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

#include <SS_Info2.hh>

Inheritance diagram for protocols::fldsgn::topology::SS_Info2:
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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...
 
basic::datacache::CacheableDataOP clone () const override
 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 (core::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 (core::Size is) const
 return owning pointer of strand given an index of strands More...
 
HelixCOP const helix (core::Size ih) const
 return owning pointer of helix given an index of helices More...
 
LoopCOP const loop (core::Size il) const
 return owning pointer of loop given an index of loops More...
 
core::Size strand_id (core::Size const nres) const
 return strand index in strands given a residue number More...
 
core::Size helix_id (core::Size const nres) const
 return helix index in helices given a residue number More...
 
core::Size loop_id (core::Size const nres) const
 return loop index in loops given a residue number More...
 
core::Size ss_element_id (core::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 (core::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< core::Sizestrand_id_
 vector for storing index of strand id for each residue position More...
 
Helices helices_
 vector of HelixOP More...
 
utility::vector1< core::Sizehelix_id_
 vector for storing index of helix id for each residue position More...
 
Loops loops_
 vector of loops More...
 
utility::vector1< core::Sizeloop_id_
 
utility::vector1< core::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

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().

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
override

make clone

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

return owning pointer of loop given an index of loops

References loops_.

core::Size protocols::fldsgn::topology::SS_Info2::loop_id ( core::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 ( core::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 ( core::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().

core::Size protocols::fldsgn::topology::SS_Info2::ss_element_id ( core::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 ( core::Size  is) const
inline
core::Size protocols::fldsgn::topology::SS_Info2::strand_id ( core::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< core::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< core::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< core::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< core::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: