#include <BinaryRNASilentStruct.hh>

Inheritance diagram for core::io::silent::BinaryRNASilentStruct:

Collaboration diagram for core::io::silent::BinaryRNASilentStruct:

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

	BinaryRNASilentStruct ()

	BinaryRNASilentStruct (core::pose::Pose const &pose, std::string tag="empty_tag")

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

virtual SilentStructOP	clone () const

	~BinaryRNASilentStruct ()

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
	Test if this BinaryRNASilentStruct is equal to the given BinaryRNASilentStruct in terms of conformation. Doesn't check energies. More...

virtual void	fill_pose (core::pose::Pose &pose) const
	Configure the conformation of the given Pose with the conformational data within this BinaryRNASilentStruct. 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 BinaryRNASilentStruct. 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 BinaryRNASilentStruct to the given std::ostream. More...

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 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)

Protected Member Functions
void	add_jump (kinematics::Jump jump)

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

void	set_fold_tree (kinematics::FoldTree const &f)

kinematics::FoldTree const &	fold_tree () const

char	secstruct (unsigned int seqpos) const

void	secstruct (unsigned int seqpos, char ss)

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...

Protected Attributes
bool	fullatom_

utility::vector1< char >	secstruct_

utility::vector1 < utility::vector1 < numeric::xyzVector< float > > >	atm_coords_

utility::vector1< kinematics::RT >	jumps_

bool	bJumps_use_IntraResStub_

kinematics::FoldTree	fold_tree_

Detailed Description

Definition at line 46 of file BinaryRNASilentStruct.hh.

Constructor & Destructor Documentation

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

Constructors.

Definition at line 85 of file BinaryRNASilentStruct.cc.

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

core::io::silent::BinaryRNASilentStruct::BinaryRNASilentStruct ( )

Definition at line 96 of file BinaryRNASilentStruct.cc.

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

Referenced by clone().

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

Definition at line 108 of file BinaryRNASilentStruct.cc.

References bJumps_use_IntraResStub_, fill_struct(), and fullatom_.

core::io::silent::BinaryRNASilentStruct::~BinaryRNASilentStruct ( )

inline

Definition at line 70 of file BinaryRNASilentStruct.hh.

Member Function Documentation

void core::io::silent::BinaryRNASilentStruct::add_jump ( kinematics::Jump jump)

inlineprotected

Definition at line 120 of file BinaryRNASilentStruct.hh.

References jumps_, and core::kinematics::Jump::rt().

Referenced by fill_struct(), and init_from_lines().

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

virtual

Definition at line 561 of file BinaryRNASilentStruct.cc.

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

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

inlinevirtual

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

Definition at line 65 of file BinaryRNASilentStruct.hh.

References BinaryRNASilentStruct().

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

virtual

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

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

Definition at line 406 of file BinaryRNASilentStruct.cc.

References atm_coords_, core::chemical::COARSE_RNA, core::chemical::ChemicalManager::get_instance(), core::io::silent::SilentStruct::one_letter_sequence(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::RNA, and core::io::serialization::size().

Referenced by get_debug_rmsd().

void core::io::silent::BinaryRNASilentStruct::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 BinaryRNASilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

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

Definition at line 420 of file BinaryRNASilentStruct.cc.

References atm_coords_, core::io::silent::SilentStruct::finish_pose(), fold_tree(), core::pose::Pose::fold_tree(), core::pose::make_pose_from_sequence(), core::chemical::ResidueType::natoms(), core::io::silent::SilentStruct::nres(), core::io::silent::SilentStruct::one_letter_sequence(), core::pose::Pose::residue_type(), secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::set_secstruct(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), and core::io::silent::tr().

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

virtual

opposite of fill_pose

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

Definition at line 118 of file BinaryRNASilentStruct.cc.

References add_jump(), core::pose::Pose::annotated_sequence(), atm_coords_, core::conformation::Residue::atom(), core::io::silent::SilentStruct::decoy_tag(), core::io::silent::SilentStruct::energies_from_pose(), fold_tree(), core::pose::Pose::fold_tree(), fold_tree_, fullatom_, core::conformation::Residue::is_coarse(), core::pose::Pose::jump(), jumps_, core::conformation::Residue::natoms(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::io::silent::SilentStruct::sequence(), core::io::silent::SilentStruct::set_tag_from_pose(), core::pose::Pose::total_residue(), core::io::silent::tr(), and core::conformation::Atom::xyz().

Referenced by BinaryRNASilentStruct().

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

inlineprotected

Definition at line 131 of file BinaryRNASilentStruct.hh.

References fold_tree_.

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

ObjexxFCL::FArray2D< Real > core::io::silent::BinaryRNASilentStruct::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.

Definition at line 549 of file BinaryRNASilentStruct.cc.

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

Referenced by CA_rmsd().

Real core::io::silent::BinaryRNASilentStruct::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.

Definition at line 527 of file BinaryRNASilentStruct.cc.

References atm_coords_, core::conformation::Residue::atom_index(), fill_pose(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().