Package ffx.potential.terms

Class BondPotentialEnergy

java.lang.Object

ffx.potential.terms.EnergyTerm

ffx.potential.terms.BondPotentialEnergy

public class BondPotentialEnergy
extends EnergyTerm

Bond potential energy term using Bond instances.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields inherited from class ffx.potential.terms.EnergyTerm

energy, forceGroup, name

Constructor Summary

Constructors

Constructor	Description
BondPotentialEnergy(String name)	Create a BondPotentialEnergy with the provided name.
BondPotentialEnergy(String name, int forceGroup)	Create a BondPotentialEnergy with the provided name and force group.
BondPotentialEnergy(String name, int forceGroup, List<Bond> bonds)	Create a BondPotentialEnergy initialized with a list of bonds and force group.
BondPotentialEnergy(String name, Collection<Bond> bonds)	Create a BondPotentialEnergy initialized with a collection of bonds.

Method Summary

Modifier and Type	Method	Description
boolean	addBond(Bond bond)	Add a Bond to this term.
boolean	addBonds(Bond[] bonds)	Add an array of Bonds to this term.
boolean	addBonds(List<Bond> bonds)	Add a list of Bonds to this term.
Bond	getBond(int index)	Get the Bond at a given index.
Bond[]	getBondArray()	Get an array of Bonds in this term.
BondedTerm[]	getBondedTermsArray()	Get an array of BondedTerms in this term.
String	getBondEnergyString()
List<Bond>	getBonds()	Get an unmodifiable view of the Bonds in this term.
int	getNumberOfBonds()	Get the number of Bonds in this term.
int	getNumberOfTerms()	Get the number of terms in this potential energy term.
void	log()	Log the details of Bond interactions.
boolean	removeBond(Bond bond)	Remove a Bond from this term.
String	toPDBString()	Get a PDB-style REMARK representation of this energy term.
String	toString()	Get a string representation of this energy term.

Methods inherited from class ffx.potential.terms.EnergyTerm

addAndGetEnergy, addAndGetRMSD, getEnergy, getForceGroup, getName, getRMSD, getTime, setEnergy, setForceGroup, setName, setRMSD, startTime, stopTime

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

BondPotentialEnergy

public BondPotentialEnergy(String name)

Create a BondPotentialEnergy with the provided name.

Parameters:

name - Name for this term.

BondPotentialEnergy

public BondPotentialEnergy(String name,
 int forceGroup)

Create a BondPotentialEnergy with the provided name and force group.

Parameters:

name - Name for this term.

forceGroup - Integer force group identifier.

BondPotentialEnergy

public BondPotentialEnergy(String name,
 int forceGroup,
 List<Bond> bonds)

Create a BondPotentialEnergy initialized with a list of bonds and force group.

Parameters:

name - Name for this term.

forceGroup - Force group identifier.

bonds - List of Bond instances to add (null-safe).

BondPotentialEnergy

public BondPotentialEnergy(String name,
 Collection<Bond> bonds)

Create a BondPotentialEnergy initialized with a collection of bonds.

Parameters:

name - Name for this term (may be null).

bonds - Collection of Bond instances to add (null-safe).

Method Details

getNumberOfTerms

public int getNumberOfTerms()

Get the number of terms in this potential energy term.

Specified by:

getNumberOfTerms in class EnergyTerm

Returns:

The number of terms, which is the same as the number of bonds.

getBondedTermsArray

public BondedTerm[] getBondedTermsArray()

Get an array of BondedTerms in this term.

Specified by:

getBondedTermsArray in class EnergyTerm

Returns:

Array of BondedTerms, which are actually Bonds in this case.

addBond

public boolean addBond(Bond bond)

Add a Bond to this term.

Parameters:

bond - Bond to add (ignored if null).

Returns:

true if the bond was added.

addBonds

public boolean addBonds(Bond[] bonds)

Add an array of Bonds to this term.

Parameters:

bonds - Array of Bond instances to add.

Returns:

true if the bonds were added.

addBonds

public boolean addBonds(List<Bond> bonds)

Add a list of Bonds to this term.

Parameters:

bonds - List of Bond instances to add.

Returns:

true if the bonds were added.

removeBond

public boolean removeBond(Bond bond)

Remove a Bond from this term.

Parameters:

bond - Bond to remove (ignored if null).

Returns:

true if the bond was present and removed.

getBond

public Bond getBond(int index)

Get the Bond at a given index.

Parameters:

index - Index in the internal list.

Returns:

Bond at the specified index.

Throws:

IndexOutOfBoundsException - if index is invalid.

getBonds

public List<Bond> getBonds()

Get an unmodifiable view of the Bonds in this term.

Returns:

Unmodifiable List of Bonds.

getBondArray

public Bond[] getBondArray()

Get an array of Bonds in this term.

Returns:

Array of Bonds.

getNumberOfBonds

public int getNumberOfBonds()

Get the number of Bonds in this term.

Returns:

The number of Bonds.

getBondEnergyString

public String getBondEnergyString()

log

public void log()

Log the details of Bond interactions.

Specified by:

log in class EnergyTerm

toPDBString

public String toPDBString()

Description copied from class: EnergyTerm

Get a PDB-style REMARK representation of this energy term.

Specified by:

toPDBString in class EnergyTerm

Returns:

A PDB REMARK string for this energy term.

toString

public String toString()

Description copied from class: EnergyTerm

Get a string representation of this energy term.

Specified by:

toString in class EnergyTerm

Returns:

A string representation of the energy term.