructCreatorOP
typedef utility::pointer::shared_ptr < SilentStructCreator const >	SilentStructCreatorCOP
typedef utility::pointer::shared_ptr < SilentStructFactory >	SilentStructFactoryOP
typedef utility::pointer::shared_ptr < SequenceFactory >	SequenceFactoryOP

Enumerations
enum	SharedSilentDataType { energynames = 1, simplesequencedata }
enum	SilentFileHeaderLine { SFHEADER_SEQUENCE_LINE = 1, SFHEADER_SCORE_TYPE_LINE, SFHEADER_SCORE_LINE }
	Enum for the types of lines that a silent file can have in its header section. More...

Functions
static basic::Tracer	pss_tr ("core.io.silent")
static basic::Tracer	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 basic::Tracer	tr ("core.io.silent.SilentStruct")
bool	SilentEnergy_sort_by_name (const SilentEnergy &score_energy1, const SilentEnergy &score_energy2)
static basic::Tracer	tr ("core.io.silent")
static basic::Tracer	tr ("core.io.silent")
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)
	figures out which decoys are already stored in silent file. More...
void	figure_out_residue_numbers_from_line (std::istream &line_stream, utility::vector1< int > &residue_numbers, utility::vector1< char > &chains, utility::vector1< std::string > &segids)
	needed for reading out RESNUM lines from silent files More...
std::string	get_outfile_name_with_tag (std::string const &silent_file, std::string const &tag)
	Changes blah.out to blah_LORES.out (if tag is "_LORES") More...
void	remove_silent_file_if_it_exists (std::string const &silent_file)
	used with -overwrite flag More...

Typedef Documentation

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

typedef utility::pointer::shared_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::shared_ptr< ProteinSilentStruct > core::io::silent::ProteinSilentStructOP

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

typedef utility::pointer::shared_ptr< ScoreJumpFileSilentStruct > core::io::silent::ScoreJumpFileSilentStructOP

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::shared_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

enum core::io::silent::SilentFileHeaderLine

Enum for the types of lines that a silent file can have in its header section.

Some silent file types (e.g. BinarySilentFiles) are initialized from their header data.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Enumerator
SFHEADER_SEQUENCE_LINE
SFHEADER_SCORE_TYPE_LINE
SFHEADER_SCORE_LINE

Function Documentation

void core::io::silent::figure_out_residue_numbers_from_line	(	std::istream &	line_stream,
		utility::vector1< int > &	residue_numbers,
		utility::vector1< char > &	chains,
		utility::vector1< std::string > &	segids
	)

needed for reading out RESNUM lines from silent files

Referenced by core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(), core::io::silent::SilentFileData::get_resnum(), and core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines().

std::string core::io::silent::get_outfile_name_with_tag	(	std::string const &	silent_file,
		std::string const &	tag
	)

Changes blah.out to blah_LORES.out (if tag is "_LORES")

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::stepwise::sampler::protein::get_basic_protein_sampler(), and protocols::rna::denovo::RNA_DeNovoProtocol::initialize_lores_silent_file().

void core::io::silent::gzip

(

)

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

References tr().

Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::boinc::boincOutputFilter(), protocols::jd2::BOINCJobDistributor::go(), and protocols::jobdist::PlainSilentFileJobDistributor::shutdown().

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

(

std::string const &

silent_file

)

figures out which decoys are already stored in silent file.

References core::io::silent::SilentFileData::read_tags_fast().

Referenced by protocols::rna::setup::RNA_MonteCarloJobDistributor::get_out_tag(), protocols::stepwise::legacy::modeler::rna::get_tag_and_silent_file_for_struct(), and protocols::rna::denovo::RNA_DeNovoProtocol::initialize_tag_is_done().

static 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().

void core::io::silent::remove_silent_file_if_it_exists

(

std::string const &

silent_file

)

used with -overwrite flag

References tr().

Referenced by protocols::rna::denovo::RNA_DeNovoProtocol::apply(), protocols::stepwise::legacy::modeler::protein::output_pose_list(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::remove_checkpoint_file(), and protocols::rna::setup::RNA_CSA_JobDistributor::write_out_silent_file().

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().

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

static

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

static

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::ScoreJumpFileSilentStruct::fill_pose(), core::io::silent::SilentStruct::fill_pose(), core::io::silent::RigidBodySilentStruct::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::SilentFileData::get_sequence(), 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::RigidBodySilentStruct::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(), remove_silent_file_if_it_exists(), core::io::silent::SilentFileData::reverse_score_filter(), and core::io::silent::SilentFileData::score_filter().

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

static

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

static

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

static

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

static

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

static