Package ffx.potential.bonded

Class TorsionTorsion

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.TorsionTorsion

All Implemented Interfaces:

BondedEnergy, LambdaInterface, ROLS, Serializable, Cloneable, Comparable<BondedTerm>, MutableTreeNode, TreeNode

public class TorsionTorsion
extends BondedTerm
implements LambdaInterface

The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ffx.potential.bonded.BondedTerm

BondedTerm.BondedComparator

Field Summary

Fields

Modifier and Type	Field	Description
final Torsion[]	torsions	The two torsions that are coupled.
TorsionTorsionType	torsionTorsionType	The force field Torsion-Torsion type in use.

Fields inherited from class ffx.potential.bonded.BondedTerm

atoms, bonds, energy, id, value

Fields inherited from class ffx.potential.bonded.MSNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ffx.potential.bonded.ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
TorsionTorsion(Bond firstBond, Angle angle, Bond lastBond, boolean reversed)	Torsion-Torsion constructor.

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	getChiralAtom()	getChiralAtom.
double	getd2EdL2()	Get the 2nd partial derivative of the energy with respect to lambda.
double	getdEdL()	Get the partial derivative of the energy with respect to lambda.
void	getdEdXdL(double[] gradient)	Get the gradient of dEdL with respect to each parameter.
double	getLambda()	Get the current value of the state variable.
void	log()	Log details for this Torsion-Torsion energy term.
void	setLambda(double lambda)	Set the current value of the state variable.
static TorsionTorsion	torsionTorsionFactory(Bond firstBond, Angle angle, Bond lastBond, ForceField forceField)	torsionTorsionFactory.
String	toString()

Methods inherited from class ffx.potential.bonded.BondedTerm

applyLambda, compareTo, containsHydrogen, containsResolution, destroy, equals, getAtom, getAtomArray, getAtomArray, getAtoms, getBond, getID, getUse, getValue, hashCode, isConstrained, isLambdaScaled, isNeuralNetwork, print, removeNeuralNetworkTerms, setAtoms, setBonds, setColor, setConstraint, setID, setID_Key, setSelected, setValue, setView

Methods inherited from class ffx.potential.bonded.MSNode

contains, drawLabel, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getExtent, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, isSelected, removeChild, setName, update

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface ffx.potential.bonded.BondedEnergy

energy, energy, update

Methods inherited from interface ffx.potential.bonded.LambdaInterface

dEdLZeroAtEnds

Field Details

torsions

public final Torsion[] torsions

The two torsions that are coupled.

torsionTorsionType

public TorsionTorsionType torsionTorsionType

The force field Torsion-Torsion type in use.

Constructor Details

TorsionTorsion

public TorsionTorsion(Bond firstBond,
 Angle angle,
 Bond lastBond,
 boolean reversed)

Torsion-Torsion constructor.

Parameters:

firstBond - a Bond object.

angle - a Angle object.

lastBond - a Bond object.

reversed - a boolean.

Method Details

torsionTorsionFactory

public static TorsionTorsion torsionTorsionFactory(Bond firstBond,
 Angle angle,
 Bond lastBond,
 ForceField forceField)

torsionTorsionFactory.

Parameters:

firstBond - the first Bond.

angle - the Angle.

lastBond - the last Bond.

forceField - the ForceField parameters to apply.

Returns:

the new TorsionTorsion, or null.

energy

public double energy(boolean gradient,
 int threadID,
 AtomicDoubleArray3D grad,
 AtomicDoubleArray3D lambdaGrad)

energy.

Evaluate the Torsion-Torsion energy.

Specified by:

energy in interface BondedEnergy

Parameters:

gradient - If true, compute the gradient.

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

a double.

getChiralAtom

public Atom getChiralAtom()

getChiralAtom.

Returns:

a Atom object.

getLambda

public double getLambda()

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

setLambda

public void setLambda(double lambda)

Set the current value of the state variable. May be ignored if lambda is not being applied.

Specified by:

setLambda in interface LambdaInterface

Parameters:

lambda - a double.

getd2EdL2

public double getd2EdL2()

Get the 2nd partial derivative of the energy with respect to lambda.

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Get the partial derivative of the energy with respect to lambda.

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

getdEdXdL

public void getdEdXdL(double[] gradient)

Get the gradient of dEdL with respect to each parameter.

Specified by:

getdEdXdL in interface LambdaInterface

Parameters:

gradient - - A double array of length the number of parameters in the model (commonly 3 * number of atoms).

log

public void log()

Log details for this Torsion-Torsion energy term.

toString

public String toString()

Overridden toString method returns the MSNode's name

Overridden toString Method returns the Term's id.

Overridden toString Method returns the Term's id.

Overrides:

toString in class BondedTerm