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>

Inheritance diagram for core::io::silent::SilentFileData:

[legend]

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_

Detailed Description

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.

Constructor & Destructor Documentation

core::io::silent::SilentFileData::SilentFileData ( SilentFileOptions const & options )

core::io::silent::SilentFileData::SilentFileData	(	std::string const &	filename,
		SilentFileOptions const &	options
	)

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
	)

core::io::silent::SilentFileData::~SilentFileData ( )

override

Destructor.

References clear_structure_map().

Member Function Documentation

bool core::io::silent::SilentFileData::_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.

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`
	)

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`
	)		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:

SAFE! in the sense that it actually copies the SilentStruct object, not just the pointer to the object.
SLOW! in the sense that copying the object takes a small amount of time.

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().

iterator core::io::silent::SilentFileData::begin ( )

inline

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().

const_iterator core::io::silent::SilentFileData::begin ( ) const

inline

Returns an iterator to the start of the members of this container.

References structure_map_.

bool core::io::silent::SilentFileData::check_if_rna_from_sequence_line ( std::string const & sequence_line )

private

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().

void core::io::silent::SilentFileData::clear ( )

inline

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().

void core::io::silent::SilentFileData::clear_shared_silent_data ( )

inline

Clears all of the data associated with this object.

References shared_silent_data_.

void core::io::silent::SilentFileData::clear_structure_map ( )

inline

Remove all of the SilentStruct objects from this object.

References structure_list_, and structure_map_.

Referenced by clear(), renumber_all_decoys(), and ~SilentFileData().

void core::io::silent::SilentFileData::comment_line ( std::string const & line )

inline

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_.

utility::vector1< std::string > core::io::silent::SilentFileData::comment_lines ( )

inline

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().

iterator core::io::silent::SilentFileData::end ( )

inline

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().

const_iterator core::io::silent::SilentFileData::end ( ) const

inline

Returns an iterator to the end of the members of this container.

References structure_map_.

std::string const& core::io::silent::SilentFileData::filename ( ) const

inline

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().

iterator core::io::silent::SilentFileData::get_iterator_for_tag ( const std::string & tag )

inline

References structure_map_.

Referenced by protocols::jd2::archive::ArchiveBase::read_structures().

const_iterator core::io::silent::SilentFileData::get_iterator_for_tag ( const std::string & tag ) const

inline

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 )

References core::io::silent::figure_out_residue_numbers_from_line(), and get_sequence().

Referenced by core::import_pose::RNA_DeNovoSetup::get_silent_resnum(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_resnum().

std::string core::io::silent::SilentFileData::get_sequence ( std::string const & filename )

References core::chemical::orbitals::strip_whitespace(), and core::io::silent::tr().

Referenced by get_resnum(), core::import_pose::RNA_DeNovoSetup::get_silent_seq(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_seq().

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().

SilentStruct const& core::io::silent::SilentFileData::get_structure ( const std::string & tag ) const

inline

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().

bool core::io::silent::SilentFileData::has_tag ( std::string const & tag ) const

inline

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[]().

bool core::io::silent::SilentFileData::is_score_type_line ( std::string const & line ) const

private

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.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

bool core::io::silent::SilentFileData::line_starts_with_other ( std::string const & line ) const

private

Are the first six characters of a line "OTHER:"?

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

bool core::io::silent::SilentFileData::line_starts_with_other_header_string ( std::string const & line ) const

private

Does a line start with another header string?

Includes strings like "ANNOTATED_SEQUENCE", "FOLD_TREE", etc.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

bool core::io::silent::SilentFileData::line_starts_with_remark ( std::string const & line ) const

private

Are the first six characters of a line "REMARK "?

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

bool core::io::silent::SilentFileData::line_starts_with_score ( std::string const & line ) const

private

Are the first six characters of a line "SCORE:"?

Both score type lines and score lines start with "SCORE:".

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

bool core::io::silent::SilentFileData::line_starts_with_sequence ( std::string const & line ) const

private

Are the first nine characters of a line "SEQUENCE:"?

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by read_stream().

void core::io::silent::SilentFileData::lines_from_header_line_collection	(	std::map< SilentFileHeaderLine, std::string > const &	header_lines,
		utility::vector1< std::string > &	all_lines
	)		const

private

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.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

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_.

void core::io::silent::SilentFileData::push_back ( SilentStructOP const & new_struct )

inline

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().

bool core::io::silent::SilentFileData::read_full_model_parameters_from_remark	(	std::string const &	line,
		bool const	header = `false`
	)

private

Look for FULL_MODEL_PARAMETERS in REMARK line from header.

References full_model_parameters_.

Referenced by read_stream().

bool core::io::silent::SilentFileData::read_silent_struct_type_from_remark	(	std::string const &	line,
		bool const	header = `false`
	)

private

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"`
	)

Parameters

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().

void core::io::silent::SilentFileData::set_filename ( std::string filename )

inline

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().

void core::io::silent::SilentFileData::set_record_source ( bool const & new_mode )

inline

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().

void core::io::silent::SilentFileData::set_verbose ( bool const setting )

inline

Sets the filename that this SilentFileData object will write to.

References verbose_.

Size core::io::silent::SilentFileData::size ( ) const

inline

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().

bool core::io::silent::SilentFileData::store_argv_in_file ( ) const

inline

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().

void core::io::silent::SilentFileData::store_argv_in_file ( bool new_setting )

inline

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_.

bool core::io::silent::SilentFileData::strict_column_mode ( ) const

inline

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().

void core::io::silent::SilentFileData::strict_column_mode ( bool new_mode )

inline

Sets value for strict column mode. See strict_column_mode() for more information.

References strict_column_mode_.

utility::vector1<SilentStructOP> core::io::silent::SilentFileData::structure_list ( )

inline

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.