Package ffx.potential.terms

Class RestrainTorsionPotentialEnergy

java.lang.Object

ffx.potential.terms.EnergyTerm

ffx.potential.terms.RestrainTorsionPotentialEnergy

public class RestrainTorsionPotentialEnergy
extends EnergyTerm

Restrain-Torsion potential energy term using Torsion instances. Method names are specific to restrain torsions for clarity.

Field Summary

Fields inherited from class ffx.potential.terms.EnergyTerm

energy, forceGroup, name

Constructor Summary

Constructors

Constructor	Description
RestrainTorsionPotentialEnergy(String name)	Create a RestrainTorsionPotentialEnergy with the provided name.
RestrainTorsionPotentialEnergy(String name, int forceGroup)	Create a RestrainTorsionPotentialEnergy with the provided name and force group.
RestrainTorsionPotentialEnergy(String name, int forceGroup, List<Torsion> restrainTorsions)	Create a RestrainTorsionPotentialEnergy initialized with a list of torsions and force group.
RestrainTorsionPotentialEnergy(String name, Collection<Torsion> restrainTorsions)	Create a RestrainTorsionPotentialEnergy initialized with a collection of torsions.

Method Summary

Modifier and Type	Method	Description
boolean	addRestrainTorsion(Torsion torsion)	Add a single restrain torsion.
boolean	addRestrainTorsions(Torsion[] torsions)	Add an array of restrain torsions.
boolean	addRestrainTorsions(List<Torsion> torsions)	Add a list of restrain torsions.
BondedTerm[]	getBondedTermsArray()	Get an array of BondedTerms in this term.
int	getNumberOfRestrainTorsions()	Get the number of restrain torsions.
int	getNumberOfTerms()	Get the number of BondedTerms in this term.
Torsion	getRestrainTorsion(int index)	Get a restrain torsion at an index.
Torsion[]	getRestrainTorsionArray()	Get an array of restrain torsions.
List<Torsion>	getRestrainTorsions()	Get an unmodifiable view of restrain torsions.
void	log()	Log the details of Restrain Torsion interactions.
boolean	removeRestrainTorsion(Torsion torsion)	Remove a restrain torsion.
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

RestrainTorsionPotentialEnergy

public RestrainTorsionPotentialEnergy(String name)

Create a RestrainTorsionPotentialEnergy with the provided name.

Parameters:

name - Name for this term.

RestrainTorsionPotentialEnergy

public RestrainTorsionPotentialEnergy(String name,
 int forceGroup)

Create a RestrainTorsionPotentialEnergy with the provided name and force group.

Parameters:

name - Name for this term.

forceGroup - Integer force group identifier.

RestrainTorsionPotentialEnergy

public RestrainTorsionPotentialEnergy(String name,
 int forceGroup,
 List<Torsion> restrainTorsions)

Create a RestrainTorsionPotentialEnergy initialized with a list of torsions and force group.

Parameters:

name - Name for this term.

forceGroup - Force group identifier.

restrainTorsions - List of Torsion instances to add (null-safe).

RestrainTorsionPotentialEnergy

public RestrainTorsionPotentialEnergy(String name,
 Collection<Torsion> restrainTorsions)

Create a RestrainTorsionPotentialEnergy initialized with a collection of torsions.

Parameters:

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

restrainTorsions - Collection of Torsion instances to add (null-safe).

Method Details

getNumberOfTerms

public int getNumberOfTerms()

Get the number of BondedTerms in this term.

Specified by:

getNumberOfTerms in class EnergyTerm

Returns:

The number of BondedTerms.

getBondedTermsArray

public BondedTerm[] getBondedTermsArray()

Get an array of BondedTerms in this term.

Specified by:

getBondedTermsArray in class EnergyTerm

Returns:

Array of BondedTerms.

addRestrainTorsion

public boolean addRestrainTorsion(Torsion torsion)

Add a single restrain torsion.

Parameters:

torsion - Torsion to add (ignored if null).

Returns:

true if added.

addRestrainTorsions

public boolean addRestrainTorsions(Torsion[] torsions)

Add an array of restrain torsions.

Parameters:

torsions - Array of Torsion instances to add.

Returns:

true if added.

addRestrainTorsions

public boolean addRestrainTorsions(List<Torsion> torsions)

Add a list of restrain torsions.

Parameters:

torsions - List of Torsion instances to add.

Returns:

true if added.

removeRestrainTorsion

public boolean removeRestrainTorsion(Torsion torsion)

Remove a restrain torsion.

Parameters:

torsion - Torsion to remove (ignored if null).

Returns:

true if removed.

getRestrainTorsion

public Torsion getRestrainTorsion(int index)

Get a restrain torsion at an index.

Parameters:

index - Index.

Returns:

Torsion.

Throws:

IndexOutOfBoundsException - if invalid index.

getRestrainTorsions

public List<Torsion> getRestrainTorsions()

Get an unmodifiable view of restrain torsions.

Returns:

List of Torsion.

getRestrainTorsionArray

public Torsion[] getRestrainTorsionArray()

Get an array of restrain torsions.

Returns:

Array of Torsion.

getNumberOfRestrainTorsions

public int getNumberOfRestrainTorsions()

Get the number of restrain torsions.

Returns:

Number of restrain torsions.

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.

log

public void log()

Log the details of Restrain Torsion interactions.

Specified by:

log in class EnergyTerm