cpsp::scth::SideChainThreading Class Reference

#include <chain_threading.h>

Detailed Description

Definition at line 43 of file chain_threading.h.


Public Member Functions
virtual Gecode::Space *	copy (bool share)
virtual std::string	print (const std::string sequence, const biu::LatticeFrame latFrame, int option=0)
	SideChainThreading (bool, SideChainThreading &)
	SideChainThreading (const std::string sequence, const biu::LatticeFrame latFrame, const biu::IndexVec neighVecs, cpsp::HCore hCore, const biu::IPointVec *shiftVec=NULL, bool withBreakingSymmetry=true)
virtual	~SideChainThreading ()
Data Fields
IntVarArray	BHs
IntVarArray	BPs
IntVarArray	Hs
IntVarArray	Ps
Private Member Functions
void	attachedToCore (cpsp::HCore *)
void	B_HsNeighbours (const biu::IndexVec *neighVecs)
void	B_PsNeighbours (const biu::IndexVec *neighVecs)
void	BsNeighbours (const std::string sequence, const biu::IndexVec neighVecs)
int	getMaxHull (const std::string *sequence)
void	inCore (cpsp::HCore *)
void	outCore (const std::string sequence, cpsp::HCore )
void	printAsDrowMoves (const std::string seq, const biu::LatticeFrame latFrame)
std::string	printAsMoves (const std::string seq, const biu::LatticeFrame latFrame)
void	printSol (const std::string seq, const biu::LatticeFrame latFrame)
void	selfAvoid ()
void	setBHDomain (const biu::LatticeFrame latFrame, cpsp::HCore hCore)
void	setHDomain (const biu::LatticeFrame latFrame, cpsp::HCore hCore)
void	setOutCoreDomain (const std::string sequence, const biu::LatticeFrame latFrame, cpsp::HCore *hCore)
Private Attributes
IntSet	BHDomain
IntSet	HDomain
IntSet	OutCoreDomain

Constructor & Destructor Documentation

cpsp::scth::SideChainThreading::SideChainThreading	(	const std::string *	sequence,
		const biu::LatticeFrame *	latFrame,
		const biu::IndexVec *	neighVecs,
		cpsp::HCore *	hCore,
		const biu::IPointVec *	shiftVec = `NULL`,
		bool	withBreakingSymmetry = `true`
	)

The constructor for threading one sequence to one Core

Parameters:

	sequence	the sequence string
	latFrame	the lattice (FCC or Cubic)
	neighVecs	the neighboring vector, for effeciency this is a parameter although it could be got from the lattice
	hCore	the HCore
	shiftVec	This is null as default (Will be adjusted automatically in the program)
	withBreakingSymmetry	The default value for breaking the symmetry is true

Definition at line 29 of file chain_threading.cpp.

cpsp::scth::SideChainThreading::SideChainThreading	(	bool	share,
		SideChainThreading &	old
	)

The copy constructor.

Definition at line 160 of file chain_threading.cpp.

cpsp::scth::SideChainThreading::~SideChainThreading ( ) [virtual]

The destructor

Definition at line 173 of file chain_threading.cpp.

Member Function Documentation

void cpsp::scth::SideChainThreading::attachedToCore ( cpsp::HCore * hCore ) [private]

All the back bones of H's are 1 distance unit far from the H-Core. This function propagates the necessary contraints for this.

Definition at line 180 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::B_HsNeighbours ( const biu::IndexVec * neighVecs ) [private]

Neighbourig constrains between the backbones and side chains os Hs

Definition at line 471 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::B_PsNeighbours ( const biu::IndexVec * neighVecs ) [private]

Neighbourig constrains between the backbones and the side chains of Ps

Definition at line 463 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::BsNeighbours	(	const std::string *	sequence,
		const biu::IndexVec *	neighVecs
	)			`[private]`

Neighbouring constrains for the backbones, each backbone should be a neighbor to the backbone of the following amino acid in the sequence.

Definition at line 479 of file chain_threading.cpp.

Gecode::Space * cpsp::scth::SideChainThreading::copy ( bool share ) [virtual]

Copy constrcutor for the gecode.

Definition at line 168 of file chain_threading.cpp.

int cpsp::scth::SideChainThreading::getMaxHull ( const std::string * sequence ) [private]

Get the maximum hull. This is a global maximum. The range for each variable is set afterward.

Returns:: the maximum possible value for the out core domain

Definition at line 524 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::inCore ( cpsp::HCore * hCore ) [private]

All H's are in the HCore, this constraint will make sure of this

Definition at line 175 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::outCore	(	const std::string *	sequence,
		cpsp::HCore *	hCore
	)			`[private]`

All none H are out of the HCore.

Definition at line 419 of file chain_threading.cpp.

std::string cpsp::scth::SideChainThreading::print	(	const std::string *	sequence,
		const biu::LatticeFrame *	latFrame,
		int	option = `0`
	)			`[virtual]`

This is the public function for printing the solutions 1 to print the solution 2 for printing the directions (U,D,L,R,F,B)

Definition at line 402 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::printAsDrowMoves	(	const std::string *	seq,
		const biu::LatticeFrame *	latFrame
	)			`[private]`

Printing for drawing. This function is justs for testing. It is private do not use it!

Definition at line 335 of file chain_threading.cpp.

std::string cpsp::scth::SideChainThreading::printAsMoves	(	const std::string *	seq,
		const biu::LatticeFrame *	latFrame
	)			`[private]`

Printing as moves and return those moves

Parameters:

	seq	The sequence
	latFrame	the lattice frame (Cubic or Lattice)

Returns:: the moves

Definition at line 209 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::printSol	(	const std::string *	seq,
		const biu::LatticeFrame *	latFrame
	)			`[private]`

Printing the solution points This function print the solutions as coordinates.

Definition at line 185 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::selfAvoid ( ) [private]

Self avoiding.

Definition at line 502 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::setBHDomain	(	const biu::LatticeFrame *	latFrame,
		cpsp::HCore *	hCore
	)			`[private]`

Settiing the BH domain (the backbones of Hs).

Definition at line 438 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::setHDomain	(	const biu::LatticeFrame *	latFrame,
		cpsp::HCore *	hCore
	)			`[private]`

Setting domain of the side chains of the Hs.

Definition at line 427 of file chain_threading.cpp.

void cpsp::scth::SideChainThreading::setOutCoreDomain	(	const std::string *	sequence,
		const biu::LatticeFrame *	latFrame,
		cpsp::HCore *	hCore
	)			`[private]`