Package ffx.potential.bonded

Class UreyBradley

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.UreyBradley

All Implemented Interfaces:

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

public class UreyBradley
extends BondedTerm

The UreyBradley class.

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
protected final Angle	angle	The Angle this UreyBradley term is based on.
final UreyBradleyType	ureyBradleyType	Force field parameters to compute the Stretch-Bend energy.

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
UreyBradley(Angle a, UreyBradleyType ureyBradleyType)	Constructor for the UreyBradley class.

Method Summary

Modifier and Type	Method	Description
int	compareTo(BondedTerm ub)
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
void	log()	log
void	setRigidScale(double rigidScale)	Setter for the field rigidScale.
static UreyBradley	ureyBradlyFactory(Angle angle, ForceField forceField)	Attempt to create a new UreyBradley for the specified Angle.

Methods inherited from class ffx.potential.bonded.BondedTerm

applyLambda, 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, toString

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

Field Details

ureyBradleyType

public final UreyBradleyType ureyBradleyType

Force field parameters to compute the Stretch-Bend energy.

angle

protected final Angle angle

The Angle this UreyBradley term is based on.

Constructor Details

UreyBradley

public UreyBradley(Angle a,
 UreyBradleyType ureyBradleyType)

Constructor for the UreyBradley class.

Parameters:

a - a Angle object.

ureyBradleyType - The Urey-Bradley type to apply.

Method Details

ureyBradlyFactory

public static UreyBradley ureyBradlyFactory(Angle angle,
 ForceField forceField)

Attempt to create a new UreyBradley for the specified Angle.

Parameters:

angle - the Angle to create the UreyBradley from.

forceField - the ForceField parameters to apply.

Returns:

a new UreyBradley, or null.

compareTo

public int compareTo(BondedTerm ub)

Specified by:

compareTo in interface Comparable<BondedTerm>

Overrides:

compareTo in class BondedTerm

energy

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

energy.

Evaluate the Urey-Bradley energy.

Parameters:

gradient - If true, compute the gradient.

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

a double.

log

public void log()

log

setRigidScale

public void setRigidScale(double rigidScale)

Setter for the field rigidScale.

Parameters:

rigidScale - a double.