Package ffx.potential.bonded

Class StretchBend

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.StretchBend

All Implemented Interfaces:

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

public class StretchBend
extends BondedTerm
implements Comparable<BondedTerm>

The StretchBend class represents a Stretch-Bend formed between three linearly 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
protected final Angle	angle	Angle this Stretch-Bend is based on.
double	angleEq	Equilibrium angle.
double	bond0Eq	First equilibrium bond distance.
double	bond1Eq	Second equilibrium bond distance.
double	force0	Force constant.
double	force1	Force constant.

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
StretchBend(Angle a)	Constructor for the Stretch-Bend class.

Method Summary

Modifier and Type	Method	Description
int	compareTo(BondedTerm sb)
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
void	log()	log
void	setRigidScale(double rigidScale)	Setter for the field rigidScale.
void	setStretchBendType(StretchBendType stretchBendType)	Setter for the field stretchBendType.
String	toString()

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

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

angleEq

public double angleEq

Equilibrium angle.

bond0Eq

public double bond0Eq

First equilibrium bond distance.

bond1Eq

public double bond1Eq

Second equilibrium bond distance.

angle

protected final Angle angle

Angle this Stretch-Bend is based on.

force0

public double force0

Force constant.

force1

public double force1

Force constant.

Constructor Details

StretchBend

public StretchBend(Angle a)

Constructor for the Stretch-Bend class.

Parameters:

a - The Angle that this stretch-bend is based on.

Method Details

compareTo

public int compareTo(BondedTerm sb)

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 Stretch-Bend 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.

log

public void log()

log

setRigidScale

public void setRigidScale(double rigidScale)

Setter for the field rigidScale.

Parameters:

rigidScale - a double.

setStretchBendType

public void setStretchBendType(StretchBendType stretchBendType)

Setter for the field stretchBendType.

Parameters:

stretchBendType - a StretchBendType object.

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