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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, boolinitialize_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 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< 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::pointer::shared_ptr< SimpleSequenceData > core::io::silent::SimpleSequenceDataOP
typedef std::map< std::string, SilentStructOP > core::io::silent::Structure_Map

Enumeration Type Documentation

Enumerator
energynames 
simplesequencedata 

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 
)
std::string core::io::silent::get_outfile_name_with_tag ( std::string const &  silent_file,
std::string const &  tag 
)
void core::io::silent::gzip ( )
std::map< std::string, bool > core::io::silent::initialize_tag_is_done ( std::string const &  silent_file)
static basic::Tracer core::io::silent::pss_tr ( "core.io.silent"  )
static
void core::io::silent::remove_silent_file_if_it_exists ( std::string const &  silent_file)
bool core::io::silent::SilentEnergy_sort_by_name ( const SilentEnergy &  score_energy1,
const SilentEnergy &  score_energy2 
)
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