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protocols::jumping::PairingLibrary Class Reference

#include <PairingLibrary.hh>

Inheritance diagram for protocols::jumping::PairingLibrary:
Inheritance graph
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Public Types

typedef std::vector
< PairingTemplate
PairingTemplateList
 
typedef std::map< std::pair
< int, int >
, PairingTemplateList
PairingTemplateMap
 

Public Member Functions

 PairingLibrary ()
 
void read_from_file (std::string const &fn)
 
void read_from_file_no_filters (std::string const &fn)
 
core::kinematics::RT get_random_beta_sheet_jump (int const orientation, int const pleating) const
 classic rosetta++ accessor More...
 
core::kinematics::RT get_random_tmh_jump (int const orientation, int const pos1, int const pos2) const
 classic rosetta++ accessor More...
 
void set_tmh_jump (core::pose::Pose pose, int const jump_number, int const orientation, int const pos1, int const pos2) const
 
void create_jump_fragments (int const orientation, int const pleating, bool bWithTorsion, core::fragment::FragDataOPs &) const override
 puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end More...
 
core::Size size () const
 
void generate_jump_frags (core::scoring::dssp::PairingsList const &pairings, core::kinematics::MoveMap const &mm, bool bWithTorsion, core::fragment::FragSet &frags_accumulator) override
 
- Public Member Functions inherited from protocols::jumping::BasePairingLibrary
 ~BasePairingLibrary () override
 

Private Attributes

PairingTemplateMap pairings_
 
core::Size num_of_pairings_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jumping::PairingLibrary::PairingLibrary ( )
inline

Member Function Documentation

void protocols::jumping::PairingLibrary::create_jump_fragments ( int const  orientation,
int const  pleating,
bool  bWithTorsion,
core::fragment::FragDataOPs frags 
) const
overridevirtual

puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end

puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating

Implements protocols::jumping::BasePairingLibrary.

References pairings_, protocols::loops::start, and protocols::loops::stop.

Referenced by generate_jump_frags(), and protocols::jumping::JumpSample::generate_jump_frags().

void protocols::jumping::PairingLibrary::generate_jump_frags ( core::scoring::dssp::PairingsList const &  pairings,
core::kinematics::MoveMap const &  mm,
bool  bWithTorsion,
core::fragment::FragSet frags_accumulator 
)
overridevirtual
kinematics::RT protocols::jumping::PairingLibrary::get_random_beta_sheet_jump ( int const  orientation,
int const  pleating 
) const
kinematics::RT protocols::jumping::PairingLibrary::get_random_tmh_jump ( int const  orientation,
int const  pos1,
int const  pos2 
) const
void protocols::jumping::PairingLibrary::read_from_file ( std::string const &  fn)
void protocols::jumping::PairingLibrary::read_from_file_no_filters ( std::string const &  fn)
void protocols::jumping::PairingLibrary::set_tmh_jump ( core::pose::Pose  pose,
int const  jump_number,
int const  orientation,
int const  pos1,
int const  pos2 
) const
core::Size protocols::jumping::PairingLibrary::size ( ) const
inline

References num_of_pairings_.

Member Data Documentation

core::Size protocols::jumping::PairingLibrary::num_of_pairings_
private
PairingTemplateMap protocols::jumping::PairingLibrary::pairings_
private

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