Package ffx.potential.bonded

Class OutOfPlaneBend

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.OutOfPlaneBend

All Implemented Interfaces:

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

public class OutOfPlaneBend
extends BondedTerm

The OutOfPlaneBend class represents an Out-Of-Plane Bend.

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
OutOfPlaneBendType	outOfPlaneBendType	Force field parameters to compute the Out-of-Plane 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
OutOfPlaneBend(Angle angle, Atom atom)	OutOfPlaneBend constructor.

Method Summary

Modifier and Type	Method	Description
int	compareTo(BondedTerm o)
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	getFirstAngleAtom()	Get the first atom of the Angle.
Atom	getFourthAtom()	The atom of this out-of-plane bend that was not part of the Angle.
Atom	getLastAngleAtom()	Get the first atom of the Angle.
Atom	getTrigonalAtom()	Get the trigonal atom of this out-of-plane bend (central atom of the Angle).
void	log()	Log details for this Out-of-Plane Bend energy term.
static OutOfPlaneBend	outOfPlaneBendFactory(Angle angle, ForceField forceField)	Attempt to create a new OutOfPlaneBend instance for a given Angle and Force Field.
void	setOutOfPlaneBendType(OutOfPlaneBendType a)	Set a reference to the force field parameters for this Angle.
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

outOfPlaneBendType

public OutOfPlaneBendType outOfPlaneBendType

Force field parameters to compute the Out-of-Plane Bend energy.

Constructor Details

OutOfPlaneBend

public OutOfPlaneBend(Angle angle,
 Atom atom)

OutOfPlaneBend constructor.

Parameters:

angle - Angle that contains 3 of 4 OutOfPlaneBend atoms.

atom - The 4th atom of the trigonal center.

Method Details

getFourthAtom

public Atom getFourthAtom()

The atom of this out-of-plane bend that was not part of the Angle.

Returns:

Fourth atom.

getTrigonalAtom

public Atom getTrigonalAtom()

Get the trigonal atom of this out-of-plane bend (central atom of the Angle).

Returns:

Fourth atom.

getFirstAngleAtom

public Atom getFirstAngleAtom()

Get the first atom of the Angle.

Returns:

Fourth atom.

getLastAngleAtom

public Atom getLastAngleAtom()

Get the first atom of the Angle.

Returns:

Fourth atom.

outOfPlaneBendFactory

public static OutOfPlaneBend outOfPlaneBendFactory(Angle angle,
 ForceField forceField)

Attempt to create a new OutOfPlaneBend instance for a given Angle and Force Field.

Parameters:

angle - the Angle to create an OutOfPlaneBend around.

forceField - the ForceField parameters to use.

Returns:

a new OutOfPlaneBend if the central atom of the angle is trigonal and a force field type exists.

compareTo

public int compareTo(BondedTerm o)

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 this Out-of-Plane Bend 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 details for this Out-of-Plane Bend energy term.

setOutOfPlaneBendType

public void setOutOfPlaneBendType(OutOfPlaneBendType a)

Set a reference to the force field parameters for this Angle.

Parameters:

a - a OutOfPlaneBendType 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