#include <DecoyStruct.hh>

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

Collaboration 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 ()

void	fill_pose (core::pose::Pose &pose)
	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)
	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...

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

virtual Real	get_debug_rmsd ()
	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
virtual	~RawStruct ()

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>="">: More...

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_

Detailed Description

Definition at line 51 of file DecoyStruct.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 55 of file DecoyStruct.hh.

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

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

inline

Definition at line 62 of file DecoyStruct.hh.

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

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

Definition at line 49 of file DecoyStruct.cc.

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::total_residue(), and core::conformation::Residue::xyz().

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

inline

Definition at line 81 of file DecoyStruct.hh.

Member Function Documentation

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

inline

Definition at line 124 of file DecoyStruct.hh.

References chi_.

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

inline

Definition at line 153 of file DecoyStruct.hh.

References chi_.

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

inline

Definition at line 128 of file DecoyStruct.hh.

References coords_.

Referenced by coords().

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

inline

Definition at line 157 of file DecoyStruct.hh.

References coords(), and coords_.

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

virtual

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.

Definition at line 91 of file DecoyStruct.cc.

References core::chemical::CENTROID, core::chemical::FA_STANDARD, fullatom(), core::chemical::ChemicalManager::get_instance(), and core::chemical::ChemicalManager::residue_type_set().

Referenced by get_debug_rmsd().

void core::io::raw_data::DecoyStruct::fill_pose	(	core::pose::Pose &	pose,
		core::chemical::ResidueTypeSet const &	residue_set
	)

virtual

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.

Definition at line 104 of file DecoyStruct.cc.

References chi_, fullatom_, core::pose::make_pose_from_sequence(), core::conformation::Residue::nchi(), 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::total_residue().