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protocols::jumping::SheetBuilder Class Reference

select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in of Rosetta++ More...

#include <SheetBuilder.hh>

Inheritance diagram for protocols::jumping::SheetBuilder:
Inheritance graph
Collaboration diagram for protocols::jumping::SheetBuilder:
Collaboration graph

Public Types

typedef utility::vector1
< core::Size

Public Member Functions

 SheetBuilder (core::fragment::SecondaryStructureOP, core::scoring::dssp::PairingsList const &, SheetTopology const &)
 SheetBuilder (SheetBuilder const &)
virtual ~SheetBuilder ()
std::string type_name () const
virtual JumpSample create_jump_sample () const
JumpSample clean_jumps (JumpSample const &js) const
 take from a given JumpSample only those Jumps, which could also have been created by create_jump_sample() More...
Size total_residue () const
- Public Member Functions inherited from protocols::jumping::BaseJumpSetup
virtual ~BaseJumpSetup ()
 Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
virtual core::fragment::FragSetOP generate_jump_frags (JumpSample const &, core::kinematics::MoveMap const &mm) const
 returns an ordered FragSet that is compatible with the JumpSample default: generate jumps from ss-library according to JumpSample More...

Protected Member Functions

virtual SheetTopology create_new_random_topol () const

Private Member Functions

bool builder_loop (core::scoring::dssp::PairingsList &jump_pairings) const
void choose_next_pairing (ObjexxFCL::FArray3D_int &, core::Size, core::Size) const
 simply random choice of pairing from pool More...
bool check_next_pairing (ObjexxFCL::FArray3D_int &, core::Size, core::Size) const
bool check_two_pairings (ObjexxFCL::FArray1A_int pairing1, ObjexxFCL::FArray1A_int pairing2, int &common_strands) const
bool check_sheet_pairings (ObjexxFCL::FArray2A_int pairing_list, const int last_pairing, const bool force_single_sheet) const
bool check_pairing_intersect (ObjexxFCL::FArray1A_int, ObjexxFCL::FArray1A_int) const
 return true if parings have a strand in common More...

Private Attributes

core::Size total_residue_
core::scoring::dssp::PairingsList pairings_
SameStrandOP same_strand_
core::fragment::SecondaryStructureOP secondary_structure_
SheetTopology sheet_sizes_
bool bForceSingleSheet_

Detailed Description

select jumps to build a given topology this class encapsulates the functionality of choose_random_pairings in of Rosetta++

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::jumping::SheetBuilder::SheetBuilder ( core::fragment::SecondaryStructureOP  ss,
core::scoring::dssp::PairingsList const &  pairings,
SheetTopology const &  sheet_topol 
protocols::jumping::SheetBuilder::SheetBuilder ( SheetBuilder const &  other)
protocols::jumping::SheetBuilder::~SheetBuilder ( )

Member Function Documentation

bool protocols::jumping::SheetBuilder::builder_loop ( core::scoring::dssp::PairingsList jump_pairings) const
bool protocols::jumping::SheetBuilder::check_next_pairing ( ObjexxFCL::FArray3D_int &  ,
core::Size  ,
) const
bool protocols::jumping::SheetBuilder::check_pairing_intersect ( ObjexxFCL::FArray1A_int  ,
) const

return true if parings have a strand in common

References same_strand_.

Referenced by check_next_pairing().

bool protocols::jumping::SheetBuilder::check_sheet_pairings ( ObjexxFCL::FArray2A_int  pairing_list,
const int  last_pairing,
const bool  force_single_sheet 
) const

References check_two_pairings().

Referenced by check_next_pairing().

bool protocols::jumping::SheetBuilder::check_two_pairings ( ObjexxFCL::FArray1A_int  pairing1,
ObjexxFCL::FArray1A_int  pairing2,
int common_strands 
) const

count how many strands are in common : 0, 1, or 2 if 1 or 2 strands are in common check if pleating of the two pairings is compatible

References core::scoring::dssp::Pairing::Pleating(), core::scoring::dssp::Pairing::Pos1(), core::scoring::dssp::Pairing::Pos2(), core::scoring::dssp::Pairing::reverse(), and same_strand_.

Referenced by check_sheet_pairings().

void protocols::jumping::SheetBuilder::choose_next_pairing ( ObjexxFCL::FArray3D_int &  ,
core::Size  ,
) const

simply random choice of pairing from pool

References pairings_, and protocols::jumping::RG().

Referenced by builder_loop().

JumpSample protocols::jumping::SheetBuilder::clean_jumps ( JumpSample const &  ) const

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

Implements protocols::jumping::BaseJumpSetup.

JumpSample protocols::jumping::SheetBuilder::create_jump_sample ( ) const
virtual SheetTopology protocols::jumping::SheetBuilder::create_new_random_topol ( ) const

Reimplemented in protocols::jumping::RandomSheetBuilder.

References sheet_sizes_.

Referenced by create_jump_sample().

Size protocols::jumping::SheetBuilder::total_residue ( ) const

References total_residue_.

std::string protocols::jumping::SheetBuilder::type_name ( ) const

Member Data Documentation

bool protocols::jumping::SheetBuilder::bForceSingleSheet_

Referenced by check_next_pairing().

core::scoring::dssp::PairingsList protocols::jumping::SheetBuilder::pairings_

Referenced by choose_next_pairing().

SameStrandOP protocols::jumping::SheetBuilder::same_strand_
core::fragment::SecondaryStructureOP protocols::jumping::SheetBuilder::secondary_structure_

Referenced by create_jump_sample().

SheetTopology protocols::jumping::SheetBuilder::sheet_sizes_
core::Size protocols::jumping::SheetBuilder::total_residue_

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