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Public Member Functions | Protected Attributes | List of all members
core::io::raw_data::DecoyStruct Class Reference

#include <DecoyStruct.hh>

Inheritance diagram for core::io::raw_data::DecoyStruct:
Inheritance graph
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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< Realchi (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>="">:

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< Realphi_
 
utility::vector1< Realpsi_
 
utility::vector1< Realomega_
 
utility::vector1
< utility::vector1< Real > > 
chi_
 
utility::vector1< Vectorcoords_
 
- Protected Attributes inherited from core::io::raw_data::RawStruct
Size nres_
 
std::string decoy_tag_
 
std::string sequence_
 

Constructor & Destructor Documentation

core::io::raw_data::DecoyStruct::DecoyStruct ( Size const  nres_in)
inline
core::io::raw_data::DecoyStruct::DecoyStruct ( )
inline
core::io::raw_data::DecoyStruct::DecoyStruct ( core::pose::Pose const &  pose,
std::string  tag = "empty_tag",
bool  fa = false 
)
core::io::raw_data::DecoyStruct::~DecoyStruct ( )
inlineoverride

Member Function Documentation

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

References chi_.

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

References chi_.

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

References coords_.

Referenced by coords().

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

References coords(), and coords_.

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().

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

data getters/setters

References fullatom_.

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

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

References fullatom(), and fullatom_.

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_, and fill_pose().

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

References omega_.

Referenced by omega().

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

References omega(), and omega_.

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

References phi_.

Referenced by phi().

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

References phi(), and phi_.

void core::io::raw_data::DecoyStruct::print_conformation ( std::ostream &  output) const
overridevirtual
Real core::io::raw_data::DecoyStruct::psi ( unsigned int  seqpos) const
inline

References psi_.

Referenced by psi().

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

References psi(), and psi_.

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().

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

References secstruct_.

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

References secstruct_.

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::io::raw_data::DecoyStruct::chi_
protected
utility::vector1< Vector > core::io::raw_data::DecoyStruct::coords_
protected
bool core::io::raw_data::DecoyStruct::fullatom_
protected
utility::vector1< Real > core::io::raw_data::DecoyStruct::omega_
protected
utility::vector1< Real > core::io::raw_data::DecoyStruct::phi_
protected
utility::vector1< Real > core::io::raw_data::DecoyStruct::psi_
protected
utility::vector1< char > core::io::raw_data::DecoyStruct::secstruct_
protected

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