#include <RNA_SilentStruct.hh>

Inheritance diagram for core::io::silent::RNA_SilentStruct:

[legend]

Public Member Functions
	RNA_SilentStruct (SilentFileOptions const &opts, Size const nres_in)
	Constructors. More...

	RNA_SilentStruct (SilentFileOptions const &opts)

	RNA_SilentStruct (SilentFileOptions const &opts, 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...

SilentStructOP	clone () const override

	~RNA_SilentStruct () override

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...

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

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

void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set, bool const metapatches=true) const override
	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...

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

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

void	print_conformation (std::ostream &output) const override
	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

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

virtual Real	CA_rmsd (RNA_SilentStruct other_pss)

Real	get_debug_rmsd () override
	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 (SilentFileOptions const &opts)

	~SilentStruct () override

	SilentStruct (SilentStruct const &)

SilentStruct &	operator= (SilentStruct const &)

SilentStructCOP	get_self_ptr () const
	self pointers More...

SilentStructOP	get_self_ptr ()

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...

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 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...

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...

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 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

◆ RNA_SilentStruct() [1/3]

core::io::silent::RNA_SilentStruct::RNA_SilentStruct	(	SilentFileOptions const &	opts,
		Size const	nres_in
	)

inline

Constructors.

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

◆ RNA_SilentStruct() [2/3]

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

inline

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

◆ RNA_SilentStruct() [3/3]

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

References fill_struct().

◆ ~RNA_SilentStruct()

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

inlineoverride

Member Function Documentation

◆ add_jump()

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

inline

References jump(), and jumps_.

Referenced by fill_struct(), and init_from_lines().

◆ CA_rmsd()

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

virtual

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

◆ chi()

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

inline

References chi_torsions_.

◆ chi_torsions()

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

inline

References chi_torsions_.

◆ clone()

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

inlineoverridevirtual

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

◆ coords() [1/2]

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

inline

References coords_.

Referenced by set_coords().

◆ coords() [2/2]

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

inline

References coords_.

◆ fill_pose() [1/2]

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

overridevirtual

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

Referenced by get_debug_rmsd().

◆ fill_pose() [2/2]

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

overridevirtual

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(), core::chemical::FULL_ATOM_t, fullatom_, jump(), 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::pose::Pose::residue_type_set_for_pose(), 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().

◆ fill_struct()

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

overridevirtual

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::kinematics::Stub::global2local(), 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(), core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::sequence(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by RNA_SilentStruct().

◆ fold_tree()

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().

◆ fullatom() [1/2]

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

inline

data getters/setters

References fullatom_.

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

◆ fullatom() [2/2]

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

inline

References fullatom(), and fullatom_.

◆ get_CA_xyz()

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

overridevirtual

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().

◆ get_debug_rmsd()

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

overridevirtual

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(), core::pose::Pose::size(), and core::conformation::Residue::xyz().