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Rosetta
2021.07
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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 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< 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 |
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().
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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().
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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().
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