#include <SilentStruct.hh>

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

Public Member Functions
	SilentStruct (SilentFileOptions const &opts)

	~SilentStruct () override

	SilentStruct (SilentStruct const &)

SilentStruct &	operator= (SilentStruct const &)

virtual SilentStructOP	clone () const =0

SilentStructCOP	get_self_ptr () const
	self pointers More...

SilentStructOP	get_self_ptr ()

virtual void	fill_pose (core::pose::Pose &pose, bool const metapatches=true) const

void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSetCOP residue_set, bool const metapatches=true) const
	non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one) and invokes the virtual method that takes the const &. More...

virtual void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) 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 void	print_submotif_info (std::ostream &out) const
	print the submotif_info 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 const &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 const &scorename, std::string const &value, int const index=-1)
	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	comment_from_line (std::string const &line, bool const include_silentfile_comments)
	Creates and adds a comment from an input REMARK line. More...

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< int > const &residue_numbers)

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

void	set_full_model_parameters (core::pose::full_model_info::FullModelParametersCOP setting)

core::pose::full_model_info::FullModelParametersCOP	full_model_parameters () const

void	set_segment_IDs (utility::vector1< std::string > const &segids)

void	fill_struct_with_residue_numbers (pose::Pose const &pose)

void	fill_other_struct_list (pose::Pose const &pose)

void	residue_numbers_into_pose (pose::Pose &pose) const

void	full_model_info_into_pose (pose::Pose &pose) const

void	figure_out_residue_numbers_from_line (std::istream &line_stream)

void	figure_out_segment_ids_from_line (std::istream &line_stream)

void	add_submotif_info_from_line (std::istream &line_stream)

void	fill_struct_with_submotif_info_list (pose::Pose const &pose)

utility::vector1 < SilentStructOP > const &	other_struct_list () const

utility::vector1 < SilentStructOP > &	nonconst_other_struct_list ()

void	add_other_struct (SilentStructOP silent_struct)

virtual void	set_force_bitflip (bool const setting)
	Sets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...

virtual bool	force_bitflip () const
	Gets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines. More...

SilentFileOptions const &	options () const

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	force_bitflip_
	If true, this forces conversion from big-endian to little-endian (or the converse) when a binary silent structure is initialized from lines (init_from_lines() function). More...

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< std::string >	pdbinfo_labels_

utility::vector1< int >	residue_numbers_

utility::vector1< char >	chains_

utility::vector1< SilentStructOP >	other_struct_list_

core::pose::full_model_info::FullModelParametersCOP	full_model_parameters_

utility::vector1< std::string >	segment_IDs_

utility::vector1 < core::pose::full_model_info::SubMotifInfoOP >	submotif_info_list_

core::Size	precision_

std::string	scoreline_prefix_

SilentFileOptions	options_

Member Typedef Documentation

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

private

Constructor & Destructor Documentation

core::io::silent::SilentStruct::SilentStruct ( SilentFileOptions const & opts )

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

overridedefault

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

default

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_, pdbinfo_labels_, silent_comments_, and core::io::silent::tr().

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

void core::io::silent::SilentStruct::add_energy	(	std::string const &	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 protocols::mean_field::max(), protocols::forge::methods::replace(), and silent_energies_.

void core::io::silent::SilentStruct::add_other_struct ( SilentStructOP silent_struct )

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

Referenced by fill_other_struct_list().

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 const &	scorename,
		std::string const &	value,
		int const	index = `-1`
	)

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

References protocols::mean_field::max(), protocols::forge::methods::replace(), and silent_energies_.

Referenced by core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_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::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo::output_silent_file(), and parse_energies().

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

References full_model_parameters_, and submotif_info_list_.

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

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

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

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

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

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

Creates and adds a comment from an input REMARK line.

Parameters

[in]	line	Input comment line, of the format "REMARK key value [value]*"
[in]	include_silentfile_comments	If true, 'REMARK XXX SILENTFILE' lines will be added to comments.

References add_comment(), core::io::silent::tr(), and protocols::hybridization::val.

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

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

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

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

inline

returns the tag associated with this SilentStruct.

References decoy_tag_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), protocols::evaluation::PoseEvaluator::apply(), core::io::silent::BinarySilentStruct::BinarySilentStruct(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), fill_struct(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::mpi_refinement::MPI_Refinement::format_silent_struct(), core::import_pose::PDBSilentStruct::init_from_lines(), core::io::silent::BinarySilentStruct::init_from_lines(), core::io::silent::RNA_SilentStruct::init_from_lines(), parse_energies(), core::import_pose::PDBSilentStruct::PDBSilentStruct(), core::io::silent::ScoreJumpFileSilentStruct::print_conformation(), core::io::silent::BinarySilentStruct::print_conformation(), core::io::silent::RNA_SilentStruct::print_conformation(), print_residue_numbers(), print_score_header(), print_scores(), print_submotif_info(), core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template(), core::io::silent::RigidBodySilentStruct::RigidBodySilentStruct(), core::io::silent::RNA_SilentStruct::RNA_SilentStruct(), core::io::silent::ScoreFileSilentStruct::ScoreFileSilentStruct(), core::io::silent::ScoreJumpFileSilentStruct::ScoreJumpFileSilentStruct(), and set_tag_from_pose().

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 protocols::cluster::calibur::aa, 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 core::io::raw_data::ScoreMap::add_arbitrary_score_data_from_pose(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), add_comment(), add_string_value(), clear_energies(), core::pose::Pose::energies(), core::pose::get_all_comments(), core::pose::get_all_score_line_strings(), protocols::mean_field::max(), 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::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), 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(), energies(), core::pose::Pose::energies(), get_all_comments(), core::io::silent::SilentFileOptions::in_silent_score_prefix(), core::io::silent::SilentFileOptions::in_silent_scores_wanted(), core::io::silent::SilentFileOptions::in_silent_scores_wanted_set(), options_, core::scoring::score_type_from_name(), protocols::kinmatch::str(), core::scoring::Energies::total_energies(), core::io::silent::tr(), and core::scoring::Energies::weights().

Referenced by core::io::silent::ScoreFileSilentStruct::fill_pose(), core::io::silent::ScoreJumpFileSilentStruct::fill_pose(), and finish_pose().

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

Returns the EnergyNames that this SilentStruct contains.

References 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(), and core::pose::Pose::data().

Referenced by fill_struct().

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

References core::io::silent::figure_out_residue_numbers_from_line(), set_chains(), set_residue_numbers(), and set_segment_IDs().

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

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

References residue_numbers_, and set_segment_IDs().

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

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

References add_other_struct(), clone(), core::pose::full_model_info::const_full_model_info(), decoy_tag_, core::pose::full_model_info::full_model_info_defined(), full_model_parameters(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and set_full_model_parameters().

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

void core::io::silent::SilentStruct::fill_pose	(	core::pose::Pose &	pose,
		bool const	metapatches = `true`
	)		const

virtual

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

References core::chemical::FULL_ATOM_t, nres_, and core::pose::Pose::residue_type_set_for_pose().

Referenced by protocols::mpi_refinement::add_poseinfo_to_ss(), protocols::evaluation::PoseEvaluator::apply(), protocols::abinitio::KinematicAbinitio::apply(), fill_pose(), protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file(), and protocols::jd3::pose_inputters::SilentFilePoseInputter::pose_from_input_source().

void core::io::silent::SilentStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSetCOP	residue_set,
		bool const	metapatches = `true`
	)		const

non-virtual interface that takes a ResidueTypeSetCOP (instead of a const & to one) and invokes the virtual method that takes the const &.

Fill a Pose with the conformation information in this SilentStruct and the ResidueTypeSetCOP provided by the caller.

References fill_pose().

void core::io::silent::SilentStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	residue_set,
		bool const	metapatches = `true`
	)		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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, 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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, 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(), core::pose::Pose::pdb_info(), pdbinfo_labels_, sequence(), set_tag_from_pose(), and core::io::silent::tr().

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

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(), set_segment_IDs(), and core::pose::Pose::size().

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

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

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::submotif_info_list(), and submotif_info_list_.

Referenced by core::io::silent::BinarySilentStruct::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(), full_model_info_into_pose(), core::io::silent::SilentFileOptions::keep_input_scores(), options_, core::pose::Pose::pdb_info(), pdbinfo_labels_, residue_numbers_into_pose(), core::io::silent::tr(), and core::pose::datacache::CacheableDataType::WRITEABLE_DATA.

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

virtual bool core::io::silent::SilentStruct::force_bitflip ( ) const

inlinevirtual

Gets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines.

References force_bitflip_.

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

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

References chains_, full_model_parameters_, residue_numbers_, segment_IDs_, core::pose::full_model_info::set_full_model_info(), core::pose::Pose::size(), submotif_info_list_, and core::pose::full_model_info::update_constraint_set_from_full_model_info().

Referenced by finish_pose().

core::pose::full_model_info::FullModelParametersCOP core::io::silent::SilentStruct::full_model_parameters ( ) const

inline

References full_model_parameters_.

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

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::io::silent::RigidBodySilentStruct, core::io::silent::BinarySilentStruct, core::import_pose::PDBSilentStruct, core::io::silent::ScoreJumpFileSilentStruct, 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

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::RigidBodySilentStruct, 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().

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), protocols::mpi_refinement::MPI_Refinement::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::mpi_refinement::MPI_Refinement::format_silent_struct(), protocols::mpi_refinement::MultiObjective::formatted_objs_values(), protocols::mpi_refinement::MultiObjective::get_fobj(), protocols::loophash::MPI_LoopHashRefine::objective_function(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::loophash::MPI_LoopHashRefine::score(), and protocols::mpi_refinement::MPI_Refinement::score().

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

References parent_remarks_map_.

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

References add_parent_remark(), and protocols::hybridization::val.

SilentStructCOP core::io::silent::SilentStruct::get_self_ptr ( ) const

inline

self pointers

Referenced by protocols::loophash::MPI_LoopHashRefine::add_structure_to_library_single_replace(), and protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_single_replace().

SilentStructOP core::io::silent::SilentStruct::get_self_ptr ( )

inline

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 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 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

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 silent_energies_.

Referenced by protocols::rna::denovo::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

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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, 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 >.

utility::vector1< SilentStructOP >& core::io::silent::SilentStruct::nonconst_other_struct_list ( )

inline

References other_struct_list_.

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

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 & )

default

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

References options_.

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

utility::vector1< SilentStructOP > const& core::io::silent::SilentStruct::other_struct_list ( ) const

inline

References other_struct_list_.

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

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(), and core::io::silent::tr().

Referenced by core::io::silent::ScoreJumpFileSilentStruct::init_from_lines(), and 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_, pdbinfo_labels_, and silent_comments_.

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

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::ProteinSilentStruct_Template< T >, core::io::silent::RNA_SilentStruct, core::io::silent::BinarySilentStruct, core::io::silent::RigidBodySilentStruct, 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 full_model_parameters_, 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 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(), nres_, residue_numbers_, and segment_IDs_.

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 protocols::comparative_modeling::features::A, decoy_tag(), protocols::mean_field::max(), options_, core::io::silent::SilentFileOptions::out_user_tag(), core::io::silent::SilentFileOptions::out_user_tag_set(), scoreline_prefix(), and silent_energies_.

Referenced by core::import_pose::PDBSilentStruct::print_header(), core::io::silent::ScoreFileSilentStruct::print_header(), 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 protocols::comparative_modeling::features::A, decoy_tag(), core::chemical::element::F, protocols::mean_field::min(), options_, core::io::silent::SilentFileOptions::out_user_tag(), core::io::silent::SilentFileOptions::out_user_tag_set(), core::io::silent::SilentFileOptions::out_weight_silent_scores(), precision(), scoreline_prefix(), and silent_energies_.

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

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

virtual

print the submotif_info in this SilentStruct, if filled.

References decoy_tag(), and submotif_info_list_.

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
	)

References core::io::silent::energynames, sequence(), core::io::silent::SilentFileData::set_shared_silent_data(), core::io::silent::simplesequencedata, and core::io::silent::tr().

bool core::io::silent::SilentStruct::read_sequence ( std::string const & line )

References sequence(), and core::io::silent::tr().

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

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

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

References chains_, core::pose::Pose::pdb_info(), residue_numbers_, segment_IDs_, and core::pose::Pose::size().

Referenced by finish_pose().

void core::io::silent::SilentStruct::scoreline_prefix ( std::string const & prefix )

References scoreline_prefix_.

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

References scoreline_prefix_.

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

core::sequence::AnnotatedSequence const& core::io::silent::SilentStruct::sequence ( ) const

inline

returns the sequence associated with this SilentStruct.

References sequence_.

void core::io::silent::SilentStruct::sequence ( core::sequence::AnnotatedSequence const & sequence )

inline

sets the sequence for this SilentStruct.

References sequence(), and sequence_.

void core::io::silent::SilentStruct::set_chains ( utility::vector1< char > const & chains )

inline

References chains_.

Referenced by figure_out_residue_numbers_from_line(), and fill_struct_with_residue_numbers().

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

inline

set the tag associate with this SilentStruct

References decoy_tag_, and other_struct_list_.

Referenced by protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate().

virtual void core::io::silent::SilentStruct::set_force_bitflip ( bool const setting )

inlinevirtual

Sets whether conversion from big-endian to little-endian (or the converse) should be forced when a binary silent structure is initialized from lines.

References force_bitflip_.

void core::io::silent::SilentStruct::set_full_model_parameters ( core::pose::full_model_info::FullModelParametersCOP setting )

inline

References full_model_parameters_.

Referenced by fill_other_struct_list().

void core::io::silent::SilentStruct::set_residue_numbers ( utility::vector1< int > const & residue_numbers )

inline

References residue_numbers_.

Referenced by figure_out_residue_numbers_from_line(), and fill_struct_with_residue_numbers().

void core::io::silent::SilentStruct::set_segment_IDs ( utility::vector1< std::string > const & segids )

inline

References segment_IDs_.

Referenced by figure_out_residue_numbers_from_line(), figure_out_segment_ids_from_line(), and fill_struct_with_residue_numbers().

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

Sets the tag from the Pose DataCache.

References core::pose::Pose::data(), decoy_tag(), and protocols::kinmatch::str().

Referenced by core::io::silent::ScoreFileSilentStruct::fill_struct(), core::io::silent::ScoreJumpFileSilentStruct::fill_struct(), core::import_pose::PDBSilentStruct::fill_struct(), and fill_struct().

void core::io::silent::SilentStruct::set_valid_energies ( utility::vector1< std::string > valid )

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

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

void core::io::silent::SilentStruct::silent_energies ( utility::vector1< SilentEnergy > const & new_se )

inline

sets the silent_energies for this SilentStruct.

References silent_energies_.

Referenced by set_valid_energies().

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

sort all the silent energies by their name.

References silent_energies_, and core::io::silent::SilentEnergy_sort_by_name().

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

private

Updates the "score" entry in the silent_energies.

References protocols::hybridization::score, and silent_energies_.

Referenced by energies_from_pose().

Member Data Documentation

utility::vector1< std::string > core::io::silent::SilentStruct::cache_remarks_

private

Referenced by add_comment(), finish_pose(), and print_comments().

utility::vector1< char > core::io::silent::SilentStruct::chains_

private

Referenced by full_model_info_into_pose(), print_residue_numbers(), residue_numbers_into_pose(), and set_chains().

std::string core::io::silent::SilentStruct::decoy_tag_

private

Referenced by decoy_tag(), fill_other_struct_list(), and set_decoy_tag().

bool core::io::silent::SilentStruct::force_bitflip_

private

If true, this forces conversion from big-endian to little-endian (or the converse) when a binary silent structure is initialized from lines (init_from_lines() function).

Referenced by force_bitflip(), and set_force_bitflip().

core::pose::full_model_info::FullModelParametersCOP core::io::silent::SilentStruct::full_model_parameters_

private

Referenced by add_submotif_info_from_line(), full_model_info_into_pose(), full_model_parameters(), print_header(), and set_full_model_parameters().