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Rosetta
2020.50
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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...
#include <SilentFileData.hh>
Classes | |
class | const_iterator |
const_iterator class for SilentFileData container. More... | |
class | iterator |
Iterator class for SilentFileData container. More... | |
Public Member Functions | |
SilentFileData (SilentFileOptions const &options) | |
SilentFileData (std::string const &filename, SilentFileOptions const &options) | |
SilentFileData (std::string const &filename, bool const store_argv_in_file, bool const strict_column_mode, std::string const &silent_struct_type, SilentFileOptions const &options) | |
bool | read_file (std::string const &filename) |
Read in the SilentStruct objects contained in the given filename. this version will throw an exception if things go wrong (boolean return value is thus always true) More... | |
bool | _read_file (std::string const &filename, bool throw_exception_on_bad_structs=false) |
Read in the SilentStruct objects contained in the given filename. this version returns with a boolean to tell you about success. More... | |
bool | read_file (std::string const &filename, utility::vector1< std::string > const &tags) |
Read in the SilentStruct objects contained in the given filename. Ignore any SilentStruct with a tag not in the tags vector. throw an exception if things go wrong (returned boolean always true) More... | |
bool | read_stream (std::istream &data, utility::vector1< std::string > const &tags, bool throw_exception_on_bad_structs, std::string filename="read_from_stream") |
bool | _read_file (std::string const &filename, utility::vector1< std::string > const &tags, bool throw_exception_on_bad_structs=false) |
Read in the SilentStruct objects contained in the given filename. Ignore any SilentStruct with a tag not in the tags vector. returns with a boolean to tell about success. More... | |
bool | store_argv_in_file () const |
Returns true if this silent-file plans on storing option.get_argv() as a comment in the silent-file, false otherwise. More... | |
void | store_argv_in_file (bool new_setting) |
Sets a boolean variable governing if this silent-file plans on storing option.get_argv() as a comment in the silent-file. More... | |
bool | write_silent_struct (SilentStruct &s, std::string const &filename, bool bWriteScoreOnly=false) const |
Write the given silent-struct to the given outfile. More... | |
bool | _write_silent_struct (SilentStruct &s, std::ostream &out, bool bWriteScoreOnly=false) const |
Write the given silent-struct, including the header, to the given ostream. More... | |
bool | write_silent_struct (SilentStruct &s, std::ostream &out, bool bWriteScoreOnly=false) const |
Write the given silent-struct, minus the header, to the given ostream. More... | |
void | write_comment (std::ostream &out, std::string const &line) const |
Write a comment to the given output stream. More... | |
Size | size () const |
Returns the number of structures contained in this container. More... | |
int | nres () const |
Returns the number of residues in the first structure in this object. Not guaranteed to be fixed for all structures in this container. More... | |
void | set_filename (std::string filename) |
Sets the filename that this SilentFileData object will write to. More... | |
void | set_verbose (bool const setting) |
Sets the filename that this SilentFileData object will write to. More... | |
SilentStructOP | operator[] (std::string tag) |
std::string const & | filename () const |
Gets the filename that this SilentFileData object will write to. More... | |
utility::vector1< std::string > | tags () const |
Return all tags in this container. More... | |
utility::vector1< std::string > | read_tags_fast (std::string const &filename) const |
quickly read a list of tags from a silent-input file. Only checks lines beginning with SCORE: strings. More... | |
utility::vector1< SilentStructOP > | structure_list () |
Function to access the vector of silent structure owning pointers ordered as they were in the input file. More... | |
std::string | get_sequence (std::string const &filename) |
std::tuple< utility::vector1 < int >, utility::vector1 < char >, utility::vector1 < std::string > > | get_resnum (std::string const &filename) |
bool | read_tags_fast (std::string const &filename, utility::vector1< std::string > &) const |
quickly read a list of tags from a silent-input file. Only checks lines beginning with SCORE: strings. More... | |
bool | matched_tags (std::string const &expression, std::string const &mode, utility::vector1< std::string > &tags_in_file) const |
return mode=first,last,all matched tags – currently matching 'expression*' to tags in file, boost::regexp possible later More... | |
bool | strict_column_mode () const |
Returns a boolean indicating whether or not the strict_column_mode is turned on when printing scores. More... | |
void | strict_column_mode (bool new_mode) |
Sets value for strict column mode. See strict_column_mode() for more information. More... | |
void | set_record_source (bool const &new_mode) |
bool | has_tag (std::string const &tag) const |
Returns true if we have a SilentStruct matching the given tag, false otherwise. More... | |
utility::vector1< std::string > | comment_lines () |
Returns a vector1 of the comment lines read in from a silent-file. Comment lines are any lines in the silent-file beginning with a # character. More... | |
void | comment_line (std::string const &line) |
Adds a comment-line that will be printed in write_all method. Comment lines are simply lines in the silent-file that begin with the # character, and are printed in the write_all method. More... | |
void | score_filter (Real const score_fraction) |
Removes the worst ( 1 - score_fraction ) percent of the decoys by score. The value of score_fraction should be between 0 and 1.0. More... | |
void | reverse_score_filter (Real const score_fraction) |
void | order_by_energy () |
Orders silent structs by energy. More... | |
void | add_structure_replace_tag_if_necessary (SilentStructOP &new_struct) |
void | add_structure (SilentStructOP const &new_struct) |
Adds a SilentStructOP to the structure_map_. If the SilentStruct's tag already exists in the structure_map_, a new tag is assigned. Careful with this method, as it stores an owning pointer. If you change the SilentStruct later, it will change your already stored structures. More... | |
bool | add_as_other_struct_if_relevant (SilentStructOP const &new_struct) |
In stepwise modeling, sometimes poses carry refs to 'other poses'. More... | |
void | push_back (SilentStructOP const &new_struct) |
push_back to provide compatibility with other std containers. More... | |
void | add_structure (SilentStruct const &new_struct) |
Saves a copy of the silent struct. This method is: More... | |
SilentStruct const & | get_structure (const std::string &tag) const |
Return a SilentStruct referred to by the given tag. Assumes that we have checked the tag!! More... | |
void | clear_structure_map () |
Remove all of the SilentStruct objects from this object. More... | |
void | clear () |
Clears all of the data associated with this object. More... | |
void | clear_shared_silent_data () |
Clears all of the data associated with this object. More... | |
~SilentFileData () override | |
Destructor. More... | |
void | write_all (std::string const &filename, bool bWriteScoreOnly=false) const |
write all SilentStruct objects in the structure_map_ to the given filename. More... | |
void | renumber_all_decoys () |
renumber all of the decoys in this SilentFileData object. This obliterates decoy tag associated with every SilentStruct object, and tries to sensibly number the decoys with similar and increasingly numbered decoy tags. More... | |
SilentStructOP | create_SilentStructOP () |
creates a SilentStructOP using command-line options. Just a wrapper around SilentStructFactory::get_instance()->get_silent_struct_in(). More... | |
SharedSilentDataOP | get_shared_silent_data (SharedSilentDataType ssdt) const |
SharedSilentData methods. More... | |
void | set_shared_silent_data (SharedSilentDataType ssdt, SharedSilentDataOP ssd_op) const |
bool | has_shared_silent_data (SharedSilentDataType ssdt) const |
iterator | begin () |
Returns an iterator to the start of the members of this container. More... | |
const_iterator | begin () const |
Returns an iterator to the start of the members of this container. More... | |
iterator | end () |
Returns an iterator to the end of the members of this container. More... | |
const_iterator | end () const |
Returns an iterator to the end of the members of this container. More... | |
iterator | get_iterator_for_tag (const std::string &tag) |
const_iterator | get_iterator_for_tag (const std::string &tag) const |
Private Member Functions | |
bool | read_silent_struct_type_from_remark (std::string const &line, bool const header=false) |
bool | read_full_model_parameters_from_remark (std::string const &line, bool const header=false) |
Look for FULL_MODEL_PARAMETERS in REMARK line from header. More... | |
bool | check_if_rna_from_sequence_line (std::string const &sequence_line) |
This is somewhat redundant if the silent file has a "REMARK RNA" line, but some older silent files didn't do that. More... | |
bool | line_starts_with_score (std::string const &line) const |
Are the first six characters of a line "SCORE:"? More... | |
bool | line_starts_with_sequence (std::string const &line) const |
Are the first nine characters of a line "SEQUENCE:"? More... | |
bool | line_starts_with_other (std::string const &line) const |
Are the first six characters of a line "OTHER:"? More... | |
bool | line_starts_with_remark (std::string const &line) const |
Are the first six characters of a line "REMARK "? More... | |
bool | line_starts_with_other_header_string (std::string const &line) const |
Does a line start with another header string? More... | |
bool | is_score_type_line (std::string const &line) const |
Is a line (that is assumed to start with "SCORE:") a score type line or a score line? More... | |
void | lines_from_header_line_collection (std::map< SilentFileHeaderLine, std::string > const &header_lines, utility::vector1< std::string > &all_lines) const |
Given a list of non-header lines read from a silent file and a map of certain types of single-occurance header lines to strings, copy the single-occurance header lines to the top of the list of lines. More... | |
Private Attributes | |
Structure_Map | structure_map_ |
mapping from tags to structure data pointers More... | |
utility::vector1< SilentStructOP > | structure_list_ |
mapping from index in a silent file to data pointers, for situations in which the ordering in the file matters. More... | |
utility::vector1< std::string > | comment_lines_ |
std::map< SharedSilentDataType, SharedSilentDataOP > | shared_silent_data_ |
std::string | filename_ |
bool | store_argv_in_file_ |
bool | strict_column_mode_ |
bool | record_source_ |
std::string | silent_struct_type_ |
bool | verbose_ |
core::pose::full_model_info::FullModelParametersOP | full_model_parameters_ |
SilentFileOptions | options_ |
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.
core::io::silent::SilentFileData::SilentFileData | ( | SilentFileOptions const & | options | ) |
core::io::silent::SilentFileData::SilentFileData | ( | std::string const & | filename, |
SilentFileOptions const & | options | ||
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core::io::silent::SilentFileData::SilentFileData | ( | std::string const & | filename, |
bool const | store_argv_in_file, | ||
bool const | strict_column_mode, | ||
std::string const & | silent_struct_type, | ||
SilentFileOptions const & | options | ||
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override |
Destructor.
References clear_structure_map().
bool core::io::silent::SilentFileData::_read_file | ( | std::string const & | filename, |
bool | throw_exception_on_bad_structs = false |
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Read in the SilentStruct objects contained in the given filename. this version returns with a boolean to tell you about success.
References protocols::mean_field::min(), options_, read_tags_fast(), core::scoring::rg, core::io::silent::SilentFileOptions::select_random(), core::io::silent::SilentFileOptions::select_random_set(), core::io::silent::SilentFileOptions::select_range_len(), core::io::silent::SilentFileOptions::select_range_mul(), core::io::silent::SilentFileOptions::select_range_start(), and core::io::silent::tr().
Referenced by read_file().
bool core::io::silent::SilentFileData::_read_file | ( | std::string const & | filename, |
utility::vector1< std::string > const & | tags, | ||
bool | throw_exception_on_bad_structs = false |
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Read in the SilentStruct objects contained in the given filename. Ignore any SilentStruct with a tag not in the tags vector. returns with a boolean to tell about success.
References read_stream().
bool core::io::silent::SilentFileData::_write_silent_struct | ( | SilentStruct & | s, |
std::ostream & | out, | ||
bool | bWriteScoreOnly = false |
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) | const |
Write the given silent-struct, including the header, to the given ostream.
Unlike write_silent_struct(), this method writes both the header and the body of the silent file to the given stream. Therefore this is probably the more appropriate method to use in high-level codes.
References core::io::silent::SilentStruct::print_header(), and write_silent_struct().
Referenced by protocols::trajectory::DbTrajectoryWriter::write_cache_to_db(), and protocols::canonical_sampling::DbTrajectoryRecorder::write_cache_to_db().
bool core::io::silent::SilentFileData::add_as_other_struct_if_relevant | ( | SilentStructOP const & | new_struct | ) |
In stepwise modeling, sometimes poses carry refs to 'other poses'.
stepwise modeling can involve holding references to 'other poses' which, taken together correspond to the full model of the pose.
References has_tag(), and structure_map_.
Referenced by add_structure().
void core::io::silent::SilentFileData::add_structure | ( | SilentStructOP const & | new_struct | ) |
Adds a SilentStructOP to the structure_map_. If the SilentStruct's tag already exists in the structure_map_, a new tag is assigned. Careful with this method, as it stores an owning pointer. If you change the SilentStruct later, it will change your already stored structures.
References add_as_other_struct_if_relevant(), add_structure_replace_tag_if_necessary(), has_tag(), structure_list_, structure_map_, and core::io::silent::tr().
Referenced by add_structure(), add_structure_replace_tag_if_necessary(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::flush(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::flush(), protocols::abinitio::AbrelaxApplication::fold(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeBase::gen_diversity_pool(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), push_back(), read_stream(), and protocols::abinitio::HedgeArchive::save_pending_decoys().
void core::io::silent::SilentFileData::add_structure | ( | SilentStruct const & | new_struct | ) |
Saves a copy of the silent struct. This method is:
References add_structure(), and core::io::silent::SilentStruct::clone().
void core::io::silent::SilentFileData::add_structure_replace_tag_if_necessary | ( | SilentStructOP & | new_struct | ) |
References add_structure(), has_tag(), and core::io::silent::tr().
Referenced by add_structure(), and protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file().
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Returns an iterator to the start of the members of this container.
References structure_map_.
Referenced by protocols::wum::SilentStructStore::add(), protocols::noesy_assign::NoesyModule::assign(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::LazySilentFilePoseInputStream(), protocols::jd2::archive::ArchiveBase::load_decoys(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), protocols::toolbox::KClusterData::load_silent_file(), nres(), order_by_energy(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::process_input_file(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), protocols::wum::SilentStructStore::read_from_stream(), protocols::abinitio::IterativeAbrelax::read_structures(), protocols::jd2::archive::ArchiveBase::read_structures(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::abinitio::HedgeArchive::restore_status(), reverse_score_filter(), protocols::toolbox::KClusterData::save_all_in_one(), protocols::toolbox::KClusterData::save_cluster_tree(), score_filter(), protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter(), protocols::jobdist::universal_main(), and write_all().
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Returns an iterator to the start of the members of this container.
References structure_map_.
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This is somewhat redundant if the silent file has a "REMARK RNA" line, but some older silent files didn't do that.
References silent_struct_type_.
Referenced by read_stream().
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Clears all of the data associated with this object.
References clear_structure_map(), comment_lines_, filename_, shared_silent_data_, store_argv_in_file_, and strict_column_mode_.
Referenced by core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose().
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Clears all of the data associated with this object.
References shared_silent_data_.
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Remove all of the SilentStruct objects from this object.
References structure_list_, and structure_map_.
Referenced by clear(), renumber_all_decoys(), and ~SilentFileData().
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Adds a comment-line that will be printed in write_all method. Comment lines are simply lines in the silent-file that begin with the # character, and are printed in the write_all method.
References comment_lines_.
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Returns a vector1 of the comment lines read in from a silent-file. Comment lines are any lines in the silent-file beginning with a # character.
References comment_lines_.
Referenced by protocols::wum::SilentStructStore::read_from_stream().
SilentStructOP core::io::silent::SilentFileData::create_SilentStructOP | ( | ) |
creates a SilentStructOP using command-line options. Just a wrapper around SilentStructFactory::get_instance()->get_silent_struct_in().
References full_model_parameters_, options_, and silent_struct_type_.
Referenced by read_stream().
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Returns an iterator to the end of the members of this container.
References structure_map_.
Referenced by protocols::wum::SilentStructStore::add(), protocols::noesy_assign::NoesyModule::assign(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::has_another_pose(), protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::jd2::archive::ArchiveBase::load_decoys(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), protocols::toolbox::KClusterData::load_silent_file(), order_by_energy(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::process_input_file(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), protocols::wum::SilentStructStore::read_from_stream(), protocols::abinitio::IterativeAbrelax::read_structures(), protocols::jd2::archive::ArchiveBase::read_structures(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::reset(), protocols::abinitio::HedgeArchive::restore_status(), reverse_score_filter(), protocols::toolbox::KClusterData::save_all_in_one(), protocols::toolbox::KClusterData::save_cluster_tree(), score_filter(), protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter(), protocols::jobdist::universal_main(), and write_all().
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Returns an iterator to the end of the members of this container.
References structure_map_.
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Gets the filename that this SilentFileData object will write to.
References filename_.
Referenced by protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), matched_tags(), read_stream(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), and set_filename().
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References structure_map_.
Referenced by protocols::jd2::archive::ArchiveBase::read_structures().
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References structure_map_.
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > core::io::silent::SilentFileData::get_resnum | ( | std::string const & | filename | ) |
std::string core::io::silent::SilentFileData::get_sequence | ( | std::string const & | filename | ) |
SharedSilentDataOP core::io::silent::SilentFileData::get_shared_silent_data | ( | SharedSilentDataType | ssdt | ) | const |
SharedSilentData methods.
Returns the SharedSilentDataOP associated with the given type.
References shared_silent_data_.
Referenced by core::io::silent::ScoreFileSilentStruct::init_from_lines(), core::import_pose::PDBSilentStruct::init_from_lines(), 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::ProteinSilentStruct_Template< T >::init_from_lines(), and write_silent_struct().
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Return a SilentStruct referred to by the given tag. Assumes that we have checked the tag!!
References structure_map_.
Referenced by protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), and protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file().
bool core::io::silent::SilentFileData::has_shared_silent_data | ( | SharedSilentDataType | ssdt | ) | const |
References shared_silent_data_.
Referenced by write_silent_struct().
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Returns true if we have a SilentStruct matching the given tag, false otherwise.
References structure_map_.
Referenced by add_as_other_struct_if_relevant(), add_structure(), add_structure_replace_tag_if_necessary(), protocols::abinitio::KinematicAbinitio::apply(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), and operator[]().
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Is a line (that is assumed to start with "SCORE:") a score type line or a score line?
Considered a score type line if and only if the second whitespace-separated chunk is "score" or "total_score"; otherwise, considered a score line.
Referenced by read_stream().
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Are the first six characters of a line "OTHER:"?
Referenced by read_stream().
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Does a line start with another header string?
Includes strings like "ANNOTATED_SEQUENCE", "FOLD_TREE", etc.
Referenced by read_stream().
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Are the first six characters of a line "REMARK "?
Referenced by read_stream().
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Are the first six characters of a line "SCORE:"?
Both score type lines and score lines start with "SCORE:".
Referenced by read_stream().
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Are the first nine characters of a line "SEQUENCE:"?
Referenced by read_stream().
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Given a list of non-header lines read from a silent file and a map of certain types of single-occurance header lines to strings, copy the single-occurance header lines to the top of the list of lines.
References core::io::silent::SFHEADER_SCORE_LINE, core::io::silent::SFHEADER_SCORE_TYPE_LINE, and core::io::silent::SFHEADER_SEQUENCE_LINE.
Referenced by read_stream().
bool core::io::silent::SilentFileData::matched_tags | ( | std::string const & | expression, |
std::string const & | mode, | ||
utility::vector1< std::string > & | tags_in_file | ||
) | const |
return mode=first,last,all matched tags – currently matching 'expression*' to tags in file, boost::regexp possible later
References filename(), and core::io::silent::tr().
Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation().
int core::io::silent::SilentFileData::nres | ( | ) | const |
Returns the number of residues in the first structure in this object. Not guaranteed to be fixed for all structures in this container.
References begin().
SilentStructOP core::io::silent::SilentFileData::operator[] | ( | std::string | tag | ) |
References has_tag(), and structure_map_.
void core::io::silent::SilentFileData::order_by_energy | ( | ) |
Orders silent structs by energy.
References begin(), end(), structure_list_, and structure_map_.
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push_back to provide compatibility with other std containers.
References add_structure().
bool core::io::silent::SilentFileData::read_file | ( | std::string const & | filename | ) |
Read in the SilentStruct objects contained in the given filename. this version will throw an exception if things go wrong (boolean return value is thus always true)
References _read_file(), options_, and core::io::silent::SilentFileOptions::read_through_errors().
Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::noesy_assign::NoesyModule::assign(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), protocols::canonical_sampling::MetropolisHastingsMover::get_checkpoints(), protocols::jd2::archive::ArchiveManager::go(), protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(), protocols::ddg::ddGMover::is_any_pdb_empty(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::LazySilentFilePoseInputStream(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), protocols::jd2::archive::ArchiveBase::load_decoys(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::optimize_weights::IterativeOptEDriver::load_pose(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_reference_pool(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), protocols::toolbox::KClusterData::load_silent_file(), protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::process_input_file(), protocols::jd2::archive::BaseArchiveManager::read_returning_decoys(), protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::abinitio::HedgeArchive::restore_status(), protocols::toolbox::KClusterData::save_all_in_one(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::comparative_modeling::ThreadingJobInputter::ThreadingJobInputter(), and protocols::jobdist::universal_main().
bool core::io::silent::SilentFileData::read_file | ( | std::string const & | filename, |
utility::vector1< std::string > const & | tags | ||
) |
Read in the SilentStruct objects contained in the given filename. Ignore any SilentStruct with a tag not in the tags vector. throw an exception if things go wrong (returned boolean always true)
References _read_file(), options_, and core::io::silent::SilentFileOptions::read_through_errors().
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Look for FULL_MODEL_PARAMETERS in REMARK line from header.
References full_model_parameters_.
Referenced by read_stream().
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The first remarks line in a silent file block described the type of silent file that is comming. For example, REMARK BINARY SILENTFILE
References silent_struct_type_, and core::io::silent::tr().
Referenced by read_stream().
bool core::io::silent::SilentFileData::read_stream | ( | std::istream & | data, |
utility::vector1< std::string > const & | tags, | ||
bool | throw_exception_on_bad_structs, | ||
std::string | filename = "read_from_stream" |
||
) |
filename | for error reporting * |
References add_structure(), check_if_rna_from_sequence_line(), comment_lines_, create_SilentStructOP(), filename(), core::io::silent::SilentFileOptions::force_silent_bitflip_on_read(), is_score_type_line(), line_starts_with_other(), line_starts_with_other_header_string(), line_starts_with_remark(), line_starts_with_score(), line_starts_with_sequence(), lines_from_header_line_collection(), options_, read_full_model_parameters_from_remark(), read_silent_struct_type_from_remark(), record_source_, core::io::silent::SFHEADER_SCORE_LINE, core::io::silent::SFHEADER_SCORE_TYPE_LINE, core::io::silent::SFHEADER_SEQUENCE_LINE, structure_map_, core::io::silent::tr(), and verbose_.
Referenced by _read_file(), core::import_pose::PoseResourceLoader::create_resource(), protocols::trajectory::DbTrajectoryReader::get_pose(), and protocols::wum::SilentStructStore::read_from_stream().
utility::vector1< std::string > core::io::silent::SilentFileData::read_tags_fast | ( | std::string const & | filename | ) | const |
quickly read a list of tags from a silent-input file. Only checks lines beginning with SCORE: strings.
Referenced by _read_file(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), core::io::silent::initialize_tag_is_done(), protocols::ddg::ddGMover::is_any_pdb_empty(), protocols::jd2::ScoreOnlyJobOutputter::read_done_jobs(), protocols::jd2::SilentFileJobOutputter::read_done_jobs(), protocols::jd2::RNA_DeNovoJobOutputter::read_done_jobs(), protocols::jd2::archive::BaseArchiveManager::read_returning_decoys(), and protocols::jobdist::PlainSilentFileJobDistributor::startup().
bool core::io::silent::SilentFileData::read_tags_fast | ( | std::string const & | filename, |
utility::vector1< std::string > & | tags_in_file | ||
) | const |
quickly read a list of tags from a silent-input file. Only checks lines beginning with SCORE: strings.
void core::io::silent::SilentFileData::renumber_all_decoys | ( | ) |
renumber all of the decoys in this SilentFileData object. This obliterates decoy tag associated with every SilentStruct object, and tries to sensibly number the decoys with similar and increasingly numbered decoy tags.
References clear_structure_map(), structure_list_, and structure_map_.
void core::io::silent::SilentFileData::reverse_score_filter | ( | Real const | score_fraction | ) |
References begin(), end(), structure_list_, structure_map_, and core::io::silent::tr().
Referenced by score_filter().
void core::io::silent::SilentFileData::score_filter | ( | Real const | score_fraction | ) |
Removes the worst ( 1 - score_fraction ) percent of the decoys by score. The value of score_fraction should be between 0 and 1.0.
References begin(), end(), reverse_score_filter(), structure_list_, structure_map_, and core::io::silent::tr().
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Sets the filename that this SilentFileData object will write to.
References filename(), and filename_.
Referenced by protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::ddg::ddGMover::apply(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::ddG::ddGData::read_mut_data(), protocols::ddG::ddGData::read_wt_data(), and protocols::ddg::ddGMover::relax_wildtype_structure().
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References record_source_.
void core::io::silent::SilentFileData::set_shared_silent_data | ( | SharedSilentDataType | ssdt, |
SharedSilentDataOP | ssd_op | ||
) | const |
References shared_silent_data_.
Referenced by core::io::silent::ScoreFileSilentStruct::init_from_lines(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::SilentStruct::read_score_headers(), and write_silent_struct().
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Sets the filename that this SilentFileData object will write to.
References verbose_.
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Returns the number of structures contained in this container.
References structure_map_.
Referenced by protocols::noesy_assign::NoesyModule::assign(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::fill_pool(), protocols::abinitio::IterativeBase::gen_diversity_pool(), protocols::toolbox::KClusterData::load_silent_file(), protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(), protocols::jd2::archive::BaseArchiveManager::read_returning_decoys(), protocols::jd2::archive::ArchiveBase::read_structures(), and protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation().
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Returns true if this silent-file plans on storing option.get_argv() as a comment in the silent-file, false otherwise.
References store_argv_in_file_.
Referenced by write_silent_struct().
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Sets a boolean variable governing if this silent-file plans on storing option.get_argv() as a comment in the silent-file.
References store_argv_in_file_.
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Returns a boolean indicating whether or not the strict_column_mode is turned on when printing scores.
If strict_column_mode() is true, then the first SilentStruct printed to this SilentFileData object sets the EnergyNames that will be printed for all other SilentStruct objects. Extra EnergyNames in subsequent SilentStruct objects are ignored. If new objects are missing energies that should be printed in strict_column_mode, missing energy values are set to zero. In !strict_column_mode(), when each SilentStruct is printed, a new SCORE: header is printed if energies differ from last printed SilentStruct.
References strict_column_mode_.
Referenced by protocols::abinitio::AbrelaxApplication::fold(), and write_silent_struct().
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Sets value for strict column mode. See strict_column_mode() for more information.
References strict_column_mode_.
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Function to access the vector of silent structure owning pointers ordered as they were in the input file.
References structure_list_.
utility::vector1< std::string > core::io::silent::SilentFileData::tags | ( | ) | const |
Return all tags in this container.
References structure_map_.
Referenced by protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::indexed_structure_store::SilentStructureStoreBackend::load_store(), protocols::ddG::ddGData::read_mut_data(), and protocols::ddG::ddGData::read_wt_data().
void core::io::silent::SilentFileData::write_all | ( | std::string const & | filename, |
bool | bWriteScoreOnly = false |
||
) | const |
write all SilentStruct objects in the structure_map_ to the given filename.
References begin(), end(), and write_silent_struct().
Referenced by protocols::jobdist::PlainSilentFileJobDistributor::dump_silent(), protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter::flush(), protocols::jd3::pose_outputters::SilentFilePoseOutputter::flush(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeBase::gen_diversity_pool(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file(), and protocols::abinitio::HedgeArchive::save_pending_decoys().
void core::io::silent::SilentFileData::write_comment | ( | std::ostream & | out, |
std::string const & | line | ||
) | const |
Write a comment to the given output stream.
Referenced by write_silent_struct().
bool core::io::silent::SilentFileData::write_silent_struct | ( | SilentStruct & | s, |
std::string const & | filename, | ||
bool | bWriteScoreOnly = false |
||
) | const |
Write the given silent-struct to the given outfile.
References core::io::silent::SilentStruct::print_header(), core::io::silent::SilentStruct::print_score_header(), store_argv_in_file(), and write_comment().
Referenced by _write_silent_struct(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::rna::denovo::RNA_DeNovoProtocol::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::ddg::ddGMover::apply(), protocols::electron_density::DockIntoDensityMover::apply_multi(), protocols::boinc::boincOutputFilter(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score(), protocols::mpi_refinement::Serial_Refine::dump_structures(), protocols::loophash::MPI_LoopHashRefine::dump_structures(), protocols::mpi_refinement::MPI_Refinement::dump_structures(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), protocols::rna::denovo::export_packer_results(), protocols::abinitio::AbrelaxApplication::fold(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), protocols::recces::RECCES_Mover::more_dump_stuff(), protocols::frag_picker::FragmentPicker::nonlocal_pairs(), protocols::jobdist::not_universal_main(), protocols::stepwise::modeler::rna::output_data(), protocols::abinitio::Protocol::output_debug_structure(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::output_debug_structure(), protocols::relax::RelaxProtocolBase::output_debug_structure(), protocols::abinitio::MembraneAbinitio::output_debug_structure(), protocols::magnesium::MgScanner::output_mg_to_silent_file(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::output_silent_file(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::stepwise::legacy::modeler::protein::output_silent_struct(), protocols::stepwise::monte_carlo::output_to_silent_file(), protocols::cluster::ClusterBase::print_clusters_silentfile(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::recalculate_rmsd_and_output_silent_file(), protocols::ddg::ddGMover::relax_wildtype_structure(), protocols::md::MDBase::report_silent(), protocols::abinitio::run_boinc_debug(), protocols::toolbox::KClusterData::save_all_in_one(), protocols::toolbox::KClusterData::save_cluster_tree(), protocols::jd2::archive::ArchiveBase::save_decoys(), protocols::wum::SilentStructStore::serialize(), protocols::jobdist::universal_main(), write_all(), protocols::jd2::write_score_tracer(), and write_silent_struct().
bool core::io::silent::SilentFileData::write_silent_struct | ( | SilentStruct & | s, |
std::ostream & | out, | ||
bool | bWriteScoreOnly = false |
||
) | const |
Write the given silent-struct, minus the header, to the given ostream.
Note that this method does not write the header to the given stream. As such, I would guess that method is meant for internal use only, even though it isn't declared as private. If you want to write a complete silent file to a stream, use the _write_silent_struct() method instead.
References core::io::silent::EnergyNames::energy_names(), core::io::silent::SilentStruct::energy_names(), core::io::silent::energynames, get_shared_silent_data(), has_shared_silent_data(), core::io::silent::SilentStruct::nonconst_other_struct_list(), options_, core::io::silent::SilentStruct::other_struct_list(), core::io::silent::SilentFileOptions::print_all_score_headers(), core::io::silent::SilentStruct::print_comments(), core::io::silent::SilentStruct::print_conformation(), core::io::silent::SilentStruct::print_header(), core::io::silent::SilentStruct::print_residue_numbers(), core::io::silent::SilentStruct::print_scores(), core::io::silent::SilentStruct::print_submotif_info(), set_shared_silent_data(), core::io::silent::SilentStruct::set_valid_energies(), strict_column_mode(), and write_silent_struct().
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Referenced by clear(), comment_line(), comment_lines(), and read_stream().
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Referenced by clear(), filename(), and set_filename().
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Referenced by create_SilentStructOP(), and read_full_model_parameters_from_remark().
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Referenced by _read_file(), create_SilentStructOP(), read_file(), read_stream(), and write_silent_struct().
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Referenced by read_stream(), and set_record_source().
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Referenced by clear(), clear_shared_silent_data(), get_shared_silent_data(), has_shared_silent_data(), and set_shared_silent_data().
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Referenced by clear(), and store_argv_in_file().
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Referenced by clear(), and strict_column_mode().
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mapping from index in a silent file to data pointers, for situations in which the ordering in the file matters.
Referenced by add_structure(), clear_structure_map(), order_by_energy(), renumber_all_decoys(), reverse_score_filter(), score_filter(), and structure_list().
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mapping from tags to structure data pointers
Referenced by add_as_other_struct_if_relevant(), add_structure(), begin(), clear_structure_map(), end(), get_iterator_for_tag(), get_structure(), has_tag(), operator[](), order_by_energy(), read_stream(), renumber_all_decoys(), reverse_score_filter(), score_filter(), size(), and tags().
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Referenced by read_stream(), and set_verbose().