Package ffx.potential.bonded

Class RestrainTorsion

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.RestrainTorsion

All Implemented Interfaces:

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

public class RestrainTorsion
extends BondedTerm
implements LambdaInterface

RestraintTorsion is a class that restrains the torsion angle defined by four atoms.

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 TorsionType	torsionType
final double	units

Fields inherited from class ffx.potential.bonded.BondedTerm

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
RestrainTorsion(Atom a1, Atom a2, Atom a3, Atom a4, TorsionType torsionType, boolean lambdaEnabled, boolean reverseLambda, double units)	Constructor for RestrainTorsion.

Method Summary

Modifier and Type	Method	Description
boolean	applyLambda()	Check if any atom of this BondedTerm has the Lambda flag set.
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	getAtom(int index)	Get the constituent Atom specified by index.
Atom[]	getAtoms()	Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
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.
double	mapLambda(double lambda)
void	setLambda(double lambda)	Set the current value of the state variable.
String	toString()

Methods inherited from class ffx.potential.bonded.BondedTerm

compareTo, containsHydrogen, containsResolution, destroy, equals, getAtomArray, getAtomArray, 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

torsionType

public final TorsionType torsionType

units

public final double units

Constructor Details

RestrainTorsion

public RestrainTorsion(Atom a1,
 Atom a2,
 Atom a3,
 Atom a4,
 TorsionType torsionType,
 boolean lambdaEnabled,
 boolean reverseLambda,
 double units)

Constructor for RestrainTorsion.

Parameters:

a1 - First torsional atom.

a2 - Second torsional atom.

a3 - Third torsional atom.

a4 - Fourth torsional atom.

torsionType - TorsionType.

lambdaEnabled - True if the lambda term is enabled.

reverseLambda - True if the lambda term should be reversed.

units - Units for the energy term.

Method Details

energy

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

Description copied from interface: BondedEnergy

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.

getLambda

public double getLambda()

Description copied from interface: LambdaInterface

Get the current value of the state variable.

Specified by:

getLambda in interface LambdaInterface

Returns:

state

getAtoms

public Atom[] getAtoms()

Description copied from class: BondedTerm

Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.

Overrides:

getAtoms in class BondedTerm

Returns:

Atoms in this BondedTerm

getAtom

public Atom getAtom(int index)

Description copied from class: BondedTerm

Get the constituent Atom specified by index.

Overrides:

getAtom in class BondedTerm

Parameters:

index - The index of the Atom to return.

Returns:

a Atom object.

applyLambda

public boolean applyLambda()

Description copied from class: BondedTerm

Check if any atom of this BondedTerm has the Lambda flag set.

Overrides:

applyLambda in class BondedTerm

Returns:

True if Lambda is applied to one of the BondedTerm atoms.

setLambda

public void setLambda(double lambda)

Description copied from interface: LambdaInterface

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()

Description copied from interface: LambdaInterface

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

Specified by:

getd2EdL2 in interface LambdaInterface

Returns:

d2EdL2

getdEdL

public double getdEdL()

Description copied from interface: LambdaInterface

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

Specified by:

getdEdL in interface LambdaInterface

Returns:

dEdL

mapLambda

public double mapLambda(double lambda)

getdEdXdL

public void getdEdXdL(double[] gradient)

Description copied from interface: LambdaInterface

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).

toString

public String toString()

Description copied from class: BondedTerm

Overridden toString method returns the MSNode's name

Overridden toString Method returns the Term's id.

Overrides:

toString in class BondedTerm