PTools Class Reference

#include <PTools.h>

List of all members.

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Detailed Description

PTools defines a variety of functions related to loop closure, including functions to calculate goal positions, computation of Jacobian, computation of Null Space, and computation of RMSD distance.

Static Public Member Functions
static void	GetGoals (PAtom *anchorPrior, PAtom *anchorEnd, PAtom *effectorPrior, PAtom *effectorEnd, Real len, Real angle1, Real angle2, Vector3 &goalPrior, Vector3 &goalEnd)
static void	GetGoals (PProtein *protein, ProteinSide side, Vector3 &goalPrior, Vector3 &goalEnd)
static ProteinSide	GetGoals (PProtein *protein, Vector3 &goalPrior, Vector3 &goalEnd)
static PProtein *	CreateSlimProtein (PProtein *protein)
static PProtein *	CreateSlimProtein (PProtein *protein, int startRes, int endRes)
static Real	EffectorAnchorDist (PProtein *loop, ProteinSide side)
static PChain *	LowestCommonChain (PChain *c1, PChain *c2)
static list< PCluster >	GetClusters (const PConformationSpace &space, ConformationDistFn distFn, Real threshold)
static int	getBackboneAtomIndex (int resIndex, const string &atomID)
static void	ComputeJacobian (PProtein *loop, vector< int > ind, double **Jac, Vector3 p, bool forward)
static void	ComputeJacobian (PProtein *loop, vector< int > ind, double **Jac, bool forward)
static void	ComputeJacobian (PProtein *loop, double **Jac)
static void	ComputePseudoInverse (double **A, int m, int n, double **Ainv)
static void	ComputeNullSpace (double **Jac, int dim, bool SixDimensional, NullSpaceRet *Ret)
static void	ProjectOnNullSpace (PProtein *loop, vector< int > ind, bool forward, double ToProject[], double AfterProject[])
static vector< vector< CDof > >	GetBBDofs (vector< PProtein * > loops)
static double	RMSDBackbone (PProtein *protein0, PProtein *protein1, int loopstart, int loopend)
static double	RMSDAllAtom (PProtein *protein0, PProtein *protein1, int loopstart, int loopend)
static bool	CopyBackbone (PProtein *lpS, PProtein *lpD, int startS, int startD, int numRes)
static bool	CopyBackbone (PProtein *lpS, PProtein *lpD)
static void	RandomNullSpacePerturb (PProtein *lp, double pert_mag)
static void	RandomNullSpacePerturb (PProtein *lp, vector< vector< CDof > > Dofs, double pert_mag)
static IKSolution	CloseAlmostClosedLoop (PProtein *lp, Vector3 endPriorGoal, Vector3 endGoal, Vector3 endNextGoal)
static int	gsl_test ()

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Member Function Documentation

void PTools::GetGoals	(	PAtom *	anchorPrior,
		PAtom *	anchorEnd,
		PAtom *	effectorPrior,
		PAtom *	effectorEnd,
		Real	len,
		Real	angle1,
		Real	angle2,
		Vector3 &	goalPrior,
		Vector3 &	goalEnd
	)			[static]

Computes goal positions for chain loop closure. This version of the overloaded function GetGoals does not make the assumption that the chain in question represents a protein, and so requires information about the location of both anchors and end effectors.

Parameters:

	anchorPrior	The anchor closest to the disconencted chain loop.
	anchorEnd	The anchor farthest from the disconnected chain loop.
	effectorPrior	The end effector whose goal is farthest from anchorPrior.
	effectorEnd	The end effector whose goal is closest to anchorPrior.
	len	Distance between goalEnd and anchorPrior.
	angle1	Angle formed by goalPrior-goalEnd-anchorPrior.
	angle2	Angle formed by goalEnd-anchorPrior-anchorEnd.
	goalPrior	Reference to the Vector3 in which to store the goal for effectorPrior.
	goalEnd	Reference to the Vector3 in which to store the goal for effectorEnd.

void PTools::GetGoals	(	PProtein *	protein,
		ProteinSide	side,
		Vector3 &	goalPrior,
		Vector3 &	goalEnd
	)			[static]

Computes goal positions for the specified protein on the specified ProteinSide.

ProteinSide PTools::GetGoals	(	PProtein *	protein,
		Vector3 &	goalPrior,
		Vector3 &	goalEnd
	)			[static]

Computes goal positions for the specified protein. The ProteinSide direction is selected automatically based on distances between anchor and end effector atoms: whichever side (start/end) has the greater C-N anchor-effector distance is used.

PProtein * PTools::CreateSlimProtein

(

PProtein *

protein

)

[static]

Caller is responsible for deallocating return.

PProtein * PTools::CreateSlimProtein	(	PProtein *	protein,
		int	startRes,
		int	endRes
	)			[static]

Real PTools::EffectorAnchorDist	(	PProtein *	loop,
		ProteinSide	side
	)			[static]

Returns the distance between the closest anchor and end effector atoms on the specified side of loop.

PChain * PTools::LowestCommonChain	(	PChain *	c1,
		PChain *	c2
	)			[static]

Returns smallest shared chain or NULL if different top-level chains.

list< PCluster > PTools::GetClusters	(	const PConformationSpace &	space,
		ConformationDistFn	distFn,
		Real	threshold
	)			[static]

Performs conformation space clustering on the specified space. The user-provided function compFn is used to determine the distance between each pair of conformations.

int PTools::getBackboneAtomIndex	(	int	resIndex,
		const string &	atomID
	)			[static]

Returns the index (of atoms in the backbone) for atom atomID in residue number resIndex.

void PTools::ComputeJacobian	(	PProtein *	loop,
		vector< int >	ind,
		double **	Jac,
		Vector3	p,
		bool	forward
	)			[static]

Computes Jacoboian of specified loop, using specified DOFs (ind), tool frame position(p) and direction (forward/backward).

void PTools::ComputeJacobian	(	PProtein *	loop,
		vector< int >	ind,
		double **	Jac,
		bool	forward
	)			[static]

Computes Jacoboian of specified loop, using specified DOFs and direction

void PTools::ComputeJacobian	(	PProtein *	loop,
		double **	Jac
	)			[static]

Computes Jacoboian of specified loop, using all backbone DOFs, C-anchor's position, and direction

void PTools::ComputePseudoInverse	(	double **	A,
		int	m,
		int	n,
		double **	Ainv
	)			[static]

Computes Singularity Robust Inverse of m x n matrix A, The result is contained in Ainv.

void PTools::ComputeNullSpace	(	double **	Jac,
		int	dim,
		bool	SixDimensional,
		NullSpaceRet *	Ret
	)			[static]

Computes Null Space of the Jacobian Jac. The dimensions of Jac are 6 x dim or 3 x dim depending on SixDimensional

void PTools::ProjectOnNullSpace	(	PProtein *	loop,
		vector< int >	ind,
		bool	forward,
		double	ToProject[],
		double	AfterProject[]
	)			[static]

Projects Vector ToProject on the null space of Jacobian of the loop, given the DOFs of loop(ind) to consider, direction of computation of Jacobian (forward). The Projected vector is returned in AfterProject.

vector< vector< CDof > > PTools::GetBBDofs

(

vector< PProtein * >

loops

)

[static]

Returns all backbone DOFs of all loops

double PTools::RMSDBackbone	(	PProtein *	protein0,
		PProtein *	protein1,
		int	loopstart,
		int	loopend
	)			[static]

Returns RMSD between backbones of two proteins protein0 and protein1 starting from residue loopstart and ending at residue loopend.

double PTools::RMSDAllAtom	(	PProtein *	protein0,
		PProtein *	protein1,
		int	loopstart,
		int	loopend
	)			[static]

Returns RMSD between all the atoms of two proteins protein0 and protein1 starting from residue loopstart and ending at residue loopend.

bool PTools::CopyBackbone	(	PProtein *	lpS,
		PProtein *	lpD,
		int	startS,
		int	startD,
		int	numRes
	)			[static]

Modifies a protein loop/ fragment specified by lpD to overlap it with a specified loop/fragment specified by lpS. The loops start respectively at startS and startD and have numRes number of residues. The N-C-alpha atoms of the starting residues of the loops should have same coordinates.

bool PTools::CopyBackbone	(	PProtein *	lpS,
		PProtein *	lpD
	)			[static]

Modifies a protein loop/ fragment specified by lpD to overlap it with a specified loop/fragment specified by lpS.

void PTools::RandomNullSpacePerturb	(	PProtein *	lp,
		double	pert_mag
	)			[static]

Finds a new conformation of loop specified by lp after a random perturbation in its null space. The magnitude of perturbation is specified by pert_mag. All Backbone DOFs of the loop are perturbed.

void PTools::RandomNullSpacePerturb	(	PProtein *	lp,
		vector< vector< CDof > >	Dofs,
		double	pert_mag
	)			[static]

Finds a new conformation of loop specified by lp after a random perturbation in its null space. The magnitude of perturbation is specified by pert_mag. Only the DOFs specified by Dofs are perturbed.

IKSolution PTools::CloseAlmostClosedLoop	(	PProtein *	lp,
		Vector3	endPriorGoal,
		Vector3	endGoal,
		Vector3	endNextGoal
	)			[static]

In many applications one might want to relax the closure constraint by a little bit and in the end the loop specified by lp has to be closed. This method finds a closed conformation closest in terms of RMSD distance to the open conformation. The pose of the closed conformation is defined by the three atoms endPriorGoal, endGoal, and endNextGoal.

int PTools::gsl_test

(

)

[static]

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

• src/core/PTools.h
• src/core/PTools.cc

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