Package ffx.potential.bonded

Class Angle

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.Angle

All Implemented Interfaces:

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

public class Angle
extends BondedTerm

The Angle class represents an angle 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
AngleType	angleType	Force field parameters to compute the angle bending energy.
int	nh	Number of hydrogen on the central atom that are not part of this Angle.

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
Angle(Bond b1, Bond b2)	Angle constructor

Method Summary

Modifier and Type	Method	Description
int	compareTo(BondedTerm a)
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	get1_3(Atom a)	If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned.
AngleType.AngleMode	getAngleMode()	Getter for the field angleMode.
AngleType	getAngleType()	Get the AngleType for this angle.
Atom	getAtom4()	Getter for the field atom4.
Atom	getCentralAtom()	getCentralAtom.
Atom	getFourthAtomOfTrigonalCenter()	If the central atom of the angle is trigonal, the 4th member of the trigonal center (that is not a part of the angle) will be returned.
void	log()	Log details for this Angle energy term.
static void	logNoAngleType(Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no AngleType exists.
void	setAngleType(AngleType a)	Set a reference to the force field parameters for this Angle.
void	setConstraint(Constraint c)	Sets the Constraint on this bond (clearing it if null).
void	setRigidScale(double rigidScale)	Setter for the field rigidScale.
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, 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

angleType

public AngleType angleType

Force field parameters to compute the angle bending energy.

nh

public int nh

Number of hydrogen on the central atom that are not part of this Angle.

Constructor Details

Angle

public Angle(Bond b1,
 Bond b2)

Angle constructor

Parameters:

b1 - Bond that forms one leg of the angle

b2 - Bond that forms the other leg of the angle

Method Details

logNoAngleType

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

Log that no AngleType exists.

Parameters:

a1 - Atom 1.

a2 - Atom 2.

a3 - Atom 3.

compareTo

public int compareTo(BondedTerm a)

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 Angle energy.

Parameters:

gradient - If true, compute the gradient.

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

a double.

get1_3

public Atom get1_3(Atom a)

If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned. These atoms are said to be 1-3 to each other.

Parameters:

a - Atom

Returns:

Atom

getAngleMode

public AngleType.AngleMode getAngleMode()

Getter for the field angleMode.

Returns:

a AngleType.AngleMode object.

getAngleType

public AngleType getAngleType()

Get the AngleType for this angle.

Returns:

This angle's AngleType.

setAngleType

public void setAngleType(AngleType a)

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

Parameters:

a - a AngleType object.

getAtom4

public Atom getAtom4()

Getter for the field atom4.

Returns:

a Atom object.

getCentralAtom

public Atom getCentralAtom()

getCentralAtom.

Returns:

a Atom object.

log

public void log()

Log details for this Angle energy term.

setConstraint

public void setConstraint(Constraint c)

Description copied from class: BondedTerm

Sets the Constraint on this bond (clearing it if null). May recursively set the Constraint on component terms (i.e. an Angle will call setConstraint on its component Bonds).

Overrides:

setConstraint in class BondedTerm

Parameters:

c - Constraint or null to clear.

setRigidScale

public void setRigidScale(double rigidScale)

Setter for the field rigidScale.

Parameters:

rigidScale - a double.

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

getFourthAtomOfTrigonalCenter

public Atom getFourthAtomOfTrigonalCenter()

If the central atom of the angle is trigonal, the 4th member of the trigonal center (that is not a part of the angle) will be returned.

Returns:

The 4th atom of a trigonal center.