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protocols::jumping::ResiduePairJumpSetup Class Reference

#include <ResiduePairJumpSetup.hh>

Inheritance diagram for protocols::jumping::ResiduePairJumpSetup:
Inheritance graph
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Classes

class  JumpDef
 

Public Types

typedef utility::vector1
< JumpDef >::const_iterator 
const_iterator
 
typedef utility::vector1
< JumpDef >::iterator 
iterator
 

Public Member Functions

std::string type_name () const override
 
 ResiduePairJumpSetup ()
 
 ResiduePairJumpSetup (core::Size total_residue)
 
void add_jump (JumpDef const &jd)
 
void add_jump (Interval const &jump, Interval const &cut_reg)
 
void add_jump (core::Size js, core::Size je, core::Size crs, core::Size cre)
 
void add_residue_pair_jump (ResiduePairJumpOP ptr)
 
void set_root (core::Size root)
 
core::Size root () const
 
core::Size size () const
 
const_iterator begin () const
 
const_iterator end () const
 
void read_file (std::string file)
 
JumpSample create_jump_sample () const override
 
JumpSample clean_jumps (JumpSample const &js) const override
 take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample() More...
 
core::fragment::FragSetOP generate_jump_frags (JumpSample const &, core::kinematics::MoveMap const &mm) const override
 returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample More...
 
core::Size total_residue () const
 
void clear ()
 
- Public Member Functions inherited from protocols::jumping::BaseJumpSetup
 ~BaseJumpSetup () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 

Private Attributes

utility::vector1< JumpDefjumps_
 
core::Size total_residue_
 
core::Size root_
 
utility::vector1
< ResiduePairJumpOP
ResiduePairJumps_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jumping::ResiduePairJumpSetup::ResiduePairJumpSetup ( )
inline
protocols::jumping::ResiduePairJumpSetup::ResiduePairJumpSetup ( core::Size  total_residue)
inline

Member Function Documentation

void protocols::jumping::ResiduePairJumpSetup::add_jump ( JumpDef const &  jd)
inline

References jumps_.

Referenced by add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_jump ( Interval const &  jump,
Interval const &  cut_reg 
)
inline

References add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_jump ( core::Size  js,
core::Size  je,
core::Size  crs,
core::Size  cre 
)
inline

References add_jump().

void protocols::jumping::ResiduePairJumpSetup::add_residue_pair_jump ( ResiduePairJumpOP  ptr)
inline

References ResiduePairJumps_.

const_iterator protocols::jumping::ResiduePairJumpSetup::begin ( ) const
inline

References jumps_.

JumpSample protocols::jumping::ResiduePairJumpSetup::clean_jumps ( JumpSample const &  ) const
inlineoverridevirtual

take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample()

Implements protocols::jumping::BaseJumpSetup.

void protocols::jumping::ResiduePairJumpSetup::clear ( )
inline

References jumps_.

JumpSample protocols::jumping::ResiduePairJumpSetup::create_jump_sample ( ) const
overridevirtual
const_iterator protocols::jumping::ResiduePairJumpSetup::end ( ) const
inline

References jumps_.

FragSetOP protocols::jumping::ResiduePairJumpSetup::generate_jump_frags ( JumpSample const &  jumps,
core::kinematics::MoveMap const &  mm 
) const
overridevirtual
void protocols::jumping::ResiduePairJumpSetup::read_file ( std::string  file)
core::Size protocols::jumping::ResiduePairJumpSetup::root ( ) const
inline

References root_.

Referenced by set_root().

void protocols::jumping::ResiduePairJumpSetup::set_root ( core::Size  root)
inline

References root(), root_, and total_residue_.

core::Size protocols::jumping::ResiduePairJumpSetup::size ( ) const
inline

References jumps_.

core::Size protocols::jumping::ResiduePairJumpSetup::total_residue ( ) const
inline

References total_residue_.

std::string protocols::jumping::ResiduePairJumpSetup::type_name ( ) const
inlineoverridevirtual

Member Data Documentation

utility::vector1< JumpDef > protocols::jumping::ResiduePairJumpSetup::jumps_
private

Referenced by add_jump(), begin(), clear(), end(), and size().

utility::vector1<ResiduePairJumpOP> protocols::jumping::ResiduePairJumpSetup::ResiduePairJumps_
private

Referenced by add_residue_pair_jump().

core::Size protocols::jumping::ResiduePairJumpSetup::root_
private

Referenced by root(), and set_root().

core::Size protocols::jumping::ResiduePairJumpSetup::total_residue_
private

Referenced by set_root(), and total_residue().


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