Package ffx.potential.parameters

Class PiOrbitalTorsionType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.PiOrbitalTorsionType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="pitors",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[2 integers and 1 real]\nProvides the values for a single pi-orbital torsional angle potential parameter.\nThe two integer modifiers give the atom class numbers for the atoms involved in the central bond of the torsional angle to be parameterized.\nThe real modifier gives the value of the 2-fold Fourier amplitude for the torsional angle between p-orbitals centered on the defined bond atom classes.\nThe default units for the stretch-torsion force constant can be controlled via the pitorsunit keyword.\n")
public final class PiOrbitalTorsionType
extends BaseType
implements Comparator<String>

The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final int[]	atomClasses	Atom classes that form this Pi-Torsion.
static final double	DEFAULT_PITORS_UNIT
double	forceConstant	Force constant.
double	piTorsUnit	Convert Pi-Torsion energy to kcal/mole.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
PiOrbitalTorsionType(int[] atomClasses, double forceConstant)	PiTorsionType Constructor.

Method Summary

Modifier and Type	Method	Description
static PiOrbitalTorsionType	average(PiOrbitalTorsionType piOrbitalTorsionType1, PiOrbitalTorsionType piOrbitalTorsionType2, int[] atomClasses)	Average two PiTorsionType instances.
int	compare(String s1, String s2)
boolean	equals(Object o)
static Element	getXMLElement(Document doc, ForceField forceField)	Create an AmoebaPiTorsionForce Element.
int	hashCode()
void	incrementClasses(int increment)	incrementClasses
static PiOrbitalTorsionType	parse(String input, String[] tokens)	Construct a PiTorsionType from an input string.
PiOrbitalTorsionType	patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
static String	sortKey(int[] c)	This method sorts the atom classes as: min, max
String	toString()
Element	toXML(Document doc)	Write PiOrbitalTorsionType to OpenMM XML format.

Methods inherited from class ffx.potential.parameters.BaseType

getKey, log, print, setKey, setKey

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Field Details

DEFAULT_PITORS_UNIT

public static final double DEFAULT_PITORS_UNIT

See Also:

• Constant Field Values

piTorsUnit

@FFXProperty(name="pitorsunit",
             propertyGroup=EnergyUnitConversion,
             defaultValue="1.0",
             description="Sets the scale factor needed to convert the energy value computed by the pi-orbital torsional angle potential into units of kcal/mole.\nThe correct value is force field dependent and typically provided in the header of the master force field parameter file.\n")
public double piTorsUnit

Convert Pi-Torsion energy to kcal/mole.

atomClasses

public final int[] atomClasses

Atom classes that form this Pi-Torsion.

forceConstant

public double forceConstant

Force constant.

Constructor Details

PiOrbitalTorsionType

public PiOrbitalTorsionType(int[] atomClasses,
 double forceConstant)

PiTorsionType Constructor.

Parameters:

atomClasses - int[]

forceConstant - double

Method Details

average

public static PiOrbitalTorsionType average(PiOrbitalTorsionType piOrbitalTorsionType1,
 PiOrbitalTorsionType piOrbitalTorsionType2,
 int[] atomClasses)

Average two PiTorsionType instances. The atom classes that define the new type must be supplied.

Parameters:

piOrbitalTorsionType1 - a PiOrbitalTorsionType object.

piOrbitalTorsionType2 - a PiOrbitalTorsionType object.

atomClasses - an array of

invalid reference

int

objects.

Returns:

a PiOrbitalTorsionType object.

parse

public static PiOrbitalTorsionType parse(String input,
 String[] tokens)

Construct a PiTorsionType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a PiTorsionType instance.

sortKey

public static String sortKey(int[] c)

This method sorts the atom classes as: min, max

Parameters:

c - atomClasses

Returns:

lookup key

compare

public int compare(String s1,
 String s2)

Specified by:

compare in interface Comparator<String>

equals

public boolean equals(Object o)

Specified by:

equals in interface Comparator<String>

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

incrementClasses

public void incrementClasses(int increment)

incrementClasses

Parameters:

increment - The increment to add to the atom classes.

patchClasses

public PiOrbitalTorsionType patchClasses(HashMap<AtomType,AtomType> typeMap)

Remap new atom classes to known internal ones.

Parameters:

typeMap - a lookup between new atom types and known atom types.

Returns:

a PiOrbitalTorsionType object.

toString

public String toString()

Basic toString method.

Nicely formatted Pi-Torsion type.

Overrides:

toString in class BaseType

getXMLElement

public static Element getXMLElement(Document doc,
 ForceField forceField)

Create an AmoebaPiTorsionForce Element.

Parameters:

doc - the Document instance.

forceField - the ForceField instance to grab constants from.

Returns:

the AmoebaPiTorsionForce Element.

toXML

public Element toXML(Document doc)

Write PiOrbitalTorsionType to OpenMM XML format.

Parameters:

doc - the Document instance.

Returns:

the PiTorsion Element.