#include <SilentStruct.hh>

Public Member Functions
	SilentStruct ()

virtual	~SilentStruct ()

	SilentStruct (SilentStruct const &)

SilentStruct &	operator= (SilentStruct const &)

virtual SilentStructOP	clone () const =0

virtual void	fill_pose (core::pose::Pose &pose) const

virtual void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const
	Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which should be implemented by classes derived from SilentStruct. More...

void	set_tag_from_pose (const core::pose::Pose &pose)
	Sets the tag from the Pose DataCache. More...

void	precision (core::Size precision)

core::Size	precision () const

void	scoreline_prefix (std::string const &prefix)

std::string	scoreline_prefix () const

virtual void	fill_struct (core::pose::Pose const &pose, std::string tag="empty_tag")
	opposite of fill_pose – superclass provides functionality used by most SilentStruct types, and is optionally called at the beginning of the subclass's fill_struct method. As of this writing, used only by protein SilentStructs More...

void	finish_pose (core::pose::Pose &pose) const
	calls optH if command line requests optH. must be called by derived classes. More...

virtual Real	get_debug_rmsd ()=0
	Do some sort of comparison between the actual RMSD of this silent-struct and the cached coordinates. Used for SilentStruct objects that are rebuild from torsions or other reduced representations of data. More...

virtual void	print_header (std::ostream &out) const
	print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines: SEQUENCE: <protein sequence>="">: More...

virtual void	print_score_header (std::ostream &out) const
	only print SCORE: header line More...

virtual void	print_scores (std::ostream &out) const
	print out a SCORE line to the given ozstream. More...

virtual void	print_conformation (std::ostream &out) const =0
	print the conformation information in SilentStruct to out. More...

virtual void	print_comments (std::ostream &out) const
	print the comments in this SilentStruct. More...

virtual void	print_residue_numbers (std::ostream &out) const
	print the resnum in this SilentStruct, if filled. More...

virtual Size	nres () const
	returns the number of residues contained by this SilentStruct. More...

void	set_decoy_tag (std::string const &tag)
	set the tag associate with this SilentStruct More...

std::string	decoy_tag () const
	returns the tag associated with this SilentStruct. More...

core::sequence::AnnotatedSequence const &	sequence () const
	returns the sequence associated with this SilentStruct. More...

void	nres (Size nres)
	returns the number of residues in this SilentStruct. More...

void	decoy_tag (std::string const &tag)
	sets the tag associated with this SilentStruct. More...

void	sequence (core::sequence::AnnotatedSequence const &sequence)
	sets the sequence for this SilentStruct. More...

void	silent_energies (utility::vector1< SilentEnergy > const &new_se)
	sets the silent_energies for this SilentStruct. More...

void	sort_silent_scores ()
	sort all the silent energies by their name. More...

bool	has_energy (std::string const scorename) const
	returns true if this SilentStruct has an energy for the given scorename, returns false otherwise. More...

core::Real	get_energy (std::string const &scorename) const
	Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...

std::string const &	get_string_value (std::string const &scorename) const
	Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0. More...

SilentEnergy const &	get_silent_energy (std::string const &scorename) const
	Returns the SilentEnergy associated with this scorename. More...

utility::vector1< SilentEnergy >	get_silent_energies ()

void	set_valid_energies (utility::vector1< std::string > valid)

virtual void	clear_energies ()
	Clear all of the energies in the SilentStruct. Doesn't just zero the energies, it entirely removes all knowledge of all energies from this SilentStruct. More...

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)=0
	Create a new SilentStruct object from the provided set of lines. This abstract method should be overwritten by derived classes. Returns false if the init_from_lines routine encounters a problem with the lines provided. More...

void	add_energy (std::string scorename, Real value, Real weight=1.0)
	add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0. More...

void	add_string_value (std::string scorename, std::string const &value)
	add a non-floating point score of a given name and value to this SilentStruct. More...

void	copy_scores (const SilentStruct &src_ss)
	Copy the score information in the given SilentStruct into this SilentStruct. More...

void	add_comment (std::string name, std::string value)
	add a named comment to this SilentStruct object. Similar to methods for playing with energies, but mapping is string => string rather than string => Real. More...

bool	has_comment (std::string const &name) const

std::string	get_comment (std::string const &name) const

void	comment_from_line (std::string const &line)

void	erase_comment (std::string const &name)

void	clear_comments ()

std::map< std::string, std::string >	get_all_comments () const

void	parse_energies (std::istream &input, utility::vector1< std::string > const &energy_names)

void	energies_from_pose (core::pose::Pose const &pose)
	Initialize this SilentStruct's energies from the given Pose. This sets energies, energy weights, and the output widths for the energies. More...

void	energies_into_pose (core::pose::Pose &pose) const
	Put the energy information from this SilentStruct into the pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct. More...

virtual ObjexxFCL::FArray2D< Real >	get_CA_xyz () const =0
	returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations. More...

utility::vector1< SilentEnergy >	energies () const
	Returns the vector of SilentEnergy objects associated with this SilentStruct object. More...

EnergyNames	energy_names () const
	Returns the EnergyNames that this SilentStruct contains. More...

void	rename_energies ()

bool	read_sequence (std::string const &line)

void	read_score_headers (std::string const &line, utility::vector1< std::string > &enames, SilentFileData &container)

std::string	one_letter_sequence () const
	strip [...] comment from seqeunce_ and return pure one-letter sequence More...

virtual core::Size	mem_footprint () const

void	print_parent_remarks (std::ostream &out) const

std::string	get_parent_remark (std::string const &name) const

bool	has_parent_remark (std::string const &name) const

void	add_parent_remark (std::string const name, std::string const value)

void	get_parent_remark_from_line (std::string const line)

void	set_residue_numbers (utility::vector1< Size > const &residue_numbers)

void	set_chains (utility::vector1< char > const &chains)

void	fill_struct_with_residue_numbers (pose::Pose const &pose)

void	residue_numbers_into_pose (pose::Pose &pose) const

void	figure_out_residue_numbers_from_line (std::istream &line_stream)

Protected Member Functions
void	detect_fullatom (core::Size pos, core::Size natoms, bool &fullatom, bool &well_defined)
	@ brief helper to detect fullatom input More...

void	extract_writeable_cacheable_data (core::pose::Pose const &pose)
	add string serialization of all WriteableCacheableData in as comments. More...

Private Types
typedef std::string	string

Private Member Functions
void	update_score ()
	Updates the "score" entry in the silent_energies. More...

Private Attributes
bool	strict_column_mode_

Size	nres_

std::string	decoy_tag_

core::sequence::AnnotatedSequence	sequence_

std::map< std::string, std::string >	parent_remarks_map_

std::map< std::string, std::string >	silent_comments_

utility::vector1< SilentEnergy >	silent_energies_

utility::vector1< std::string >	cache_remarks_

utility::vector1< Size >	residue_numbers_

utility::vector1< char >	chains_

core::Size	precision_

std::string	scoreline_prefix_

Member Typedef Documentation

typedef std::string core::io::silent::SilentStruct::string

private

Constructor & Destructor Documentation

core::io::silent::SilentStruct::SilentStruct ( )

core::io::silent::SilentStruct::~SilentStruct ( )

virtual

core::io::silent::SilentStruct::SilentStruct ( SilentStruct const & src )

Member Function Documentation

void core::io::silent::SilentStruct::add_comment	(	std::string	name,
		std::string	value
	)

add a named comment to this SilentStruct object. Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

References cache_remarks_, silent_comments_, and core::io::silent::tr.

Referenced by comment_from_line(), energies_from_pose(), extract_writeable_cacheable_data(), and core::io::silent::BinarySilentStruct::init_from_lines().

void core::io::silent::SilentStruct::add_energy	(	std::string	scorename,
		Real	value,
		Real	weight = `1.0`
	)

add a score of a given name and value to this SilentStruct. Takes an optional weight that defaults to 1.0.

References core::sequence::end, and silent_energies_.

Referenced by core::io::silent::RNA_SilentStruct::init_from_lines(), and parse_energies().

void core::io::silent::SilentStruct::add_parent_remark	(	std::string const	name,
		std::string const	value
	)

References parent_remarks_map_, and core::io::silent::tr.

Referenced by get_parent_remark_from_line().

void core::io::silent::SilentStruct::add_string_value	(	std::string	scorename,
		std::string const &	value
	)

add a non-floating point score of a given name and value to this SilentStruct.

References core::sequence::end, and silent_energies_.

Referenced by energies_from_pose(), and parse_energies().

void core::io::silent::SilentStruct::clear_comments ( )

References silent_comments_.

virtual void core::io::silent::SilentStruct::clear_energies ( )

inlinevirtual

Clear all of the energies in the SilentStruct. Doesn't just zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

References silent_energies_.

Referenced by energies_from_pose().

virtual SilentStructOP core::io::silent::SilentStruct::clone ( ) const

pure virtual

Implemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.

Referenced by core::io::silent::SilentFileData::add_structure().

void core::io::silent::SilentStruct::comment_from_line ( std::string const & line )

References add_comment(), key, and core::io::silent::tr.

void core::io::silent::SilentStruct::copy_scores ( const SilentStruct & src_ss )

Copy the score information in the given SilentStruct into this SilentStruct.

References core::sequence::end, and silent_energies_.

std::string core::io::silent::SilentStruct::decoy_tag ( ) const

inline

returns the tag associated with this SilentStruct.

References decoy_tag_.

void core::io::silent::SilentStruct::decoy_tag ( std::string const & tag )

inline

sets the tag associated with this SilentStruct.

References decoy_tag_.

void core::io::silent::SilentStruct::detect_fullatom	(	core::Size	pos,
		core::Size	natoms,
		bool &	fullatom,
		bool &	well_defined
	)

protected

@ brief helper to detect fullatom input

@ brief helper to detect fullatom input @ detail

References core::chemical::aa_vrt, core::chemical::num_canonical_aas, core::sequence::AnnotatedSequence::one_letter(), sequence(), and core::io::silent::tr.

Referenced by core::io::silent::BinarySilentStruct::init_from_lines().

utility::vector1< SilentEnergy > core::io::silent::SilentStruct::energies ( ) const

inline

Returns the vector of SilentEnergy objects associated with this SilentStruct object.

References silent_energies_.

Referenced by energies_into_pose(), and energy_names().

void core::io::silent::SilentStruct::energies_from_pose ( core::pose::Pose const & pose )

Initialize this SilentStruct's energies from the given Pose. This sets energies, energy weights, and the output widths for the energies.

References add_comment(), add_string_value(), clear_energies(), core::pose::Pose::data(), core::sequence::end, core::pose::Pose::energies(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), basic::datacache::BasicDataCache::get_raw_const_ptr(), basic::datacache::BasicDataCache::has(), core::scoring::name_from_score_type(), silent_energies_, core::scoring::Energies::total_energies(), core::io::silent::tr, update_score(), and core::scoring::Energies::weights().

Referenced by fill_struct(), and core::io::silent::RNA_SilentStruct::fill_struct().

void core::io::silent::SilentStruct::energies_into_pose ( core::pose::Pose & pose ) const

Put the energy information from this SilentStruct into the pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

References core::pose::add_comment(), core::pose::add_score_line_string(), core::pose::Pose::data(), core::sequence::end, energies(), core::pose::Pose::energies(), get_all_comments(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), option, runtime_assert, core::scoring::score_type_from_name(), basic::datacache::BasicDataCache::set(), in::file::silent_score_prefix, in::file::silent_scores_wanted, core::scoring::Energies::total_energies(), core::io::silent::tr, user, weights, and core::scoring::Energies::weights().

Referenced by finish_pose().

EnergyNames core::io::silent::SilentStruct::energy_names ( ) const

Returns the EnergyNames that this SilentStruct contains.

References core::sequence::end, energies(), and core::io::silent::EnergyNames::energy_names().

Referenced by core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::erase_comment ( std::string const & name )

References silent_comments_.

void core::io::silent::SilentStruct::extract_writeable_cacheable_data ( core::pose::Pose const & pose )

protected

add string serialization of all WriteableCacheableData in as comments.

Parameters

pose	a pose containing a datacache with WriteableCacheableData.

References add_comment(), core::pose::Pose::data(), basic::datacache::DataMap::get(), and ss.

Referenced by fill_struct().

void core::io::silent::SilentStruct::figure_out_residue_numbers_from_line ( std::istream & line_stream )

References utility::get_resnum_and_chain(), set_chains(), and set_residue_numbers().

Referenced by core::io::silent::BinarySilentStruct::init_from_lines(), and core::io::silent::RNA_SilentStruct::init_from_lines().

void core::io::silent::SilentStruct::fill_pose ( core::pose::Pose & pose ) const

virtual

Reimplemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, and core::import_pose::PDBSilentStruct.

References core::chemical::FA_STANDARD, nres_, and runtime_assert.

void core::io::silent::SilentStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	residue_set
	)		const

virtual

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which should be implemented by classes derived from SilentStruct.

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSet provided by the caller. This is a virtual method which must be implemented by classes derived from SilentStruct.

Reimplemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

References core::io::silent::tr.

void core::io::silent::SilentStruct::fill_struct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`
	)

virtual

opposite of fill_pose – superclass provides functionality used by most SilentStruct types, and is optionally called at the beginning of the subclass's fill_struct method. As of this writing, used only by protein SilentStructs

Reimplemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

References core::pose::Pose::annotated_sequence(), decoy_tag(), energies_from_pose(), extract_writeable_cacheable_data(), sequence(), set_tag_from_pose(), and core::io::silent::tr.

Referenced by core::io::silent::BinarySilentStruct::fill_struct(), and core::io::silent::ProteinSilentStruct_Template< T >::fill_struct().

void core::io::silent::SilentStruct::fill_struct_with_residue_numbers ( pose::Pose const & pose )

References core::pose::Pose::pdb_info(), set_chains(), set_residue_numbers(), and core::pose::Pose::total_residue().

Referenced by core::io::silent::BinarySilentStruct::fill_struct(), and core::io::silent::RNA_SilentStruct::fill_struct().

void core::io::silent::SilentStruct::finish_pose ( core::pose::Pose & pose ) const

calls optH if command line requests optH. must be called by derived classes.

References cache_remarks_, core::pose::Pose::data(), energies_into_pose(), basic::datacache::WriteableCacheableMap::insert(), in::file::keep_input_scores, option, core::pose::Pose::pdb_info(), residue_numbers_into_pose(), basic::datacache::BasicDataCache::set(), core::io::silent::tr, and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

Referenced by core::io::silent::BinarySilentStruct::fill_pose(), and core::io::silent::RNA_SilentStruct::fill_pose().

std::map< std::string, std::string > core::io::silent::SilentStruct::get_all_comments ( ) const

References silent_comments_.

Referenced by energies_into_pose().

virtual ObjexxFCL::FArray2D< Real > core::io::silent::SilentStruct::get_CA_xyz ( ) const

pure virtual

returns the positions of the CA atoms in this ProteinSilentStruct. Useful for RMS calculations.

Implemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

std::string core::io::silent::SilentStruct::get_comment ( std::string const & name ) const

References silent_comments_.

virtual Real core::io::silent::SilentStruct::get_debug_rmsd ( )

pure virtual

Do some sort of comparison between the actual RMSD of this silent-struct and the cached coordinates. Used for SilentStruct objects that are rebuild from torsions or other reduced representations of data.

Implemented in core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

core::Real core::io::silent::SilentStruct::get_energy ( std::string const & scorename ) const

Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0.

References get_silent_energy(), has_energy(), and core::io::silent::SilentEnergy::value().

std::string core::io::silent::SilentStruct::get_parent_remark ( std::string const & name ) const

References parent_remarks_map_, and utility_exit_with_message.

void core::io::silent::SilentStruct::get_parent_remark_from_line ( std::string const line )

References add_parent_remark(), key, and utility_exit_with_message.

utility::vector1< SilentEnergy > core::io::silent::SilentStruct::get_silent_energies ( )

inline

References silent_energies_.

SilentEnergy const & core::io::silent::SilentStruct::get_silent_energy ( std::string const & scorename ) const

Returns the SilentEnergy associated with this scorename.

References core::sequence::end, has_energy(), and silent_energies_.

Referenced by get_energy(), get_string_value(), and set_valid_energies().

std::string const & core::io::silent::SilentStruct::get_string_value ( std::string const & scorename ) const

Returns the energy associated with the given scorename if this SilentStruct has an energy for that scorename. Otherwise returns 0.

References get_silent_energy(), has_energy(), and core::io::silent::SilentEnergy::string_value().

bool core::io::silent::SilentStruct::has_comment ( std::string const & name ) const

References silent_comments_.

bool core::io::silent::SilentStruct::has_energy ( std::string const scorename ) const

returns true if this SilentStruct has an energy for the given scorename, returns false otherwise.

References core::sequence::end, and silent_energies_.

Referenced by get_energy(), get_silent_energy(), get_string_value(), and set_valid_energies().

bool core::io::silent::SilentStruct::has_parent_remark ( std::string const & name ) const

References parent_remarks_map_.

virtual bool core::io::silent::SilentStruct::init_from_lines	(	utility::vector1< std::string > const &	lines,
		SilentFileData &	container
	)

pure virtual

Create a new SilentStruct object from the provided set of lines. This abstract method should be overwritten by derived classes. Returns false if the init_from_lines routine encounters a problem with the lines provided.

Implemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.

virtual core::Size core::io::silent::SilentStruct::mem_footprint ( ) const

inlinevirtual

Reimplemented in core::io::silent::ProteinSilentStruct_Template< T >.

virtual Size core::io::silent::SilentStruct::nres ( ) const

inlinevirtual

returns the number of residues contained by this SilentStruct.

References nres_.

void core::io::silent::SilentStruct::nres ( Size nres )

inline

returns the number of residues in this SilentStruct.

References nres(), and nres_.

std::string core::io::silent::SilentStruct::one_letter_sequence ( ) const

strip [...] comment from seqeunce_ and return pure one-letter sequence

References core::sequence::AnnotatedSequence::one_letter_sequence(), and sequence().

Referenced by core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::init_from_lines(), and print_header().

SilentStruct & core::io::silent::SilentStruct::operator= ( SilentStruct const & src )

References cache_remarks_, chains_, decoy_tag_, nres_, precision_, residue_numbers_, scoreline_prefix_, sequence_, silent_comments_, silent_energies_, and strict_column_mode_.

void core::io::silent::SilentStruct::parse_energies	(	std::istream &	input,
		utility::vector1< std::string > const &	energy_names
	)

References add_energy(), add_string_value(), decoy_tag(), tag, and core::io::silent::tr.

Referenced by core::io::silent::BinarySilentStruct::init_from_lines().

void core::io::silent::SilentStruct::precision ( core::Size precision )

References precision(), and precision_.

core::Size core::io::silent::SilentStruct::precision ( ) const

References precision_.

Referenced by precision(), and print_scores().

void core::io::silent::SilentStruct::print_comments ( std::ostream & out ) const

virtual

print the comments in this SilentStruct.

References cache_remarks_, core::sequence::end, and silent_comments_.

Referenced by print_scores().

virtual void core::io::silent::SilentStruct::print_conformation ( std::ostream & out ) const

pure virtual

print the conformation information in SilentStruct to out.

Implemented in core::io::silent::RNA_SilentStruct, core::io::silent::ProteinSilentStruct_Template< T >, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

Referenced by core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::print_header ( std::ostream & out ) const

virtual

print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines: SEQUENCE: <protein sequence>="">:

Reimplemented in core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::ScoreJumpFileSilentStruct, and core::io::silent::ScoreFileSilentStruct.

References one_letter_sequence(), and print_score_header().

Referenced by core::io::silent::SilentFileData::_write_silent_struct(), core::io::silent::ScoreJumpFileSilentStruct::print_header(), core::io::silent::BinarySilentStruct::print_header(), core::io::silent::RNA_SilentStruct::print_header(), and core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::print_parent_remarks ( std::ostream & out ) const

References core::sequence::end, and parent_remarks_map_.

void core::io::silent::SilentStruct::print_residue_numbers ( std::ostream & out ) const

virtual

print the resnum in this SilentStruct, if filled.

References chains_, decoy_tag(), make_tag_with_dashes(), nres_, and residue_numbers_.

Referenced by core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::print_score_header ( std::ostream & out ) const

virtual

only print SCORE: header line

References decoy_tag(), core::sequence::end, option, scoreline_prefix(), silent_energies_, tag, user, and out::user_tag.

Referenced by print_header(), and core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::print_scores ( std::ostream & out ) const

virtual

print out a SCORE line to the given ozstream.

References decoy_tag(), core::sequence::end, option, precision(), print_comments(), scoreline_prefix(), silent_energies_, tag, user, out::user_tag, weight, and out::file::weight_silent_scores.

Referenced by core::io::silent::SilentFileData::write_silent_struct().

void core::io::silent::SilentStruct::read_score_headers	(	std::string const &	line,
		utility::vector1< std::string > &	enames,
		SilentFileData &	container
	)