protocols::jumping::SheetBuilder Class Reference

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

#include <SheetBuilder.hh>

Inheritance diagram for protocols::jumping::SheetBuilder:

Collaboration diagram for protocols::jumping::SheetBuilder:

Public Types
typedef utility::vector1 < core::Size >	SheetTopology

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 jumping_pairings.cc of Rosetta++

Member Typedef Documentation

typedef utility::vector1< core::Size > protocols::jumping::SheetBuilder::SheetTopology

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 ( )

virtual

Member Function Documentation

bool protocols::jumping::SheetBuilder::builder_loop ( core::scoring::dssp::PairingsList &  jump_pairings) const

private

References check_next_pairing(), choose_next_pairing(), for(), same_strand_, core::scoring::sheet, sheet_sizes_, and protocols::jumping::tr().

Referenced by create_jump_sample().

bool protocols::jumping::SheetBuilder::check_next_pairing ( ObjexxFCL::FArray3D_int &  , core::Size  , core::Size    ) const

private

References bForceSingleSheet_, check_pairing_intersect(), check_sheet_pairings(), sheet_sizes_, and total_residue_.

Referenced by builder_loop().

bool protocols::jumping::SheetBuilder::check_pairing_intersect ( ObjexxFCL::FArray1A_int  , ObjexxFCL::FArray1A_int    ) const

private

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

private

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

private

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  , core::Size    ) const

private

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

inlinevirtual

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

Implements protocols::jumping::BaseJumpSetup.

References builder_loop(), create_new_random_topol(), protocols::jumping::JumpSample::is_valid(), secondary_structure_, sheet_sizes_, total_residue_, and protocols::jumping::tr().

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

inlineprotectedvirtual

Reimplemented in protocols::jumping::RandomSheetBuilder.

References sheet_sizes_.

Referenced by create_jump_sample().

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

inline

References total_residue_.

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

inlinevirtual

Implements protocols::jumping::BaseJumpSetup.

Member Data Documentation

bool protocols::jumping::SheetBuilder::bForceSingleSheet_

private

Referenced by check_next_pairing().

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

private

Referenced by choose_next_pairing().

SameStrandOP protocols::jumping::SheetBuilder::same_strand_

private

Referenced by builder_loop(), check_pairing_intersect(), and check_two_pairings().

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

private

Referenced by create_jump_sample().

SheetTopology protocols::jumping::SheetBuilder::sheet_sizes_

mutableprivate

Referenced by builder_loop(), check_next_pairing(), create_jump_sample(), and create_new_random_topol().

core::Size protocols::jumping::SheetBuilder::total_residue_

private

Referenced by check_next_pairing(), create_jump_sample(), and total_residue().

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

• src/protocols/jumping/SheetBuilder.hh
• src/protocols/jumping/SheetBuilder.cc