Package ffx.potential.bonded

Class AngleTorsion

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.AngleTorsion

All Implemented Interfaces:

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

public class AngleTorsion
extends BondedTerm
implements LambdaInterface

The AngleTorsion class represents an angle torsion coupling between four 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
AngleType	angleType1	First angle force field type.
AngleType	angleType2	Second angle force field type.

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
AngleTorsion(Angle an1, Angle an2)	AngleTorsion constructor.
AngleTorsion(Bond b1, Bond b2, Bond b3)	Create a AngleTorsion from 3 connected bonds (no error checking)
AngleTorsion(String n)	AngleTorsion Constructor.

Method Summary

Modifier and Type	Method	Description
static String	angleTorsionForm()	Returns the mathematical form of an angle-torsion as an OpenMM-parsable String.
boolean	compare(Atom a0, Atom a1, Atom a2, Atom a3)	compare
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
double[]	getConstants()	Returns the array of stretch-torsion constants, in units of kcal/mol/degree.
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.
void	log()	Log details for this Angle-Torsion energy term.
void	setLambda(double lambda)	Set the current value of the state variable.
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

angleType1

public AngleType angleType1

First angle force field type.

angleType2

public AngleType angleType2

Second angle force field type.

Constructor Details

AngleTorsion

public AngleTorsion(Angle an1,
 Angle an2)

AngleTorsion constructor.

Parameters:

an1 - Angle that combines to form the Torsional Angle

an2 - Angle that combines to form the Torsional Angle

AngleTorsion

public AngleTorsion(Bond b1,
 Bond b2,
 Bond b3)

Create a AngleTorsion from 3 connected bonds (no error checking)

Parameters:

b1 - Bond

b2 - Bond

b3 - Bond

AngleTorsion

public AngleTorsion(String n)

AngleTorsion Constructor.

Parameters:

n - Torsion id

Method Details

angleTorsionForm

public static String angleTorsionForm()

Returns the mathematical form of an angle-torsion as an OpenMM-parsable String.

Returns:

Mathematical form of the angle-torsion coupling.

compare

public boolean compare(Atom a0,
 Atom a1,
 Atom a2,
 Atom a3)

compare

Parameters:

a0 - a Atom object.

a1 - a Atom object.

a2 - a Atom object.

a3 - a Atom object.

Returns:

a boolean.

energy

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

energy.

Evaluate the Angle-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.

get1_4

public Atom get1_4(Atom a)

If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned. These atoms are said to be 1-4 to each other.

Parameters:

a - Atom

Returns:

Atom

getConstants

public double[] getConstants()

Returns the array of stretch-torsion constants, in units of kcal/mol/degree.

Returns:

Stretch-torsion constants.

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 Angle-Torsion energy term.

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