Package ffx.potential.bonded

Class Torsion

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.Torsion

All Implemented Interfaces:

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

public class Torsion
extends BondedTerm
implements LambdaInterface

The Torsion class represents a torsional angle formed 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
TorsionType	torsionType	The force field 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
Torsion(Bond b1, Bond b2, Bond b3)	Create a Torsion from 3 connected bonds (no error checking)

Method Summary

Modifier and Type	Method	Description
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	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.
double	getTorsionScale()	Get the torsion scale up factor.
void	log()	Log details for this Torsional Angle energy term.
static void	logNoTorsionType(Atom a0, Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no TorsionType exists.
double	measure()	Compute the torsional angle in degrees.
void	setLambda(double lambda)	Set the current value of the state variable.
void	setTorsionScale(double torsionScale)	Set the torsion scale up factor.
void	setTorsionType(TorsionType torsionType)	Set the torsion type.
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

torsionType

public TorsionType torsionType

The force field Torsion type in use.

Constructor Details

Torsion

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

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

Parameters:

b1 - The first Bond.

b2 - The middle Bond.

b3 - The last Bond.

Method Details

logNoTorsionType

public static void logNoTorsionType(Atom a0,
 Atom a1,
 Atom a2,
 Atom a3,
 ForceField forceField)

Log that no TorsionType exists.

Parameters:

a0 - Atom 0.

a1 - Atom 1.

a2 - Atom 2.

a3 - Atom 3.

setTorsionType

public void setTorsionType(TorsionType torsionType)

Set the torsion type.

Parameters:

torsionType - The TorsionType.

setTorsionScale

public void setTorsionScale(double torsionScale)

Set the torsion scale up factor.

Parameters:

torsionScale - The torsion scale up factor.

getTorsionScale

public double getTorsionScale()

Get the torsion scale up factor.

Returns:

The torsion scale up factor.

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.

measure

public double measure()

Compute the torsional angle in degrees.

Returns:

The torsion in degrees.

energy

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

energy.

Evaluate the Torsional Angle 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

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 Torsional Angle 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