meshi.geometry
Class Torsion

java.lang.Object
  meshi.geometry.Torsion

All Implemented Interfaces:

Updateable

Direct Known Subclasses:

QuickAndDirtyTorsion

public class Torsion
extends java.lang.Object
implements Updateable

--------------------------- Torsion ----------------------------------- Addapted from Ron Elber's MOIL (ephi). Below is the MOIL documentation calculate dihedral energies and forces according to T.schlick, J.comput.chem, vol 10, 7 (1989) with local variant (no delta funcion involved) V = sum [ k(n)(1 + cos(n*phi + delta)] (1=< n <= 3) delta is either 0 or pi, so the formula become less complicated upon expansion. As of version 1.41 Nir Kalisman changed the derivation of the torsion so now it is stable also at +-PI

Field Summary

protected double	a0x
protected double	a0y
protected double	a0z
protected double	a1x
protected double	a1y
protected double	a1z
protected double	a2x
protected double	a2y
protected double	a2z
protected double	aa
protected double	ab
protected double	ac
private Angle	ANGLE1
private Angle	ANGLE2
private Atom	atm1
private Atom	atm2
private Atom	atm3
private Atom	atm4
Atom	atom1
Atom	atom2
Atom	atom3
Atom	atom4
protected double	aux1
protected double	aux2
protected double	aux3
protected double	aux4
protected double	ax
protected double	ay
protected double	az
protected double	b0x
protected double	b0y
protected double	b0z
protected double	b1x
protected double	b1y
protected double	b1z
protected double	b2x
protected double	b2y
protected double	b2z
protected double	bb
protected double	bc
protected double	bx
protected double	by
protected double	bz
protected double	c0x
protected double	c0y
protected double	c0z
protected double	cc
protected double	co1
protected double	cosTorsion
protected double	cross123x
protected double	cross123y
protected double	cross123z
protected double	cross234x
protected double	cross234y
protected double	cross234z
protected double	cx
protected double	cy
protected double	cz
protected double	dCosTorsionDx1
protected double	dCosTorsionDx2
protected double	dCosTorsionDx3
protected double	dCosTorsionDx4
protected double	dCosTorsionDy1
protected double	dCosTorsionDy2
protected double	dCosTorsionDy3
protected double	dCosTorsionDy4
protected double	dCosTorsionDz1
protected double	dCosTorsionDz2
protected double	dCosTorsionDz3
protected double	dCosTorsionDz4
protected double	den
Distance	distance1
Distance	distance2
Distance	distance3
protected DistanceMatrix	distanceMatrix
protected double	dTorsionDx1
protected double	dTorsionDx2
protected double	dTorsionDx3
protected double	dTorsionDx4
protected double	dTorsionDy1
protected double	dTorsionDy2
protected double	dTorsionDy3
protected double	dTorsionDy4
protected double	dTorsionDz1
protected double	dTorsionDz2
protected double	dTorsionDz3
protected double	dTorsionDz4
protected double	dx1
protected double	dy1
protected double	dz1
protected double	factor1
protected double	factor4
protected double	invBB
protected double	normCross123squared
protected double	normCross234squared
private int	numberOfUpdates
protected double	sinSign
protected double	tmpSQRT
protected double	torsion
protected int	torsionCode
protected java.lang.String	torsionName
private boolean	torsionNeeded
protected java.lang.String	torsionResName
protected int	torsionResNum
protected double	uu
protected double	uu2
protected double	uv
protected double	ux
protected double	uy
protected double	uz
protected double	vv
protected double	vv2
protected double	vx
protected double	vy
protected double	vz

Constructor Summary

	Torsion(Angle angle1, Angle angle2, DistanceMatrix distanceMatrix)
protected	Torsion(Atom atom1, Atom atom2, Atom atom3, Atom atom4, Distance distance1, Distance distance2, Distance distance3) This constructor should be used only by DisposableAngle.

Method Summary

double	acos(double cos) Calculate the arc-cosine function.
protected void	assignName() Assigns a meaningful name to a torsion.
AtomList	atoms()
double	cosTorsion()
double	dCosTorsionDx1()
double	dCosTorsionDx2()
double	dCosTorsionDx3()
double	dCosTorsionDx4()
double	dCosTorsionDy1()
double	dCosTorsionDy2()
double	dCosTorsionDy3()
double	dCosTorsionDy4()
double	dCosTorsionDz1()
double	dCosTorsionDz2()
double	dCosTorsionDz3()
double	dCosTorsionDz4()
static double	dot(double d1, double d2, double d3, double e1, double e2, double e3)
double	dTorsionDx1()
double	dTorsionDx2()
double	dTorsionDx3()
double	dTorsionDx4()
double	dTorsionDy1()
double	dTorsionDy2()
double	dTorsionDy3()
double	dTorsionDy4()
double	dTorsionDz1()
double	dTorsionDz2()
double	dTorsionDz3()
double	dTorsionDz4()
boolean	equivalent(Torsion other)
void	freeze()
boolean	frozen()
int	getTorsionCode()
java.lang.String	getTorsionName()
java.lang.String	getTorsionResName()
int	getTorsionResNum()
java.lang.String	name()
boolean	proper()
double	torsion()
java.lang.String	toString()
private void	type1()
private void	type2()
private void	type3()
protected void	update()
void	update(int numberOfUpdates)
void	updateCosine()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atom1

public final Atom atom1

atom2

public final Atom atom2

atom3

public final Atom atom3

atom4

public final Atom atom4

atm1

private Atom atm1

atm2

private Atom atm2

atm3

private Atom atm3

atm4

private Atom atm4

ANGLE1

private Angle ANGLE1

ANGLE2

private Angle ANGLE2

torsionName

protected java.lang.String torsionName

torsionCode

protected int torsionCode

torsionResNum

protected int torsionResNum

torsionResName

protected java.lang.String torsionResName

distance1

public final Distance distance1

distance2

public final Distance distance2

distance3

public final Distance distance3

dCosTorsionDx1

protected double dCosTorsionDx1

dCosTorsionDy1

protected double dCosTorsionDy1

dCosTorsionDz1

protected double dCosTorsionDz1

dCosTorsionDx2

protected double dCosTorsionDx2

dCosTorsionDy2

protected double dCosTorsionDy2

dCosTorsionDz2

protected double dCosTorsionDz2

dCosTorsionDx3

protected double dCosTorsionDx3

dCosTorsionDy3

protected double dCosTorsionDy3

dCosTorsionDz3

protected double dCosTorsionDz3

dCosTorsionDx4

protected double dCosTorsionDx4

dCosTorsionDy4

protected double dCosTorsionDy4

dCosTorsionDz4

protected double dCosTorsionDz4

cosTorsion

protected double cosTorsion

dTorsionDx1

protected double dTorsionDx1

dTorsionDy1

protected double dTorsionDy1

dTorsionDz1

protected double dTorsionDz1

dTorsionDx2

protected double dTorsionDx2

dTorsionDy2

protected double dTorsionDy2

dTorsionDz2

protected double dTorsionDz2

dTorsionDx3

protected double dTorsionDx3

dTorsionDy3

protected double dTorsionDy3

dTorsionDz3

protected double dTorsionDz3

dTorsionDx4

protected double dTorsionDx4

dTorsionDy4

protected double dTorsionDy4

dTorsionDz4

protected double dTorsionDz4

torsion

protected double torsion

ax

protected double ax

ay

protected double ay

az

protected double az

bx

protected double bx

by

protected double by

bz

protected double bz

cx

protected double cx

cy

protected double cy

cz

protected double cz

ab

protected double ab

bc

protected double bc

ac

protected double ac

aa

protected double aa

bb

protected double bb

cc

protected double cc

uu

protected double uu

vv

protected double vv

uv

protected double uv

den

protected double den

co1

protected double co1

a0x

protected double a0x

a0y

protected double a0y

a0z

protected double a0z

b0x

protected double b0x

b0y

protected double b0y

b0z

protected double b0z

c0x

protected double c0x

c0y

protected double c0y

c0z

protected double c0z

uu2

protected double uu2

vv2

protected double vv2

a1x

protected double a1x

a1y

protected double a1y

a1z

protected double a1z

b1x

protected double b1x

b1y

protected double b1y

b1z

protected double b1z

a2x

protected double a2x

a2y

protected double a2y

a2z

protected double a2z

b2x

protected double b2x

b2y

protected double b2y

b2z

protected double b2z

ux

protected double ux

uy

protected double uy

uz

protected double uz

vx

protected double vx

vy

protected double vy

vz

protected double vz

dx1

protected double dx1

dy1

protected double dy1

dz1

protected double dz1

sinSign

protected double sinSign

cross123x

protected double cross123x

cross123y

protected double cross123y

cross123z

protected double cross123z

cross234x

protected double cross234x

cross234y

protected double cross234y

cross234z

protected double cross234z

normCross123squared

protected double normCross123squared

normCross234squared

protected double normCross234squared

factor1

protected double factor1

factor4

protected double factor4

tmpSQRT

protected double tmpSQRT

invBB

protected double invBB

aux1

protected double aux1

aux2

protected double aux2

aux3

protected double aux3

aux4

protected double aux4

distanceMatrix

protected DistanceMatrix distanceMatrix

numberOfUpdates

private int numberOfUpdates

torsionNeeded

private boolean torsionNeeded

Constructor Detail

Torsion

public Torsion(Angle angle1,
               Angle angle2,
               DistanceMatrix distanceMatrix)

Torsion

protected Torsion(Atom atom1,
                  Atom atom2,
                  Atom atom3,
                  Atom atom4,
                  Distance distance1,
                  Distance distance2,
                  Distance distance3)

This constructor should be used only by DisposableAngle.

Method Detail

type1

private void type1()

type2

private void type2()

type3

private void type3()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

cosTorsion

public double cosTorsion()

dCosTorsionDx1

public double dCosTorsionDx1()

dCosTorsionDy1

public double dCosTorsionDy1()

dCosTorsionDz1

public double dCosTorsionDz1()

dCosTorsionDx2

public double dCosTorsionDx2()

dCosTorsionDy2

public double dCosTorsionDy2()

dCosTorsionDz2

public double dCosTorsionDz2()

dCosTorsionDx3

public double dCosTorsionDx3()

dCosTorsionDy3

public double dCosTorsionDy3()

dCosTorsionDz3

public double dCosTorsionDz3()

dCosTorsionDx4

public double dCosTorsionDx4()

dCosTorsionDy4

public double dCosTorsionDy4()

dCosTorsionDz4

public double dCosTorsionDz4()

torsion

public double torsion()

dTorsionDx1

public double dTorsionDx1()

dTorsionDy1

public double dTorsionDy1()

dTorsionDz1

public double dTorsionDz1()

dTorsionDx2

public double dTorsionDx2()

dTorsionDy2

public double dTorsionDy2()

dTorsionDz2

public double dTorsionDz2()

dTorsionDx3

public double dTorsionDx3()

dTorsionDy3

public double dTorsionDy3()

dTorsionDz3

public double dTorsionDz3()

dTorsionDx4

public double dTorsionDx4()

dTorsionDy4

public double dTorsionDy4()

dTorsionDz4

public double dTorsionDz4()

updateCosine

public void updateCosine()

update

public void update(int numberOfUpdates)

Specified by:

update in interface Updateable

acos

public double acos(double cos)

Calculate the arc-cosine function. This method simply calls Math.acos, extending classes however may use approximations in order to save time.

update

protected void update()

proper

public boolean proper()

equivalent

public boolean equivalent(Torsion other)

dot

public static double dot(double d1,
                         double d2,
                         double d3,
                         double e1,
                         double e2,
                         double e3)

frozen

public boolean frozen()

freeze

public void freeze()

getTorsionName

public java.lang.String getTorsionName()

getTorsionCode

public int getTorsionCode()

getTorsionResNum

public int getTorsionResNum()

getTorsionResName

public java.lang.String getTorsionResName()

assignName

protected void assignName()

Assigns a meaningful name to a torsion. This method assigns (if possible): - name (phi, psi, chi1 etc.) to the torsion object. - number corresponding to this name. - the number in the chain of the residue to which this torsion belong - the name of the residue to which this torsion belong The names to numbers conversion is: PHI - 0 PSI - 1 OMG - 2 (Omega - on the C(n)-N(n+1) bond - very close to 180 (trans) or 0 (cis)) CHI1 - 3 (CHI-1 torsion on the CA-CB bond) CHI2 - 4 CHI3 - 5 CHI4 - 6 CHI5 - 7 (Not used any more) ALPHA - 8 (torsion made by four consecutive Ca's) OOP - 9 (Out of plain torsion) proximal - (-1) - A torsion with no biological name that could also be between two successive residues. These torsions are mainly relevent ro the plane energies. The residue names and the residue numbers of the proximal torsions are left undefined, and only the torsion code and torsion anme are updated.

name

public java.lang.String name()

atoms

public AtomList atoms()