Package ffx.potential.terms

Class AnglePotentialEnergy

java.lang.Object

ffx.potential.terms.EnergyTerm

ffx.potential.terms.AnglePotentialEnergy

public class AnglePotentialEnergy
extends EnergyTerm

Angle potential energy term using Angle 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
AnglePotentialEnergy(String name)	Create an AnglePotentialEnergy with the provided name.
AnglePotentialEnergy(String name, int forceGroup)	Create an AnglePotentialEnergy with the provided name and force group.
AnglePotentialEnergy(String name, int forceGroup, List<Angle> angles)	Create an AnglePotentialEnergy initialized with a list of angles and force group.
AnglePotentialEnergy(String name, Collection<Angle> angles)	Create an AnglePotentialEnergy initialized with a collection of angles.

Method Summary

Modifier and Type	Method	Description
boolean	addAngle(Angle angle)	Add an Angle to this term.
boolean	addAngles(Angle[] angles)	Add an array of Angles to this term.
boolean	addAngles(List<Angle> angles)	Add a list of Angles to this term.
Angle	getAngle(int index)	Get the Angle at a given index.
Angle[]	getAngleArray()	Get an array of Angles in this term.
String	getAngleEnergyString()	Get the String used for OpenMM angle energy expressions.
List<Angle>	getAngles()	Get an unmodifiable view of the Angles in this term.
BondedTerm[]	getBondedTermsArray()	Get an array of BondedTerms in this term.
String	getInPlaneAngleEnergyString()
int	getNumberOfAngles()	Get the number of Angles in this term.
int	getNumberOfTerms()	Get the number of terms in this potential energy term.
void	log()	Log the details of Angle interactions.
boolean	removeAngle(Angle angle)	Remove an Angle 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

AnglePotentialEnergy

public AnglePotentialEnergy(String name)

Create an AnglePotentialEnergy with the provided name.

Parameters:

name - Name for this term.

AnglePotentialEnergy

public AnglePotentialEnergy(String name,
 int forceGroup)

Create an AnglePotentialEnergy with the provided name and force group.

Parameters:

name - Name for this term.

forceGroup - Integer force group identifier.

AnglePotentialEnergy

public AnglePotentialEnergy(String name,
 int forceGroup,
 List<Angle> angles)

Create an AnglePotentialEnergy initialized with a list of angles and force group.

Parameters:

name - Name for this term.

forceGroup - Force group identifier.

angles - List of Angle instances to add (null-safe).

AnglePotentialEnergy

public AnglePotentialEnergy(String name,
 Collection<Angle> angles)

Create an AnglePotentialEnergy initialized with a collection of angles.

Parameters:

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

angles - Collection of Angle 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 angles.

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 Angles in this case.

addAngle

public boolean addAngle(Angle angle)

Add an Angle to this term.

Parameters:

angle - Angle to add (ignored if null).

Returns:

true if the angle was added.

addAngles

public boolean addAngles(Angle[] angles)

Add an array of Angles to this term.

Parameters:

angles - Array of Angle instances to add.

Returns:

true if the angles were added.

addAngles

public boolean addAngles(List<Angle> angles)

Add a list of Angles to this term.

Parameters:

angles - List of Angle instances to add.

Returns:

true if the angles were added.

removeAngle

public boolean removeAngle(Angle angle)

Remove an Angle from this term.

Parameters:

angle - Angle to remove (ignored if null).

Returns:

true if the angle was present and removed.

getAngle

public Angle getAngle(int index)

Get the Angle at a given index.

Parameters:

index - Index in the internal list.

Returns:

Angle at the specified index.

Throws:

IndexOutOfBoundsException - if index is invalid.

getAngles

public List<Angle> getAngles()

Get an unmodifiable view of the Angles in this term.

Returns:

Unmodifiable List of Angles.

getAngleArray

public Angle[] getAngleArray()

Get an array of Angles in this term.

Returns:

Array of Angles.

getNumberOfAngles

public int getNumberOfAngles()

Get the number of Angles in this term.

Returns:

The number of Angles.

getAngleEnergyString

public String getAngleEnergyString()

Get the String used for OpenMM angle energy expressions.

Returns:

String representing the angle energy expression.

getInPlaneAngleEnergyString

public String getInPlaneAngleEnergyString()

log

public void log()

Log the details of Angle 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.