Package ffx.potential.bonded

Class PiOrbitalTorsion

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.PiOrbitalTorsion

All Implemented Interfaces:

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

public class PiOrbitalTorsion
extends BondedTerm
implements LambdaInterface

The Pi-Orbital Torsion 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
PiOrbitalTorsionType	piOrbitalTorsionType	A reference to the Pi-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
PiOrbitalTorsion(Bond middleBond)	Pi-Orbital Torsion constructor.

Method Summary

Modifier and Type	Method	Description
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
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.
Bond	getMiddleBond()	Get the middle bond that the Pi-Orbital Torsion is formed around.
void	log()	Log details for this Pi-Orbital Torsion energy term.
static PiOrbitalTorsion	piOrbitalTorsionFactory(Bond bond, ForceField forceField)	Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.
void	setLambda(double lambda)	Set the current value of the state variable.
void	setPiOrbitalTorsionType(PiOrbitalTorsionType piOrbitalTorsionType)	Set the PiOrbitalTorsionType.
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

piOrbitalTorsionType

public PiOrbitalTorsionType piOrbitalTorsionType

A reference to the Pi-Torsion type in use.

Constructor Details

PiOrbitalTorsion

public PiOrbitalTorsion(Bond middleBond)

Pi-Orbital Torsion constructor.

Parameters:

middleBond - a Bond object.

Method Details

getMiddleBond

public Bond getMiddleBond()

Get the middle bond that the Pi-Orbital Torsion is formed around.

Returns:

The middle bond.

setPiOrbitalTorsionType

public void setPiOrbitalTorsionType(PiOrbitalTorsionType piOrbitalTorsionType)

Set the PiOrbitalTorsionType.

Parameters:

piOrbitalTorsionType - The PiOrbitalTorsionType.

piOrbitalTorsionFactory

public static PiOrbitalTorsion piOrbitalTorsionFactory(Bond bond,
 ForceField forceField)

Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.

Parameters:

bond - the Bond to create a PiOrbitalTorsion around.

forceField - the ForceField parameters to use.

Returns:

a new PiOrbitalTorsion, or null.

energy

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

energy.

Evaluate the Pi-Orbital 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.

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 Pi-Orbital Torsion energy term.

toString

public String toString()

Overridden toString method returns the MSNode's name

Overridden toString Method returns the Term's id.

Over-ridden toString Method returns the Term's id.

Overrides:

toString in class BondedTerm