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protocols::fldsgn::topology::SS_Info2 Class Reference

#include <SS_Info2.hh>

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Public Member Functions

 SS_Info2 ()
 default constructor More...
 
 SS_Info2 (String const &secstruct)
 value constructor More...
 
 SS_Info2 (Pose const &pose, String const &secstruct="")
 value constructor More...
 
 SS_Info2 (SS_Info2 const &s)
 copy constructor More...
 
 ~SS_Info2 ()
 destructor More...
 
basic::datacache::CacheableDataOP clone () const
 make clone More...
 
void initialize (String const &secstruct)
 initialize parameters of this class More...
 
void initialize (Pose const &pose, String const &secstruct="")
 initialize parameters of this class More...
 
bool bbpos_is_set () const
 get flag for telling whether bb_pos_ was initiliazed by pose or not More...
 
String secstruct () const
 string of secondary structure elements More...
 
char secstruct (Size ii) const
 
BB_Pos const & bb_pos () const
 get xyz-coordinates of backbone structure More...
 
Strands const & strands () const
 return strands More...
 
Helices const & helices () const
 return helices More...
 
Loops const & loops () const
 return loops More...
 
StrandCOP const strand (Size is) const
 return owning pointer of strand given an index of strands More...
 
HelixCOP const helix (Size ih) const
 return owning pointer of helix given an index of helices More...
 
LoopCOP const loop (Size il) const
 return owning pointer of loop given an index of loops More...
 
Size strand_id (Size const nres) const
 return strand index in strands given a residue number More...
 
Size helix_id (Size const nres) const
 return helix index in helices given a residue number More...
 
Size loop_id (Size const nres) const
 return loop index in loops given a residue number More...
 
Size ss_element_id (Size const nres) const
 return the index of secondary structure element given a residue number More...
 
void set_SSorient (Pose const &pose)
 set orientation vector of secondary structures given a pose More...
 
void set_SSorient ()
 set orientation vector of secondary structures given a pose which is defined in the constructor More...
 
void clear_data ()
 clear data More...
 

Private Types

typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef std::string String
 
typedef
protocols::fldsgn::topology::BB_Pos 
BB_Pos
 

Private Member Functions

void resize (Size const nres)
 resize vectors More...
 
void identify_ss (String const &secstruct)
 identify secondary structures More...
 

Private Attributes

bool bbpos_is_set_
 flag for telling whether bb_pos_ was initiliazed by pose or not More...
 
String secstruct_
 string of secondary structure elements More...
 
BB_Pos bb_pos_
 xyz-coordinates of backbone More...
 
Strands strands_
 vector of StrandOP More...
 
utility::vector1< Sizestrand_id_
 vector for storing index of strand id for each residue position More...
 
Helices helices_
 vector of HelixOP More...
 
utility::vector1< Sizehelix_id_
 vector for storing index of helix id for each residue position More...
 
Loops loops_
 vector of loops More...
 
utility::vector1< Sizeloop_id_
 
utility::vector1< Sizess_element_id_
 vector for storing index of secondary structure element for each residue position More...
 

Friends

std::ostream & operator<< (std::ostream &out, const SS_Info2 &ssinfo)
 output info of SS_Info2 More...
 

Member Typedef Documentation

typedef std::string protocols::fldsgn::topology::SS_Info2::String
private

Constructor & Destructor Documentation

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( )

default constructor

Referenced by clone().

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( String const &  secstruct)

value constructor

References initialize().

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( Pose const &  pose,
String const &  secstruct = "" 
)

value constructor

References initialize().

protocols::fldsgn::topology::SS_Info2::SS_Info2 ( SS_Info2 const &  s)

copy constructor

protocols::fldsgn::topology::SS_Info2::~SS_Info2 ( )

destructor

Member Function Documentation

BB_Pos const& protocols::fldsgn::topology::SS_Info2::bb_pos ( ) const
inline
bool protocols::fldsgn::topology::SS_Info2::bbpos_is_set ( ) const
inline

get flag for telling whether bb_pos_ was initiliazed by pose or not

References bbpos_is_set_.

void protocols::fldsgn::topology::SS_Info2::clear_data ( )
basic::datacache::CacheableDataOP protocols::fldsgn::topology::SS_Info2::clone ( ) const

make clone

References SS_Info2().

Helices const& protocols::fldsgn::topology::SS_Info2::helices ( ) const
inline
HelixCOP const protocols::fldsgn::topology::SS_Info2::helix ( Size  ih) const
inline

return owning pointer of helix given an index of helices

References helices_.

Size protocols::fldsgn::topology::SS_Info2::helix_id ( Size const  nres) const
inline

return helix index in helices given a residue number

References helix_id_.

void protocols::fldsgn::topology::SS_Info2::identify_ss ( String const &  secstruct)
private

identify secondary structures

identify the region of each secondary structure element

References helices_, helix_id_, loop_id_, loops_, ss_element_id_, strand_id_, and strands_.

Referenced by initialize().

void protocols::fldsgn::topology::SS_Info2::initialize ( String const &  secstruct)

initialize parameters of this class

References clear_data(), identify_ss(), resize(), secstruct(), and secstruct_.

Referenced by SS_Info2().

void protocols::fldsgn::topology::SS_Info2::initialize ( Pose const &  pose,
String const &  secstruct = "" 
)
LoopCOP const protocols::fldsgn::topology::SS_Info2::loop ( Size  il) const
inline

return owning pointer of loop given an index of loops

References loops_.

Size protocols::fldsgn::topology::SS_Info2::loop_id ( Size const  nres) const
inline

return loop index in loops given a residue number

References loop_id_.

Loops const& protocols::fldsgn::topology::SS_Info2::loops ( ) const
inline

return loops

References loops_.

void protocols::fldsgn::topology::SS_Info2::resize ( Size const  nres)
private
String protocols::fldsgn::topology::SS_Info2::secstruct ( ) const
inline

string of secondary structure elements

References secstruct_.

Referenced by initialize().

char protocols::fldsgn::topology::SS_Info2::secstruct ( Size  ii) const
inline

References secstruct_.

void protocols::fldsgn::topology::SS_Info2::set_SSorient ( Pose const &  pose)
void protocols::fldsgn::topology::SS_Info2::set_SSorient ( )

set orientation vector of secondary structures given a pose which is defined in the constructor

References bb_pos_, helices_, and strands_.

Referenced by initialize(), and set_SSorient().

Size protocols::fldsgn::topology::SS_Info2::ss_element_id ( Size const  nres) const
inline

return the index of secondary structure element given a residue number

References ss_element_id_.

StrandCOP const protocols::fldsgn::topology::SS_Info2::strand ( Size  is) const
inline

return owning pointer of strand given an index of strands

References strands_.

Referenced by protocols::fldsgn::topology::StrandPairingSet::initialize_by_dimer_pairs().

Size protocols::fldsgn::topology::SS_Info2::strand_id ( Size const  nres) const
inline
Strands const& protocols::fldsgn::topology::SS_Info2::strands ( ) const
inline

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const SS_Info2 ssinfo 
)
friend

output info of SS_Info2

Member Data Documentation

BB_Pos protocols::fldsgn::topology::SS_Info2::bb_pos_
private

xyz-coordinates of backbone

Referenced by bb_pos(), clear_data(), initialize(), resize(), and set_SSorient().

bool protocols::fldsgn::topology::SS_Info2::bbpos_is_set_
private

flag for telling whether bb_pos_ was initiliazed by pose or not

Referenced by bbpos_is_set(), initialize(), and set_SSorient().

Helices protocols::fldsgn::topology::SS_Info2::helices_
private
utility::vector1< Size > protocols::fldsgn::topology::SS_Info2::helix_id_
private

vector for storing index of helix id for each residue position

Referenced by clear_data(), helix_id(), identify_ss(), and resize().

utility::vector1< Size > protocols::fldsgn::topology::SS_Info2::loop_id_
private
Loops protocols::fldsgn::topology::SS_Info2::loops_
private

vector of loops

Referenced by identify_ss(), loop(), and loops().

String protocols::fldsgn::topology::SS_Info2::secstruct_
private

string of secondary structure elements

Referenced by clear_data(), initialize(), and secstruct().

utility::vector1< Size > protocols::fldsgn::topology::SS_Info2::ss_element_id_
private

vector for storing index of secondary structure element for each residue position

Referenced by clear_data(), identify_ss(), resize(), and ss_element_id().

utility::vector1< Size > protocols::fldsgn::topology::SS_Info2::strand_id_
private

vector for storing index of strand id for each residue position

Referenced by clear_data(), identify_ss(), resize(), and strand_id().

Strands protocols::fldsgn::topology::SS_Info2::strands_
private

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