#include <silent.fwd.hh>

Public Member Functions
	ProteinSilentStruct_Template (core::pose::Pose const &pose, std::string tag="empty_tag", bool fa=false)

	ProteinSilentStruct_Template (Size const nres_in)
	Constructors. More...

	ProteinSilentStruct_Template ()

virtual SilentStructOP	clone () const
	Returns a new ProteinSilentStruct with a copy of the information in this ProteinSilentStruct. More...

	~ProteinSilentStruct_Template ()

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

virtual bool	init_from_lines (utility::vector1< std::string > const &lines, SilentFileData &container)
	Tells this ProteinSilentStruct object to initialize itself from. More...

virtual void	fill_pose (core::pose::Pose &pose) const
	Configure the conformation of the given Pose with the conformational data within this ProteinSilentStruct. 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 ProteinSilentStruct. 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="empty_tag")
	opposite of fill_pose More...

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

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

virtual void	fullatom (bool fullatom)

Real	phi (Size const seqpos) const

Real	psi (Size const seqpos) const

Real	omega (Size const seqpos) const

char	secstruct (Size const seqpos) const

Real	chi (Size const seqpos, Size const chi_num) const

Size	n_chi (Size const seqpos) const
	returns the number of chis at this position. More...

numeric::xyzVector< T > const &	coords (Size const seqpos) const

utility::vector1 < numeric::xyzVector< T > > const &	coords () const

void	phi (Size const seqpos, Real const phi)

void	psi (Size const seqpos, Real const psi)

void	omega (Size const seqpos, Real const omega)

void	secstruct (Size const seqpos, char const ss)

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

void	chain_endings (utility::vector1< Size > const &endings)
	set the list of chain endings More...

void	add_chain_ending (Size const seqpos)
	add a chain ending to the list More...

void	chi (Size const seqpos, utility::vector1< T > const &chis)

void	chi (Size const seqpos, Size const chi_num, Real const chi)

Size	max_chi () const

void	coords (Size const seqpos, numeric::xyzVector< T > const &coords)

void	fold_tree (kinematics::FoldTree const &f)

kinematics::FoldTree const &	fold_tree () const

bool	is_symmetric () const

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

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

void	add_jump (kinematics::Jump const &jump)

void	add_rt (kinematics::RT const &rt)

Size	njumps () const
	returns the number of jumps held in this container. More...

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

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

virtual Real	CA_rmsd (ProteinSilentStruct_Template< T > 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...

virtual core::Size	mem_footprint () const
	end accessors More...

template<>
bool	is_single_precision ()

template<>
bool	is_single_precision ()

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_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_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...

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)

Static Public Member Functions
static bool	is_single_precision ()

Protected Member Functions
void	parse_chain_endings (std::istream &stream)
	parse the chain endings string from an input stream More...

std::string	chain_endings_str () const
	return the chain endings string More...

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...

Protected Attributes
bool	fullatom_

utility::vector1< char >	secstruct_

utility::vector1< T >	phi_

utility::vector1< T >	psi_

utility::vector1< T >	omega_

utility::vector1 < numeric::xyzVector< T > >	coords_

utility::vector1< kinematics::RT >	jumps_

bool	bJumps_use_IntraResStub_

kinematics::FoldTree	fold_tree_

core::conformation::symmetry::SymmetryInfoOP	symminfo_

utility::vector1< Size >	chain_endings_

Static Protected Attributes
static const Size	max_chi_ = 4

Private Types
typedef SilentStruct	Parent

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

void	resize_chi ()

Private Attributes
utility::vector1 < utility::vector1< T > >	chi_

Member Typedef Documentation

template<class T>

typedef SilentStruct core::io::silent::ProteinSilentStruct_Template< T >::Parent

private

Constructor & Destructor Documentation

template<class T>

core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`,
		bool	fa = `false`
	)

inline

References core::io::silent::ProteinSilentStruct_Template< T >::bJumps_use_IntraResStub_, core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::symminfo_, and tag.

template<class T>

core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template ( Size const nres_in )

inline

Constructors.

References core::io::silent::ProteinSilentStruct_Template< T >::bJumps_use_IntraResStub_, core::io::silent::SilentStruct::decoy_tag(), core::io::silent::ProteinSilentStruct_Template< T >::fullatom_, core::io::silent::SilentStruct::nres(), core::io::silent::ProteinSilentStruct_Template< T >::resize(), and core::io::silent::ProteinSilentStruct_Template< T >::symminfo_.

template<class T>

core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template ( )

inline

References core::io::silent::ProteinSilentStruct_Template< T >::bJumps_use_IntraResStub_, core::io::silent::SilentStruct::decoy_tag(), core::io::silent::ProteinSilentStruct_Template< T >::fullatom(), core::io::silent::SilentStruct::nres(), and core::io::silent::ProteinSilentStruct_Template< T >::symminfo_.

template<class T>

core::io::silent::ProteinSilentStruct_Template< T >::~ProteinSilentStruct_Template ( )

inline

Member Function Documentation

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::add_chain_ending ( Size const seqpos )

add a chain ending to the list

Remarks: All positions in the list must be strictly less than the number of residues in the data. If this condition is not met the routine will fail-fast, so remember to resize() properly prior to calling this function.

References nres, core::io::silent::pss_tr, and utility_exit.

template<class T>

void core::io::silent::ProteinSilentStruct_Template< T >::add_jump ( kinematics::Jump const & jump )

inline

References core::io::silent::ProteinSilentStruct_Template< T >::jumps_, and core::kinematics::Jump::rt().

template<class T>

void core::io::silent::ProteinSilentStruct_Template< T >::add_rt ( kinematics::RT const & rt )

inline

References core::io::silent::ProteinSilentStruct_Template< T >::jumps_.

template<class T >

Real core::io::silent::ProteinSilentStruct_Template< T >::CA_rmsd ( ProteinSilentStruct_Template< T > other_pss )

virtual

References core::io::silent::ProteinSilentStruct_Template< T >::get_CA_xyz(), nres, numeric::model_quality::rms_wrapper(), and rmsd.

template<class T>

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

inline

References core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T >

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

set the list of chain endings

Remarks: All positions in the list must be strictly less than the number of residues in the data. If this condition is not met the routine will fail-fast, so remember to resize() properly prior to calling this function.

References nres, core::io::silent::pss_tr, and utility_exit.

template<class T >

std::string core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_str ( ) const

protected

return the chain endings string

References begin, core::sequence::end, and ss.

template<class T >

Real core::io::silent::ProteinSilentStruct_Template< T >::chi	(	Size const	seqpos,
		Size const	chi_num
	)		const

References core::io::silent::pss_tr, and utility_exit_with_message.

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::chi	(	Size const	seqpos,
		utility::vector1< T > const &	chis
	)

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::chi	(	Size const	seqpos,
		Size const	chi_num,
		Real const	chi
	)

References core::io::serialization::size(), and utility_exit_with_message.

template<class T>

virtual SilentStructOP core::io::silent::ProteinSilentStruct_Template< T >::clone ( ) const

inlinevirtual

Returns a new ProteinSilentStruct with a copy of the information in this ProteinSilentStruct.

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

template<class T>

numeric::xyzVector<T> const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( Size const seqpos ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::coords_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T>

utility::vector1< numeric::xyzVector<T> > const& core::io::silent::ProteinSilentStruct_Template< T >::coords ( ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::coords_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::coords().

template<class T>

void core::io::silent::ProteinSilentStruct_Template< T >::coords	(	Size const	seqpos,
		numeric::xyzVector< T > const &	coords
	)

inline

References core::io::silent::ProteinSilentStruct_Template< T >::coords(), and core::io::silent::ProteinSilentStruct_Template< T >::coords_.

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::fill_pose ( core::pose::Pose & pose ) const

virtual

Configure the conformation of the given Pose with the conformational data within this ProteinSilentStruct. 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::pss_tr.

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::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 ProteinSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the user-specified residue types.

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

References core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), empty, core::sequence::end, fold_tree, core::pose::Pose::fold_tree(), fullatom, core::pose::initialize_disulfide_bonds(), core::chemical::ResidueType::is_protein(), length, core::pose::make_pose_from_sequence(), core::pose::named_stub_id_to_stub_id(), core::chemical::ResidueType::nchi(), nres, core::scoring::omega, core::io::silent::pss_tr, core::pose::Pose::residue_type(), runtime_assert, sequence, core::pose::Pose::set_chi(), core::pose::Pose::set_jump(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), basic::SILENT_FILL_POSE, basic::SILENT_SET_POSE_COORDS, start, and utility_exit_with_message.

template<class T >

void core::io::silent::ProteinSilentStruct_Template< T >::fill_struct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`
	)

virtual

opposite of fill_pose

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

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::chemical::aa_vrt, core::conformation::Conformation::chain_endings(), core::conformation::Residue::chi(), core::pose::Pose::conformation(), core::io::silent::SilentStruct::fill_struct(), fold_tree, core::pose::Pose::fold_tree(), fullatom, core::pose::Pose::is_fullatom(), core::pose::is_ideal_pose(), core::pose::Pose::jump(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::nchi(), core::scoring::omega, core::io::silent::pss_tr, resi, core::pose::Pose::residue(), core::pose::Pose::secstruct(), basic::SILENT_FILL_STRUCT, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template().

template<class T>

void core::io::silent::ProteinSilentStruct_Template< T >::fold_tree ( kinematics::FoldTree const & f )

inline

References core::io::silent::ProteinSilentStruct_Template< T >::fold_tree_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T>

kinematics::FoldTree const& core::io::silent::ProteinSilentStruct_Template< T >::fold_tree ( ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::fold_tree_.

template<class T>

bool core::io::silent::ProteinSilentStruct_Template< T >::fullatom ( ) const

inline

data getters/setters

References core::io::silent::ProteinSilentStruct_Template< T >::fullatom_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::fullatom(), and core::io::silent::ProteinSilentStruct_Template< T >::ProteinSilentStruct_Template().

template<class T>

virtual void core::io::silent::ProteinSilentStruct_Template< T >::fullatom ( bool fullatom )

inlinevirtual

References core::io::silent::ProteinSilentStruct_Template< T >::fullatom(), and core::io::silent::ProteinSilentStruct_Template< T >::fullatom_.

template<class T >

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

virtual

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

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

References nres.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::CA_rmsd().

template<class T >

Real core::io::silent::ProteinSilentStruct_Template< T >::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 core::pose::Pose::residue(), numeric::model_quality::rms_wrapper(), rmsd, core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

template<class T >

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

virtual

Tells this ProteinSilentStruct object to initialize itself from.

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

References core::sequence::end, core::io::silent::energynames, fold_tree, fullatom, core::io::silent::SilentFileData::get_shared_silent_data(), nres, core::scoring::omega, core::io::silent::pss_tr, sequence, core::io::silent::simplesequencedata, ss, and tag.

template<>

bool core::io::silent::ProteinSilentStruct_Template< float >::is_single_precision ( )

template<>

bool core::io::silent::ProteinSilentStruct_Template< core::Real >::is_single_precision ( )

template<class T>

static bool core::io::silent::ProteinSilentStruct_Template< T >::is_single_precision ( )

static

template<class T>

bool core::io::silent::ProteinSilentStruct_Template< T >::is_symmetric ( ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::symminfo_.

template<class T>

kinematics::RT const& core::io::silent::ProteinSilentStruct_Template< T >::jump ( Size const jump_num ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::jumps_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T >

Size core::io::silent::ProteinSilentStruct_Template< T >::max_chi ( ) const

template<class T >

core::Size core::io::silent::ProteinSilentStruct_Template< T >::mem_footprint ( ) const

virtual

end accessors

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

References sum().

template<class T >

Size core::io::silent::ProteinSilentStruct_Template< T >::n_chi ( Size const seqpos ) const

returns the number of chis at this position.

template<class T>

Size core::io::silent::ProteinSilentStruct_Template< T >::njumps ( ) const

inline

returns the number of jumps held in this container.

References core::io::silent::ProteinSilentStruct_Template< T >::jumps_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T>

Real core::io::silent::ProteinSilentStruct_Template< T >::omega ( Size const seqpos ) const

inline

References core::io::silent::ProteinSilentStruct_Template< T >::omega_.

Referenced by core::io::silent::ProteinSilentStruct_Template< T >::omega(), and core::io::silent::ProteinSilentStruct_Template< T >::operator=().

template<class T>

void core::io::silent::ProteinSilentStruct_Template< T >::omega	(	Size const	seqpos,
		Real const	omega
	)

inline

References core::io::silent::ProteinSilentStruct_Template< T >::omega(), and core::io::silent::ProteinSilentStruct_Template< T >::omega_.

template<class T >

ProteinSilentStruct_Template< T > & core::io::silent::ProteinSilentStruct_Template< T >::operator= ( ProteinSilentStruct_Template< T > const & src )