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>

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(), s, same_strand_, 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 j, and 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