why this inheritance pathway? this makes no sense! More...

#include <BinarySilentStruct.hh>

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

	BinarySilentStruct ()

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

virtual SilentStructOP	clone () const

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

	~BinarySilentStruct ()

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

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
	Initialize object from a set of lines. More...

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

virtual ObjexxFCL::FArray2D< Real >	get_CA_xyz () const
	returns the positions of the CA atoms More...

virtual Real	CA_rmsd (BinarySilentStruct other_pss)

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

void	add_jump (kinematics::Jump jump)

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

void	fold_tree (kinematics::FoldTree f)

kinematics::FoldTree const &	fold_tree () const

bool	fullatom () const

virtual void	fullatom (bool fullatom)

char	secstruct (unsigned int seqpos) const

void	secstruct (unsigned int seqpos, char ss)

void	symmetry_info (core::conformation::symmetry::SymmetryInfo &s)

core::conformation::symmetry::SymmetryInfoCOP	symmetry_info () const

bool	is_symmetric () const

void	parse_chain_endings (std::istream &stream)

void	chain_endings (utility::vector1< Size > const &endings)

std::string	chain_endings_str () const

utility::vector1< Size > const &	chain_endings () const

void	add_chain_ending (Size const seqpos)

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)

Private Types
typedef SilentStruct	Parent

Private Attributes
bool	fullatom_

utility::vector1< char >	secstruct_

utility::vector1< kinematics::RT >	jumps_

bool	bJumps_use_IntraResStub_

kinematics::FoldTree	fold_tree_

core::conformation::symmetry::SymmetryInfoOP	symminfo_

utility::vector1< Size >	chain_endings_

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

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...

Detailed Description

why this inheritance pathway? this makes no sense!

Member Typedef Documentation

typedef SilentStruct core::io::silent::BinarySilentStruct::Parent

private

Constructor & Destructor Documentation

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

Constructors.

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

core::io::silent::BinarySilentStruct::BinarySilentStruct ( )

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

Referenced by clone().

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

References bJumps_use_IntraResStub_, fill_struct(), and symminfo_.

core::io::silent::BinarySilentStruct::~BinarySilentStruct ( )

inline

Member Function Documentation

void core::io::silent::BinarySilentStruct::add_chain_ending ( Size const seqpos )

References chain_endings_, is_symmetric(), core::io::silent::SilentStruct::nres(), symmetry_info(), core::io::silent::tr, and utility_exit.

Referenced by parse_chain_endings().

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

inline

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

Referenced by fill_struct(), and init_from_lines().

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

virtual

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

void core::io::silent::BinarySilentStruct::chain_endings ( utility::vector1< Size > const & endings )

References chain_endings_, is_symmetric(), core::io::silent::SilentStruct::nres(), symmetry_info(), core::io::silent::tr, and utility_exit.

utility::vector1< Size > const& core::io::silent::BinarySilentStruct::chain_endings ( ) const

inline

References chain_endings_.

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

std::string core::io::silent::BinarySilentStruct::chain_endings_str ( ) const

References begin, chain_endings(), core::sequence::end, and ss.

Referenced by print_conformation().

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

inlinevirtual

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

References BinarySilentStruct().

Referenced by fill_struct().

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

virtual

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

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

References core::chemical::CENTROID, core::chemical::FA_STANDARD, fullatom(), and core::io::silent::tr.

Referenced by get_debug_rmsd().

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

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

References core::pose::Pose::annotated_sequence(), atm_coords_, core::pose::Pose::batch_set_xyz(), bJumps_use_IntraResStub_, chain_endings(), core::conformation::Conformation::chain_endings(), core::scoring::Energies::clear(), core::pose::Pose::conformation(), empty, core::pose::Pose::energies(), core::io::silent::SilentStruct::finish_pose(), fold_tree(), core::pose::Pose::fold_tree(), fullatom(), core::pose::initialize_disulfide_bonds(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), is_symmetric(), j, jump(), core::kinematics::FoldTree::jump_edge(), length, core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_sequence(), core::pose::symmetry::make_symmetric_pose(), core::conformation::Residue::name(), core::pose::named_stub_id_to_stub_id(), core::conformation::Residue::natoms(), core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), core::io::silent::SilentStruct::one_letter_sequence(), core::pose::Pose::residue(), runtime_assert, secstruct_, core::io::silent::SilentStruct::sequence(), core::pose::Pose::set_jump(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), start, core::kinematics::Edge::start(), core::kinematics::Edge::stop(), symmetry_info(), core::io::silent::tr, and utility_exit_with_message.

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

virtual

opposite of fill_pose

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

References add_jump(), atm_coords_, core::conformation::Residue::atom(), chain_endings(), core::conformation::Conformation::chain_endings(), clone(), core::pose::Pose::conformation(), core::io::silent::SilentStruct::fill_struct(), core::io::silent::SilentStruct::fill_struct_with_residue_numbers(), fold_tree(), core::pose::Pose::fold_tree(), fold_tree_, fullatom(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), is_symmetric(), j, core::pose::Pose::jump(), jumps_, core::conformation::Residue::natoms(), core::kinematics::FoldTree::num_jump(), resi, core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::pose::symmetry::symmetry_info(), symmetry_info(), core::pose::Pose::total_residue(), core::io::silent::tr, and core::conformation::Atom::xyz().

Referenced by BinarySilentStruct().

void core::io::silent::BinarySilentStruct::fold_tree ( kinematics::FoldTree f )

inline

References fold_tree_.

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

inline

References fold_tree_.

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

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

inline

References fullatom_.

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

virtual void core::io::silent::BinarySilentStruct::fullatom ( bool fullatom )

inlinevirtual

References fullatom(), and fullatom_.

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

virtual

returns the positions of the CA atoms

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

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

Referenced by CA_rmsd().

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

virtual

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

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

References atm_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::BinarySilentStruct::init_from_lines	(	utility::vector1< std::string > const &	lines,
		SilentFileData &	container
	)

virtual

Initialize object from a set of lines.

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

bool core::io::silent::BinarySilentStruct::is_symmetric ( ) const

inline

References symminfo_.

Referenced by add_chain_ending(), chain_endings(), fill_pose(), fill_struct(), and print_conformation().

kinematics::RT const& core::io::silent::BinarySilentStruct::jump ( Size jump_num ) const

inline

References jumps_.

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

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

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

References exit, and utility_exit_with_message.

void core::io::silent::BinarySilentStruct::parse_chain_endings ( std::istream & stream )

References add_chain_ending(), and s.

Referenced by init_from_lines().

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

virtual

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

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

References atm_coords_, begin, chain_endings(), chain_endings_str(), core::io::silent::SilentStruct::decoy_tag(), empty, utility::encode6bit(), core::sequence::end, fold_tree(), is_symmetric(), jump(), core::io::silent::SilentStruct::nres(), core::kinematics::FoldTree::num_jump(), option, secstruct_, core::io::silent::SilentStruct::sequence(), core::io::serialization::size(), symmetry_info(), and user.

Referenced by core::pose::compare_binary_protein_silent_struct().

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

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

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

References atm_coords_, fold_tree_, core::kinematics::FoldTree::is_simple_tree(), core::io::silent::SilentStruct::nres(), secstruct_, and core::kinematics::FoldTree::simple_tree().

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

char core::io::silent::BinarySilentStruct::secstruct ( unsigned int seqpos ) const

inline

References secstruct_.

void core::io::silent::BinarySilentStruct::secstruct	(	unsigned int	seqpos,
		char	ss
	)

inline

References secstruct_.

void core::io::silent::BinarySilentStruct::symmetry_info ( core::conformation::symmetry::SymmetryInfo & s )

inline

References symminfo_.

core::conformation::symmetry::SymmetryInfoCOP core::io::silent::BinarySilentStruct::symmetry_info ( ) const

inline

References symminfo_.

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

Member Data Documentation

utility::vector1< utility::vector1< numeric::xyzVector<float> > > core::io::silent::BinarySilentStruct::atm_coords_

private

Referenced by fill_pose(), fill_struct(), get_CA_xyz(), get_debug_rmsd(), init_from_lines(), print_conformation(), and resize().

bool core::io::silent::BinarySilentStruct::bJumps_use_IntraResStub_

private

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

utility::vector1< Size > core::io::silent::BinarySilentStruct::chain_endings_

private

Referenced by add_chain_ending(), chain_endings(), and init_from_lines().

kinematics::FoldTree core::io::silent::BinarySilentStruct::fold_tree_

private

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

bool core::io::silent::BinarySilentStruct::fullatom_

private

Referenced by BinarySilentStruct(), fullatom(), and init_from_lines().

utility::vector1< kinematics::RT > core::io::silent::BinarySilentStruct::jumps_

private

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

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

private

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

core::conformation::symmetry::SymmetryInfoOP core::io::silent::BinarySilentStruct::symminfo_

private

Referenced by BinarySilentStruct(), is_symmetric(), and symmetry_info().

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

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

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation