#include <DecoyStruct.hh>

Inheritance diagram for core::io::raw_data::DecoyStruct:

Public Member Functions
	DecoyStruct (Size const nres_in)

	DecoyStruct ()

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

void	resize (Size const nres_in)
	Resize this silent-struct to the appropriate number of residues. More...

	~DecoyStruct () override

void	fill_pose (core::pose::Pose &pose) override
	Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct. More...

void	fill_pose (core::pose::Pose &pose, core::chemical::ResidueTypeSet const &residue_set) override
	Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct. More...

void	print_conformation (std::ostream &output) const override
	Print the conformation information contained in this object to the given ozstream. More...

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

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

Real	phi (unsigned int seqpos) const

Real	psi (unsigned int seqpos) const

Real	omega (unsigned int seqpos) const

char	secstruct (unsigned int seqpos) const

utility::vector1< Real >	chi (unsigned int seqpos) const

Vector	coords (unsigned int seqpos) const

void	fullatom (bool fullatom)

void	phi (unsigned int seqpos, Real phi)

void	psi (unsigned int seqpos, Real psi)

void	omega (unsigned int seqpos, Real omega)

void	secstruct (unsigned int seqpos, char ss)

void	chi (unsigned int seqpos, utility::vector1< Real > chis)

void	coords (unsigned int seqpos, Vector coords)

Public Member Functions inherited from core::io::raw_data::RawStruct
	~RawStruct () override

virtual void	print_header (std::ostream &out, std::map< std::string, core::Real > const &score_map, std::map< std::string, std::string > const &string_map=(std::map< std::string, std::string >()), bool print_sequence=true) const
	print out a header line to the given ozstream. In a rosetta++ silent-file, this contained the lines SEQUENCE: <protein sequence>\nSCORE: More...

virtual void	print_scores (std::ostream &out, std::map< std::string, core::Real > const &score_map, std::map< std::string, std::string > const &string_map=(std::map< std::string, std::string >())) const
	print out a SCORE line to the given ozstream. More...

Size	nres ()
	data access methods. More...

std::string	decoy_tag ()
	returns the tag associated with this RawStruct More...

std::string	sequence ()
	returns the sequence for this RawStruct More...

void	nres (Size nres)
	returns the number of residues in this RawStruct More...

void	decoy_tag (std::string tag)
	sets the tag associated with this RawStruct More...

void	sequence (std::string sequence)
	sets the sequence for this RawStruct More...

Protected Attributes
bool	fullatom_

utility::vector1< char >	secstruct_

utility::vector1< Real >	phi_

utility::vector1< Real >	psi_

utility::vector1< Real >	omega_

utility::vector1< utility::vector1< Real > >	chi_

utility::vector1< Vector >	coords_

Protected Attributes inherited from core::io::raw_data::RawStruct
Size	nres_

std::string	decoy_tag_

std::string	sequence_

Constructor & Destructor Documentation

◆ DecoyStruct() [1/3]

core::io::raw_data::DecoyStruct::DecoyStruct ( Size const nres_in )

inline

References fullatom_, core::io::raw_data::RawStruct::nres_, and resize().

◆ DecoyStruct() [2/3]

core::io::raw_data::DecoyStruct::DecoyStruct ( )

inline

References core::io::raw_data::RawStruct::decoy_tag_, fullatom_, and core::io::raw_data::RawStruct::nres_.

◆ DecoyStruct() [3/3]

core::io::raw_data::DecoyStruct::DecoyStruct	(	core::pose::Pose const &	pose,
		std::string	tag = `"empty_tag"`,
		bool	fa = `false`
	)

References core::conformation::Residue::chi(), chi_, coords_, core::io::raw_data::RawStruct::decoy_tag_, fullatom(), core::conformation::Residue::mainchain_torsion(), omega_, phi_, psi_, core::pose::Pose::residue(), resize(), core::pose::Pose::secstruct(), secstruct_, core::pose::Pose::sequence(), core::io::raw_data::RawStruct::sequence_, core::pose::Pose::size(), and core::conformation::Residue::xyz().

◆ ~DecoyStruct()

core::io::raw_data::DecoyStruct::~DecoyStruct ( )

inlineoverride

Member Function Documentation

◆ chi() [1/2]

utility::vector1< Real > core::io::raw_data::DecoyStruct::chi ( unsigned int seqpos ) const

inline

References chi_.

◆ chi() [2/2]

void core::io::raw_data::DecoyStruct::chi	(	unsigned int	seqpos,
		utility::vector1< Real >	chis
	)

inline

References chi_.

◆ coords() [1/2]

Vector core::io::raw_data::DecoyStruct::coords ( unsigned int seqpos ) const

inline

References coords_.

Referenced by coords().

◆ coords() [2/2]

void core::io::raw_data::DecoyStruct::coords	(	unsigned int	seqpos,
		Vector	coords
	)

inline

References coords(), and coords_.

◆ fill_pose() [1/2]

void core::io::raw_data::DecoyStruct::fill_pose ( core::pose::Pose & pose )

overridevirtual

Fill a Pose with the conformation information in this RawStruct and the FA_STANDARD ResidueTypeSet. This is a virtual method which must be implemented by classes derived from RawStruct.

Implements core::io::raw_data::RawStruct.

References core::chemical::CENTROID_t, 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::raw_data::DecoyStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	residue_set
	)

overridevirtual

Fill a Pose with the conformation information in this RawStruct and the ResidueTypeSet provided by the caller. This is a virtual method which must be implemented by classes derived from RawStruct.

Implements core::io::raw_data::RawStruct.

References chi_, fullatom_, core::pose::make_pose_from_sequence(), omega_, phi_, psi_, core::pose::Pose::residue(), secstruct_, core::io::raw_data::RawStruct::sequence_, core::pose::Pose::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), and core::pose::Pose::size().

◆ fullatom() [1/2]

bool core::io::raw_data::DecoyStruct::fullatom ( ) const

inline

data getters/setters

References fullatom_.

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

◆ fullatom() [2/2]

void core::io::raw_data::DecoyStruct::fullatom ( bool fullatom )

inline

References fullatom(), and fullatom_.

◆ get_debug_rmsd()

Real core::io::raw_data::DecoyStruct::get_debug_rmsd ( )

overridevirtual

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

Reimplemented from core::io::raw_data::RawStruct.

References coords_, fill_pose(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

◆ omega() [1/2]

Real core::io::raw_data::DecoyStruct::omega ( unsigned int seqpos ) const

inline

References omega_.

Referenced by omega().

◆ omega() [2/2]

void core::io::raw_data::DecoyStruct::omega	(	unsigned int	seqpos,
		Real	omega
	)

inline

References omega(), and omega_.

◆ phi() [1/2]

Real core::io::raw_data::DecoyStruct::phi ( unsigned int seqpos ) const

inline

References phi_.

Referenced by phi().

◆ phi() [2/2]

void core::io::raw_data::DecoyStruct::phi	(	unsigned int	seqpos,
		Real	phi
	)

inline

References phi(), and phi_.

◆ print_conformation()

void core::io::raw_data::DecoyStruct::print_conformation ( std::ostream & output ) const

overridevirtual

Print the conformation information contained in this object to the given ozstream.

Reimplemented from core::io::raw_data::RawStruct.

References chi_, coords_, core::io::raw_data::RawStruct::decoy_tag_, core::chemical::element::F, fullatom_, core::chemical::element::I, core::io::raw_data::RawStruct::nres_, omega_, phi_, psi_, and secstruct_.

Referenced by core::io::raw_data::DecoyFileData::write_struct().

◆ psi() [1/2]

Real core::io::raw_data::DecoyStruct::psi ( unsigned int seqpos ) const

inline

References psi_.

Referenced by psi().

◆ psi() [2/2]

void core::io::raw_data::DecoyStruct::psi	(	unsigned int	seqpos,
		Real	psi
	)

inline

References psi(), and psi_.

◆ resize()

void core::io::raw_data::DecoyStruct::resize ( Size const nres_in )

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

References chi_, coords_, core::io::raw_data::RawStruct::nres_, omega_, phi_, psi_, and secstruct_.

Referenced by DecoyStruct().

◆ secstruct() [1/2]

char core::io::raw_data::DecoyStruct::secstruct ( unsigned int seqpos ) const

inline

References secstruct_.

◆ secstruct() [2/2]

void core::io::raw_data::DecoyStruct::secstruct	(	unsigned int	seqpos,
		char	ss
	)

inline

References secstruct_.

Member Data Documentation

◆ chi_

utility::vector1< utility::vector1< Real > > core::io::raw_data::DecoyStruct::chi_

protected

Referenced by chi(), DecoyStruct(), fill_pose(), print_conformation(), and resize().

◆ coords_

utility::vector1< Vector > core::io::raw_data::DecoyStruct::coords_

protected

Referenced by coords(), DecoyStruct(), get_debug_rmsd(), print_conformation(), and resize().

◆ fullatom_

bool core::io::raw_data::DecoyStruct::fullatom_

protected

Referenced by DecoyStruct(), fill_pose(), fullatom(), and print_conformation().

◆ omega_

utility::vector1< Real > core::io::raw_data::DecoyStruct::omega_

protected

Referenced by DecoyStruct(), fill_pose(), omega(), print_conformation(), and resize().

◆ phi_

utility::vector1< Real > core::io::raw_data::DecoyStruct::phi_

protected

Referenced by DecoyStruct(), fill_pose(), phi(), print_conformation(), and resize().

◆ psi_

utility::vector1< Real > core::io::raw_data::DecoyStruct::psi_

protected

Referenced by DecoyStruct(), fill_pose(), print_conformation(), psi(), and resize().

◆ secstruct_

utility::vector1< char > core::io::raw_data::DecoyStruct::secstruct_

protected

Referenced by DecoyStruct(), fill_pose(), print_conformation(), resize(), and secstruct().

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

src/core/io/raw_data/DecoyStruct.hh
src/core/io/raw_data/DecoyStruct.cc

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ DecoyStruct() [1/3]

◆ DecoyStruct() [2/3]

◆ DecoyStruct() [3/3]

◆ ~DecoyStruct()

Member Function Documentation

◆ chi() [1/2]

◆ chi() [2/2]

◆ coords() [1/2]

◆ coords() [2/2]

◆ fill_pose() [1/2]

◆ fill_pose() [2/2]

◆ fullatom() [1/2]

◆ fullatom() [2/2]

◆ get_debug_rmsd()

◆ omega() [1/2]

◆ omega() [2/2]

◆ phi() [1/2]

◆ phi() [2/2]

◆ print_conformation()

◆ psi() [1/2]

◆ psi() [2/2]

◆ resize()

◆ secstruct() [1/2]

◆ secstruct() [2/2]

Member Data Documentation

◆ chi_

◆ coords_

◆ fullatom_

◆ omega_

◆ phi_

◆ psi_

◆ secstruct_