Package ffx.potential.bonded

Class BondedTerm

java.lang.Object

javax.swing.tree.DefaultMutableTreeNode

ffx.potential.bonded.MSNode

ffx.potential.bonded.BondedTerm

All Implemented Interfaces:

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

Direct Known Subclasses:

Angle, AngleTorsion, Bond, ImproperTorsion, OutOfPlaneBend, PiOrbitalTorsion, RestrainDistance, RestrainPosition, RestraintTorsion, StretchBend, StretchTorsion, Torsion, TorsionTorsion, UreyBradley

public abstract class BondedTerm
extends MSNode
implements BondedEnergy, Comparable<BondedTerm>

The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BondedTerm.BondedComparator

Field Summary

Fields

Modifier and Type	Field	Description
protected Atom[]	atoms	Atoms that are used to form this term.
protected Bond[]	bonds	Bonds that are used to form this term.
protected double	energy	Energy of the term (kcal/mol).
protected String	id	ID of this BondedTerm.
protected double	value	Value of the term (e.g.

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
BondedTerm()	Default Constructor
BondedTerm(String i)	Constructor which sets the Term's id.

Method Summary

Modifier and Type	Method	Description
boolean	applyLambda()	Check if any atom of this BondedTerm has the Lambda flag set.
int	compareTo(BondedTerm t)
boolean	containsHydrogen()	containsHydrogen
boolean	containsResolution(Atom.Resolution resolution)	Checks if at least one atom in this BondedTerm is of the given resolution.
boolean	destroy()	destroy
final boolean	equals(Object object)
Atom	getAtom(int index)	Get the constituent Atom specified by index.
Atom[]	getAtomArray()	Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Atom[]	getAtomArray(boolean returnCopy)	Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Atom[]	getAtoms()	Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Bond	getBond(int index)	Get the constituent Bond specified by index.
String	getID()	Get the Term's id.
boolean	getUse()	This method returns true if any atom is being used.
double	getValue()	Get the Term's value.
int	hashCode()
boolean	isConstrained()	Check if this BondedTerm is constrained.
boolean	isLambdaScaled()	Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).
boolean	isNeuralNetwork()	This method returns true if any atom is marked as being part of a neural network.
void	print()	Prints the MSNode's name
static <T extends BondedTerm> void	removeNeuralNetworkTerms(List<T> list)	This method removes terms from a list that are marked as being part of a neural network.
void	setAtoms(Atom[] a)	Add a constituent Atom to the Term.
void	setBonds(Bond[] b)	Add constituent Bonds to the Term.
void	setColor(RendererCache.ColorModel newColorModel, org.jogamp.vecmath.Color3f color, org.jogamp.java3d.Material mat)	setColor
void	setConstraint(Constraint c)	Sets the Constraint on this bond (clearing it if null).
void	setID(String i)	Sets the Term's id.
final void	setID_Key(boolean reverse)	setID_Key
void	setSelected(boolean b)	Setter for the field selected.
void	setValue(double v)	Sets the Term's value.
void	setView(RendererCache.ViewModel newViewModel, List<org.jogamp.java3d.BranchGroup> newShapes)	setView
String	toString()

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, energy, update

Field Details

id

protected String id

ID of this BondedTerm.

atoms

protected Atom[] atoms

Atoms that are used to form this term.

bonds

protected Bond[] bonds

Bonds that are used to form this term.

value

protected double value

Value of the term (e.g. bond length, angle, dihedral angle, etc).

energy

protected double energy

Energy of the term (kcal/mol).

Constructor Details

BondedTerm

public BondedTerm()

Default Constructor

BondedTerm

public BondedTerm(String i)

Constructor which sets the Term's id.

Parameters:

i - a String object.

Method Details

applyLambda

public boolean applyLambda()

Check if any atom of this BondedTerm has the Lambda flag set.

Returns:

True if Lambda is applied to one of the BondedTerm atoms.

compareTo

public int compareTo(BondedTerm t)

Specified by:

compareTo in interface Comparable<BondedTerm>

containsHydrogen

public boolean containsHydrogen()

containsHydrogen

Returns:

a boolean.

isNeuralNetwork

public boolean isNeuralNetwork()

This method returns true if any atom is marked as being part of a neural network.

Returns:

True if any atom is marked as being part of a neural network.

removeNeuralNetworkTerms

public static <T extends BondedTerm> void removeNeuralNetworkTerms(List<T> list)

This method removes terms from a list that are marked as being part of a neural network.

Type Parameters:

T - The Bonded term class.

Parameters:

list - The list to check.

containsResolution

public boolean containsResolution(Atom.Resolution resolution)

Checks if at least one atom in this BondedTerm is of the given resolution.

Parameters:

resolution - a Atom.Resolution object.

Returns:

true if at least one atom in this term is of the specified resolution.

destroy

public boolean destroy()

destroy

Overrides:

destroy in class MSNode

Returns:

a boolean.

equals

public final boolean equals(Object object)

MSNode equality := same class and same name. Consider replacing with a Comparator<MSNode> for cases where non-reference equality is desired.

Overridden method that returns true if object is equals to this, is of the same Class and has the same id.

Overrides:

equals in class MSNode

getAtom

public Atom getAtom(int index)

Get the constituent Atom specified by index.

Parameters:

index - The index of the Atom to return.

Returns:

a Atom object.

getAtoms

public Atom[] getAtoms()

Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.

Returns:

Atoms in this BondedTerm

getAtomArray

public Atom[] getAtomArray()

Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure. Returns a new array, not a reference to the original array.

Returns:

Atoms in this BondedTerm

getAtomArray

public Atom[] getAtomArray(boolean returnCopy)

Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.

Parameters:

returnCopy - If true, return a new copy of the Atom array.

Returns:

Atoms in this BondedTerm

getBond

public Bond getBond(int index)

Get the constituent Bond specified by index.

Parameters:

index - The index of the Bond to return.

Returns:

a Bond object.

getID

public String getID()

Get the Term's id.

Returns:

a String object.

getUse

public boolean getUse()

This method returns true if any atom is being used.

Returns:

True if any atom is being used.

setID

public void setID(String i)

Sets the Term's id.

Parameters:

i - a String object.

getValue

public double getValue()

Get the Term's value.

Returns:

a double.

setValue

public void setValue(double v)

Sets the Term's value.

Parameters:

v - a double.

hashCode

public int hashCode()

Overrides:

hashCode in class MSNode

isConstrained

public boolean isConstrained()

Check if this BondedTerm is constrained.

Returns:

If constrained.

isLambdaScaled

public boolean isLambdaScaled()

Check if this BondedTerm is lambda-sensitive (e.g., a softcore dihedral).

Returns:

True if Lambda affects the energy of this term.

print

public void print()

Prints the MSNode's name

Prints the toString method to stdout

Overrides:

print in class MSNode

setAtoms

public void setAtoms(Atom[] a)

Add a constituent Atom to the Term.

Parameters:

a - an array of Atom objects.

setBonds

public void setBonds(Bond[] b)

Add constituent Bonds to the Term.

Parameters:

b - an array of Bond objects.

setColor

public void setColor(RendererCache.ColorModel newColorModel,
 org.jogamp.vecmath.Color3f color,
 org.jogamp.java3d.Material mat)

setColor

Specified by:

setColor in interface ROLS

Overrides:

setColor in class MSNode

Parameters:

newColorModel - a RendererCache.ColorModel object.

color - a Color3f object.

mat - a Material object.

setConstraint

public void setConstraint(Constraint c)

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).

Parameters:

c - Constraint or null to clear.

setID_Key

public final void setID_Key(boolean reverse)

setID_Key

Parameters:

reverse - a boolean.

setSelected

public void setSelected(boolean b)

Setter for the field selected.

Overrides:

setSelected in class MSNode

Parameters:

b - a boolean.

setView

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

setView

Specified by:

setView in interface ROLS

Overrides:

setView in class MSNode

Parameters:

newViewModel - a RendererCache.ViewModel object.

newShapes - a List object.

toString

public String toString()

Overridden toString method returns the MSNode's name

Overridden toString Method returns the Term's id.

Overrides:

toString in class MSNode