Rosetta 3.4
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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  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
< 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

void encode6bit (const unsigned char *memory, unsigned int length, std::string &jar)
int decode6bit (unsigned char *memory, const std::string &jar)
void swap4_aligned (void *v, long ndata)
unsigned char code_to_6bit (unsigned char _6bit)
unsigned char code_from_6bit (unsigned char _8bit)
void encode_24_to_32 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char &o0, unsigned char &o1, unsigned char &o2, unsigned char &o3)
void decode_32_to_24 (unsigned char i0, unsigned char i1, unsigned char i2, unsigned char i3, unsigned char &o0, unsigned char &o1, unsigned char &o2)
static basic::Tracer tr ("core.io.silent")
static basic::Tracer pss_tr ("core.io.silent")
static basic::Tracer tr ("core.io.silent.ScoreFileSilentStruct")
static
numeric::random::RandomGenerator 
RG (21458)
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().

Typedef Documentation

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

Enumeration Type Documentation

Enumerator:
energynames 
simplesequencedata 

Function Documentation

unsigned char core::io::silent::code_from_6bit ( unsigned char  _8bit) [inline]

Referenced by decode_32_to_24().

unsigned char core::io::silent::code_to_6bit ( unsigned char  _6bit) [inline]

uuencode

Referenced by encode_24_to_32().

int core::io::silent::decode6bit ( unsigned char *  memory,
const std::string &  jar 
)
void core::io::silent::decode_32_to_24 ( unsigned char  i0,
unsigned char  i1,
unsigned char  i2,
unsigned char  i3,
unsigned char &  o0,
unsigned char &  o1,
unsigned char &  o2 
) [inline]

References code_from_6bit().

Referenced by decode6bit().

void core::io::silent::encode6bit ( const unsigned char *  memory,
unsigned int  length,
std::string &  jar 
)
void core::io::silent::encode_24_to_32 ( unsigned char  i0,
unsigned char  i1,
unsigned char  i2,
unsigned char &  o0,
unsigned char &  o1,
unsigned char &  o2,
unsigned char &  o3 
) [inline]

References code_to_6bit().

Referenced by encode6bit().

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 
)
void core::io::silent::swap4_aligned ( void *  v,
long  ndata 
) [inline]
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::RNA_SilentStruct::fill_pose(), core::io::silent::BinaryRNASilentStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::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::RNA_SilentStruct::init_from_lines(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), 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_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.ScoreFileSilentStruct"  ) [static]
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