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core::io::silent Namespace Reference

Classes

class  ProteinSilentStruct_SinglePrecCreator
 creator for the ProteinSilentStruct_SinglePrec class More...
 
class  ProteinSilentStructCreator
 creator for the ProteinSilentStruct class More...
 
class  RNA_SilentStructCreator
 creator for the RNA_SilentStruct class More...
 
class  BinarySilentStructCreator
 creator for the BinarySilentStruct class More...
 
class  ScoreFileSilentStructCreator
 creator for the ScoreFileSilentStruct class More...
 
class  ScoreJumpFileSilentStructCreator
 creator for the ScoreJumpFileSilentStruct class More...
 
class  RigidBodySilentStructCreator
 creator for the RigidBodySilentStruct class More...
 
class  BinarySilentStruct
 why this inheritance pathway? this makes no sense! More...
 
class  EnergyNames
 
class  ProteinSilentStruct_Template
 
class  RigidBodySilentStruct
 
class  RNA_SilentStruct
 
class  ScoreFileSilentStruct
 
class  ScoreJumpFileSilentStruct
 
class  SharedSilentData
 
class  SimpleSequenceData
 
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...
 

Typedefs

typedef utility::pointer::shared_ptr< BinarySilentStructBinarySilentStructOP
 
typedef utility::pointer::shared_ptr< EnergyNamesEnergyNamesOP
 
typedef utility::pointer::shared_ptr< ScoreJumpFileSilentStructScoreJumpFileSilentStructOP
 
typedef ProteinSilentStruct_Template< float > ProteinSilentStruct_SinglePrec
 
typedef ProteinSilentStruct_Template< core::RealProteinSilentStruct
 
typedef utility::pointer::shared_ptr< SharedSilentDataSharedSilentDataOP
 
typedef utility::pointer::shared_ptr< SimpleSequenceDataSimpleSequenceDataOP
 
typedef utility::pointer::shared_ptr< SilentStructSilentStructOP
 
typedef utility::pointer::shared_ptr< SilentStruct const > SilentStructCOP
 
typedef utility::pointer::shared_ptr< ProteinSilentStructProteinSilentStructOP
 
typedef utility::pointer::shared_ptr< RNA_SilentStructRNA_SilentStructOP
 
typedef std::map< std::string, SilentStructOPStructure_Map
 
typedef utility::vector1< SilentStructOPSilentStructOPs
 
typedef utility::pointer::shared_ptr< SilentFileDataSilentFileDataOP
 
typedef utility::pointer::shared_ptr< SilentFileOptionsSilentFileOptionsOP
 
typedef utility::pointer::shared_ptr< SilentFileOptions const > SilentFileOptionsCOP
 
typedef utility::pointer::shared_ptr< SilentStructCreatorSilentStructCreatorOP
 
typedef utility::pointer::shared_ptr< SilentStructCreator const > SilentStructCreatorCOP
 
typedef utility::pointer::shared_ptr< SilentStructFactorySilentStructFactoryOP
 
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

◆ BinarySilentStructOP

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

◆ EnergyNamesOP

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

◆ ProteinSilentStruct

◆ ProteinSilentStruct_SinglePrec

◆ ProteinSilentStructOP

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

◆ RNA_SilentStructOP

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

◆ ScoreJumpFileSilentStructOP

◆ SequenceFactoryOP

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

◆ SharedSilentDataOP

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

◆ SilentFileDataOP

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

◆ SilentFileOptionsCOP

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

◆ SilentFileOptionsOP

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

◆ SilentStructCOP

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

◆ SilentStructCreatorCOP

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

◆ SilentStructCreatorOP

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

◆ SilentStructFactoryOP

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

◆ SilentStructOP

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

◆ SilentStructOPs

◆ SimpleSequenceDataOP

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

◆ Structure_Map

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

Enumeration Type Documentation

◆ SharedSilentDataType

Enumerator
energynames 
simplesequencedata 

◆ 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

◆ figure_out_residue_numbers_from_line()

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 
)

◆ get_outfile_name_with_tag()

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

◆ gzip()

void core::io::silent::gzip ( )

◆ initialize_tag_is_done()

std::map< std::string, bool > core::io::silent::initialize_tag_is_done ( std::string const &  silent_file)

◆ pss_tr()

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

◆ remove_silent_file_if_it_exists()

void core::io::silent::remove_silent_file_if_it_exists ( std::string const &  silent_file)

◆ SilentEnergy_sort_by_name()

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

◆ tr() [1/8]

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::BinarySilentStruct::fill_pose(), core::io::silent::SilentStruct::fill_pose(), core::io::silent::RigidBodySilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::SilentStruct::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::RigidBodySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::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().

◆ tr() [2/8]

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

◆ tr() [3/8]

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

◆ tr() [4/8]

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

◆ tr() [5/8]

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

◆ tr() [6/8]

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

◆ tr() [7/8]

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

◆ tr() [8/8]

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