#include <SilentStruct.hh>

Inheritance diagram for core::io::silent::SilentStruct:

Collaboration diagram for core::io::silent::SilentStruct:

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")=0
	opposite of fill_pose 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 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)

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

core::Size	precision_

std::string	scoreline_prefix_

Detailed Description

Definition at line 54 of file SilentStruct.hh.

Member Typedef Documentation

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

private

Definition at line 56 of file SilentStruct.hh.

Constructor & Destructor Documentation

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

Definition at line 92 of file SilentStruct.cc.

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

virtual

Definition at line 96 of file SilentStruct.cc.

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

Definition at line 98 of file SilentStruct.cc.

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.

Definition at line 430 of file SilentStruct.cc.

References silent_comments_.

Referenced by comment_from_line(), energies_from_pose(), and core::io::silent::BinaryProteinSilentStruct::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.

Definition at line 306 of file SilentStruct.cc.

References core::sequence::end, protocols::forge::methods::replace(), and silent_energies_.

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

Definition at line 876 of file SilentStruct.cc.

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.

Definition at line 328 of file SilentStruct.cc.

References core::sequence::end, protocols::forge::methods::replace(), and silent_energies_.

Referenced by protocols::rna::RNA_DeNovoProtocol::add_number_base_pairs(), protocols::simple_filters::BatchEvaluator::apply(), protocols::constraints_additional::ConstraintEvaluator::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), energies_from_pose(), protocols::swa::monte_carlo::RNA_SWA_MonteCarloMover::output_silent_file(), and parse_energies().

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

Definition at line 480 of file SilentStruct.cc.

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.

Definition at line 195 of file SilentStruct.hh.

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::BinaryRNASilentStruct, core::io::silent::BinaryProteinSilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.

Referenced by protocols::wum::SilentStructStore::add(), and core::io::silent::SilentFileData::add_structure().

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

Definition at line 434 of file SilentStruct.cc.

References add_comment(), 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.

Definition at line 405 of file SilentStruct.cc.

References core::sequence::end, protocols::forge::methods::replace(), and silent_energies_.

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

inline

returns the tag associated with this SilentStruct.

Definition at line 141 of file SilentStruct.hh.

References decoy_tag_.

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

inline

sets the tag associated with this SilentStruct.

Definition at line 156 of file SilentStruct.hh.

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

Definition at line 820 of file SilentStruct.cc.

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

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

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

inline

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

Definition at line 256 of file SilentStruct.hh.

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.

Definition at line 534 of file SilentStruct.cc.

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(), 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 core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::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.

Definition at line 612 of file SilentStruct.cc.

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(), core::scoring::ScoreTypeManager::is_score_type(), core::scoring::ScoreTypeManager::score_type_from_name(), core::scoring::Energies::total_energies(), core::io::silent::tr(), and core::scoring::Energies::weights().

Referenced by finish_pose().

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

Returns the EnergyNames that this SilentStruct contains.

Definition at line 696 of file SilentStruct.cc.

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)

Definition at line 476 of file SilentStruct.cc.

References silent_comments_.

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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, and core::import_pose::PDBSilentStruct.

Definition at line 116 of file SilentStruct.cc.

References core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), nres_, and core::chemical::ChemicalManager::residue_type_set().

Referenced by protocols::evaluation::PoseEvaluator::apply(), and protocols::abinitio::KinematicAbinitio::apply().

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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::import_pose::PDBSilentStruct, and core::io::silent::ScoreFileSilentStruct.

Definition at line 129 of file SilentStruct.cc.

References core::io::silent::tr().

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

pure virtual

opposite of fill_pose

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

Referenced by protocols::abinitio::AbrelaxApplication::process_decoy().

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.

Definition at line 136 of file SilentStruct.cc.

References energies_into_pose(), core::pose::Pose::pdb_info(), and core::io::silent::tr().

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

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

Definition at line 457 of file SilentStruct.cc.

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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, and core::io::silent::ScoreFileSilentStruct.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate(), and protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate().

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

Definition at line 465 of file SilentStruct.cc.

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::import_pose::PDBSilentStruct, core::io::silent::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, 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.

Definition at line 351 of file SilentStruct.cc.

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

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::loophash::MPI_LoopHashRefine_Emperor::add_structures_to_library(), protocols::abinitio::KinematicAbinitio::dump_jump_log(), protocols::loophash::MPI_LoopHashRefine::format_silent_struct(), protocols::loophash::MPI_LoopHashRefine::objective_function(), protocols::loophash::WorkUnit_LoopHash::run(), and protocols::loophash::MPI_LoopHashRefine::score().

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

Definition at line 853 of file SilentStruct.cc.

References parent_remarks_map_.

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

Definition at line 890 of file SilentStruct.cc.

References add_parent_remark().

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

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

inline

Definition at line 188 of file SilentStruct.hh.

References silent_energies_.

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

Returns the SilentEnergy associated with this scorename.

Definition at line 369 of file SilentStruct.cc.

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.

Definition at line 358 of file SilentStruct.cc.

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

Referenced by protocols::loophash::MPI_LoopHashRefine::format_silent_struct().

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

Definition at line 461 of file SilentStruct.cc.

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.

Definition at line 294 of file SilentStruct.cc.

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

Referenced by protocols::rna::RNA_DeNovoProtocol::add_chem_shift_info(), 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

Definition at line 869 of file SilentStruct.cc.

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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, 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 >.

Definition at line 274 of file SilentStruct.hh.

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

inlinevirtual

returns the number of residues contained by this SilentStruct.

Definition at line 131 of file SilentStruct.hh.

References nres_.

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

inline

returns the number of residues in this SilentStruct.

Definition at line 151 of file SilentStruct.hh.

References nres(), and nres_.

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

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

Definition at line 777 of file SilentStruct.cc.

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

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

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

Definition at line 104 of file SilentStruct.cc.

References decoy_tag_, nres_, precision_, 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
	)

Definition at line 485 of file SilentStruct.cc.

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

Referenced by core::io::silent::BinaryRNASilentStruct::init_from_lines(), and core::io::silent::BinaryProteinSilentStruct::init_from_lines().

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

Definition at line 758 of file SilentStruct.cc.

References precision(), and precision_.

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

Definition at line 762 of file SilentStruct.cc.

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.

Definition at line 269 of file SilentStruct.cc.

References 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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, core::import_pose::PDBSilentStruct, 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::BinaryProteinSilentStruct, core::io::silent::BinaryRNASilentStruct, and core::io::silent::ScoreFileSilentStruct.

Definition at line 199 of file SilentStruct.cc.

References one_letter_sequence(), and print_score_header().

Referenced by core::io::silent::SilentFileData::_write_silent_struct(), core::io::silent::BinaryRNASilentStruct::print_header(), core::io::silent::BinaryProteinSilentStruct::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

Definition at line 839 of file SilentStruct.cc.

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

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

virtual

only print SCORE: header line

Definition at line 204 of file SilentStruct.cc.

References protocols::comparative_modeling::features::A, decoy_tag(), core::sequence::end, scoreline_prefix(), and silent_energies_.

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.

Definition at line 231 of file SilentStruct.cc.

References protocols::comparative_modeling::features::A, decoy_tag(), core::sequence::end, precision(), print_comments(), scoreline_prefix(), and silent_energies_.

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
	)