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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  BinaryProteinSilentStructCreator
 creator for the BinaryProteinSilentStruct class More...
 
class  ScoreFileSilentStructCreator
 creator for the ScoreFileSilentStruct class More...
 
class  BinaryRNASilentStructCreator
 creator for the BinaryRNASilentStruct class More...
 
class  BinaryProteinSilentStruct
 why this inheritance pathway? this makes no sense! More...
 
class  BinaryRNASilentStruct
 
class  EnergyNames
 
class  ProteinSilentStruct_Template
 
class  RNA_SilentStruct
 
class  ScoreFileSilentStruct
 
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  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...
 

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
< BinaryProteinSilentStruct
BinaryProteinSilentStructOP
 
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

static basic::Tracer tr ("core.io.silent")
 
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")
 
static
numeric::random::RandomGenerator 
RG (21458)
 
static basic::Tracer tr ("core.io.silent")
 
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...
 

Typedef Documentation

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

Enumeration Type Documentation

Enumerator
energynames 
simplesequencedata 

Function Documentation

void core::io::silent::gzip ( )
static basic::Tracer core::io::silent::pss_tr ( "core.io.silent"  )
static
static numeric::random::RandomGenerator core::io::silent::RG ( 21458  )
static
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.ScoreFileSilentStruct"  )
static
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::BinaryProteinSilentStruct::add_chain_ending(), 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::BinaryProteinSilentStruct::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::BinaryProteinSilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::RNA_SilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), core::io::silent::SilentStruct::finish_pose(), core::io::silent::ScoreFileSilentStruct::get_CA_xyz(), core::io::silent::ScoreFileSilentStruct::get_debug_rmsd(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), gzip(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::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().

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