#include <RNA_SilentStruct.hh>

Public Member Functions
	RNA_SilentStruct (Size const nres_in)
	Constructors. More...

	RNA_SilentStruct ()

	RNA_SilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag", bool fa=true)

void	resize (Size const nres_in)
	Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues. More...

virtual SilentStructOP	clone () const

	~RNA_SilentStruct ()

RNA_SilentStruct &	operator= (RNA_SilentStruct const &src)
	Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation. Doesn't check energies. More...

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
	Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should be of the format. More...

virtual void	fill_pose (core::pose::Pose &pose) const
	Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types. More...

virtual void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) const
	Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types. More...

virtual void	fill_struct (core::pose::Pose const &pose, std::string tag)
	opposite of fill_pose More...

virtual void	print_header (std::ostream &out) const
	print header information More...

virtual void	print_conformation (std::ostream &output) const
	Prints the conformation information within this RNA_SilentStruct to the given std::ostream. More...

bool	fullatom () const
	data getters/setters More...

void	fullatom (bool fullatom)

char	secstruct (Size seqpos) const

utility::vector1< Real >	mainchain_torsions (Size seqpos) const

utility::vector1< Real >	chi_torsions (Size seqpos) const

Real	mainchain_torsion (Size const &seqpos, Size const &torsion_num) const

Real	chi (Size const &seqpos, Size const &torsion_num) const

Vector	coords (Size seqpos) const

utility::vector1< Vector >	coords () const

void	set_secstruct (Size const &seqpos, char const &ss)

void	set_mainchain_torsions (Size const &seqpos, utility::vector1< Real > &torsions)

void	set_chi_torsions (Size const &seqpos, utility::vector1< Real > &torsions)

void	set_coords (Size const &seqpos, Vector const &coords)

void	set_non_main_chain_sugar_coords (Size const &seqpos, utility::vector1< Vector > const &vecs)

void	set_fold_tree (kinematics::FoldTree const &f)

kinematics::FoldTree const &	fold_tree () const

void	add_jump (kinematics::Jump const &jump)

kinematics::Jump const &	jump (Size const &jump_num) const

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

virtual Real	CA_rmsd (RNA_SilentStruct other_pss)

virtual Real	get_debug_rmsd ()
	calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct. More...

Public Member Functions inherited from core::io::silent::SilentStruct
	SilentStruct ()

virtual	~SilentStruct ()

	SilentStruct (SilentStruct const &)

SilentStruct &	operator= (SilentStruct const &)

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

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

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...

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 Attributes
bool	fullatom_

bool	non_main_chain_sugar_coords_defined_

utility::vector1< char >	secstruct_

utility::vector1 < utility::vector1< Real > >	mainchain_torsions_

utility::vector1 < utility::vector1< Real > >	chi_torsions_

utility::vector1< Vector >	coords_

utility::vector1 < utility::vector1< Vector > >	non_main_chain_sugar_coords_

utility::vector1 < kinematics::Jump >	jumps_

kinematics::FoldTree	fold_tree_

Additional Inherited Members
Protected Member Functions inherited from core::io::silent::SilentStruct
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...

Constructor & Destructor Documentation

core::io::silent::RNA_SilentStruct::RNA_SilentStruct ( Size const nres_in )

inline

Constructors.

References fullatom_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), and resize().

core::io::silent::RNA_SilentStruct::RNA_SilentStruct ( )

inline

References core::io::silent::SilentStruct::decoy_tag(), fullatom_, non_main_chain_sugar_coords_defined_, and core::io::silent::SilentStruct::nres().

Referenced by clone().

core::io::silent::RNA_SilentStruct::RNA_SilentStruct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`,
		bool	fa = `true`
	)

References fill_struct().

core::io::silent::RNA_SilentStruct::~RNA_SilentStruct ( )

inline

Member Function Documentation

void core::io::silent::RNA_SilentStruct::add_jump ( kinematics::Jump const & jump )

inline

References jumps_.

Referenced by fill_struct(), and init_from_lines().

Real core::io::silent::RNA_SilentStruct::CA_rmsd ( RNA_SilentStruct other_pss )

virtual

References get_CA_xyz(), core::io::silent::SilentStruct::nres(), numeric::model_quality::rms_wrapper(), and rmsd.

Real core::io::silent::RNA_SilentStruct::chi	(	Size const &	seqpos,
		Size const &	torsion_num
	)		const

inline

References chi_torsions_.

utility::vector1< Real > core::io::silent::RNA_SilentStruct::chi_torsions ( Size seqpos ) const

inline

References chi_torsions_.

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

inlinevirtual

Implements core::io::silent::SilentStruct.

References RNA_SilentStruct().

Vector core::io::silent::RNA_SilentStruct::coords ( Size seqpos ) const

inline

References coords_.

utility::vector1< Vector > core::io::silent::RNA_SilentStruct::coords ( ) const

inline

References coords_.

Referenced by set_coords().

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

virtual

Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

Reimplemented from core::io::silent::SilentStruct.

References fullatom(), and core::chemical::RNA.

Referenced by get_debug_rmsd().

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

virtual

Configure the conformation of the given Pose with the conformational data within this RNA_SilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

Reimplemented from core::io::silent::SilentStruct.

References core::pose::rna::apply_non_main_chain_sugar_coords(), core::id::BB, core::id::CHI, chi_torsions_, core::io::silent::SilentStruct::finish_pose(), fold_tree(), core::pose::Pose::fold_tree(), fullatom_, jump(), length, mainchain_torsions_, core::pose::make_pose_from_sequence(), non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::pose::Pose::residue(), core::chemical::RNA, secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::set_jump(), core::pose::Pose::set_secstruct(), core::pose::Pose::set_torsion(), core::io::silent::tr, and core::conformation::Residue::xyz().

void core::io::silent::RNA_SilentStruct::fill_struct	(	core::pose::Pose const &	pose,
		std::string	tag
	)

virtual

opposite of fill_pose

Reimplemented from core::io::silent::SilentStruct.

References add_jump(), core::conformation::Residue::chi(), chi_torsions_, coords_, core::io::silent::SilentStruct::decoy_tag(), core::io::silent::SilentStruct::energies_from_pose(), core::io::silent::SilentStruct::fill_struct_with_residue_numbers(), fold_tree(), core::pose::Pose::fold_tree(), fold_tree_, fullatom(), core::pose::Pose::jump(), jumps_, core::conformation::Residue::mainchain_torsions(), mainchain_torsions_, core::chemical::rna::non_main_chain_sugar_atoms, non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::kinematics::FoldTree::num_jump(), resi, core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::sequence(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by RNA_SilentStruct().

kinematics::FoldTree const& core::io::silent::RNA_SilentStruct::fold_tree ( ) const

inline

References fold_tree_.

Referenced by fill_pose(), fill_struct(), init_from_lines(), and print_conformation().

bool core::io::silent::RNA_SilentStruct::fullatom ( ) const

inline

data getters/setters

References fullatom_.

Referenced by fill_pose(), fill_struct(), and fullatom().

void core::io::silent::RNA_SilentStruct::fullatom ( bool fullatom )

inline

References fullatom(), and fullatom_.

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

virtual

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

Implements core::io::silent::SilentStruct.

References coords_, and core::io::silent::SilentStruct::nres().

Referenced by CA_rmsd().

Real core::io::silent::RNA_SilentStruct::get_debug_rmsd ( )

virtual

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this RNA_SilentStruct and the C-alpha atoms from this RNA_SilentStruct.

Implements core::io::silent::SilentStruct.

References coords_, fill_pose(), core::pose::Pose::residue(), numeric::model_quality::rms_wrapper(), rmsd, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

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

virtual

Tells this RNA_SilentStruct object to initialize itself from the given set of lines. Lines should be of the format.

Implements core::io::silent::SilentStruct.

References core::io::silent::SilentStruct::add_energy(), add_jump(), core::io::silent::SilentStruct::decoy_tag(), core::sequence::end, core::io::silent::energynames, core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(), fold_tree(), fold_tree_, fullatom_, core::io::silent::SilentFileData::get_shared_silent_data(), jump(), length, core::io::silent::SilentStruct::nres(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), resize(), runtime_assert, core::io::silent::SilentStruct::sequence(), set_chi_torsions(), set_coords(), set_fold_tree(), set_mainchain_torsions(), set_non_main_chain_sugar_coords(), set_secstruct(), core::io::silent::SilentFileData::set_shared_silent_data(), core::kinematics::FoldTree::simple_tree(), core::io::silent::simplesequencedata, core::io::serialization::size(), ss, tag, and core::io::silent::tr.

kinematics::Jump const& core::io::silent::RNA_SilentStruct::jump ( Size const & jump_num ) const

inline

References jumps_.

Referenced by fill_pose(), init_from_lines(), and print_conformation().

Real core::io::silent::RNA_SilentStruct::mainchain_torsion	(	Size const &	seqpos,
		Size const &	torsion_num
	)		const

inline

References mainchain_torsions_.

utility::vector1< Real > core::io::silent::RNA_SilentStruct::mainchain_torsions ( Size seqpos ) const

inline

References mainchain_torsions_.

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

Test if this RNA_SilentStruct is equal to the given RNA_SilentStruct in terms of conformation. Doesn't check energies.

References exit, and utility_exit_with_message.

void core::io::silent::RNA_SilentStruct::print_conformation ( std::ostream & output ) const

virtual

Prints the conformation information within this RNA_SilentStruct to the given std::ostream.

Implements core::io::silent::SilentStruct.

References chi_torsions_, coords_, core::io::silent::SilentStruct::decoy_tag(), fold_tree(), fullatom_, jump(), mainchain_torsions_, non_main_chain_sugar_coords_, non_main_chain_sugar_coords_defined_, core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::chemical::rna::NUM_RNA_CHI_TORSIONS(), core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), secstruct_, core::io::serialization::size(), core::kinematics::FoldTree::size(), and core::io::silent::tr.

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

virtual

print header information

Reimplemented from core::io::silent::SilentStruct.

References core::io::silent::SilentStruct::print_header().

void core::io::silent::RNA_SilentStruct::resize ( Size const nres_in )

Re-dimension the storage capacity of this RNA_SilentStruct to the given number of residues.

Resize this silent-struct to the appropriate number of residues.

References chi_torsions_, coords_, fold_tree_, mainchain_torsions_, non_main_chain_sugar_coords_, core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().

Referenced by fill_struct(), init_from_lines(), and RNA_SilentStruct().

char core::io::silent::RNA_SilentStruct::secstruct ( Size seqpos ) const

inline

References secstruct_.

void core::io::silent::RNA_SilentStruct::set_chi_torsions	(	Size const &	seqpos,
		utility::vector1< Real > &	torsions
	)

inline

References chi_torsions_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_coords	(	Size const &	seqpos,
		Vector const &	coords
	)

inline

References coords(), and coords_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_fold_tree ( kinematics::FoldTree const & f )

inline

References fold_tree_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_mainchain_torsions	(	Size const &	seqpos,
		utility::vector1< Real > &	torsions
	)

inline

References mainchain_torsions_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_non_main_chain_sugar_coords	(	Size const &	seqpos,
		utility::vector1< Vector > const &	vecs
	)

inline

References non_main_chain_sugar_coords_, and non_main_chain_sugar_coords_defined_.

Referenced by init_from_lines().

void core::io::silent::RNA_SilentStruct::set_secstruct	(	Size const &	seqpos,
		char const &	ss
	)

inline

References secstruct_.

Referenced by init_from_lines().

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::io::silent::RNA_SilentStruct::chi_torsions_

protected

Referenced by chi(), chi_torsions(), fill_pose(), fill_struct(), print_conformation(), resize(), and set_chi_torsions().

utility::vector1< Vector > core::io::silent::RNA_SilentStruct::coords_

protected

Referenced by coords(), fill_struct(), get_CA_xyz(), get_debug_rmsd(), print_conformation(), resize(), and set_coords().

kinematics::FoldTree core::io::silent::RNA_SilentStruct::fold_tree_

protected

Referenced by fill_struct(), fold_tree(), init_from_lines(), resize(), and set_fold_tree().

bool core::io::silent::RNA_SilentStruct::fullatom_

protected

Referenced by fill_pose(), fullatom(), init_from_lines(), print_conformation(), and RNA_SilentStruct().

utility::vector1< kinematics::Jump > core::io::silent::RNA_SilentStruct::jumps_

protected

Referenced by add_jump(), fill_struct(), and jump().

utility::vector1< utility::vector1< Real > > core::io::silent::RNA_SilentStruct::mainchain_torsions_

protected

Referenced by fill_pose(), fill_struct(), mainchain_torsion(), mainchain_torsions(), print_conformation(), resize(), and set_mainchain_torsions().

utility::vector1< utility::vector1< Vector > > core::io::silent::RNA_SilentStruct::non_main_chain_sugar_coords_

protected

Referenced by fill_pose(), fill_struct(), print_conformation(), resize(), and set_non_main_chain_sugar_coords().

bool core::io::silent::RNA_SilentStruct::non_main_chain_sugar_coords_defined_

protected

Referenced by fill_pose(), fill_struct(), print_conformation(), RNA_SilentStruct(), and set_non_main_chain_sugar_coords().

utility::vector1< char > core::io::silent::RNA_SilentStruct::secstruct_

protected

Referenced by fill_pose(), fill_struct(), print_conformation(), resize(), secstruct(), and set_secstruct().

The documentation for this class was generated from the following files:

symlinks/rosetta/src/core/io/silent/RNA_SilentStruct.hh
symlinks/rosetta/src/core/io/silent/RNA_SilentStruct.cc

Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation