Class Bond

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

ffx.potential.bonded.Bond

All Implemented Interfaces:

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

public class Bond
extends BondedTerm

The Bond class represents a covalent bond formed between two atoms.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class BondedTerm

BondedTerm.BondedComparator

Field Summary

Fields

Modifier and Type	Field	Description
BondType	bondType	The force field BondType for this bond.

Fields inherited from class BondedTerm

atoms, bonds, energy, id, value

Fields inherited from class MSNode

selected

Fields inherited from class DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Fields inherited from interface ROLS

MaxLengthScale

Constructor Summary

Constructors

Constructor	Description
Bond(Atom a1, Atom a2)	Bond constructor.
Bond(String n)	Simple Bond constructor that is intended to be used with the equals method.

Method Summary

Modifier and Type	Method	Description
int	compareTo(BondedTerm b)
double	energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad)	energy.
Atom	get1_2(Atom a)	Find the other Atom in this Bond.
BondType	getBondType()	Return the BondType for this Bond.
double	getCurrentDistance()	Gets the current distance between the two Atoms in this Bond.
void	log()	Log details for this Bond energy term.
static void	logNoBondType(Atom a1, Atom a2, ForceField forceField)	Log that no BondType exists.
void	removeFromParent()
void	setBondType(BondType bondType)	Set a reference to the force field parameters.
void	setColor(Atom a)	Set the color of this Bond's Java3D shapes based on the passed Atom.
void	setRigidScale(double rigidScale)	Setter for the field rigidScale.
void	setView(RendererCache.ViewModel newViewModel, List<org.jogamp.java3d.BranchGroup> newShapes)	setView
void	setWire(org.jogamp.java3d.LineArray l, int i)	setWire
void	update()	update

Methods inherited from class 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, toString

Methods inherited from class MSNode

contains, drawLabel, getAngleList, getAngleTorsionList, getAtomList, getAtomList, getBondList, getCenter, getChildList, getExtent, getFirstActiveHeavyAtom, getImproperTorsionList, getList, getList, getMSCount, getMSNode, getMW, getName, getOutOfPlaneBendList, getPiOrbitalTorsionList, getStretchBendList, getStretchTorsionList, getTorsionList, getTorsionTorsionList, getTotalMass, getUreyBradleyList, isSelected, removeChild, setName

Methods inherited from class 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, setAllowsChildren, setParent, setUserObject

Methods inherited from class Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface BondedEnergy

energy, energy

Field Details

bondType

public BondType bondType

The force field BondType for this bond.

Constructor Details

Bond

public Bond(String n)

Simple Bond constructor that is intended to be used with the equals method.

Parameters:

n - Bond id

Bond

public Bond(Atom a1,
 Atom a2)

Bond constructor.

Parameters:

a1 - Atom number 1.

a2 - Atom number 2.

Method Details

logNoBondType

public static void logNoBondType(Atom a1,
 Atom a2,
 ForceField forceField)

Log that no BondType exists.

Parameters:

a1 - Atom 1.

a2 - Atom 2.

forceField - The force field in use.

compareTo

public int compareTo(BondedTerm b)

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 Bond energy.

Parameters:

gradient - If true, compute the gradient.

threadID - The thread ID.

grad - a AtomicDoubleArray3D object.

lambdaGrad - a AtomicDoubleArray3D object.

Returns:

a double.

get1_2

public Atom get1_2(Atom a)

Find the other Atom in this Bond. These two atoms are said to be 1-2.

Parameters:

a - The known Atom.

Returns:

The other Atom that makes up this Bond, or Null if Atom a is not part of this Bond.

getCurrentDistance

public double getCurrentDistance()

Gets the current distance between the two Atoms in this Bond.

Returns:

Current distance.

log

public void log()

Log details for this Bond energy term.

removeFromParent

public void removeFromParent()

Specified by:

removeFromParent in interface MutableTreeNode

Overrides:

removeFromParent in class DefaultMutableTreeNode

setBondType

public void setBondType(BondType bondType)

Set a reference to the force field parameters.

Parameters:

bondType - a BondType object.

getBondType

public BondType getBondType()

Return the BondType for this Bond.

Returns:

Returns the BondType.

setColor

public void setColor(Atom a)

Set the color of this Bond's Java3D shapes based on the passed Atom.

Parameters:

a - Atom

setRigidScale

public void setRigidScale(double rigidScale)

Setter for the field rigidScale.

Parameters:

rigidScale - a double.

setView

public void setView(RendererCache.ViewModel newViewModel,
 List<org.jogamp.java3d.BranchGroup> newShapes)

setView

Polymorphic setView method.

Specified by:

setView in interface ROLS

Overrides:

setView in class BondedTerm

Parameters:

newViewModel - a RendererCache.ViewModel object.

newShapes - a List object.

setWire

public void setWire(org.jogamp.java3d.LineArray l,
 int i)

setWire

Parameters:

l - a LineArray object.

i - The index of the LineArray to use.

update

public void update()

update

Update recomputes bonds length, Wireframe vertices, and Cylinder Transforms

Specified by:

update in interface BondedEnergy

Specified by:

update in interface ROLS

Overrides:

update in class MSNode