Package ffx.potential.parameters

Class AngleTorsionType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.AngleTorsionType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="angtors",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[4 integers and 6 reals]\nProvides the values for a single bond angle bending-torsional angle parameter.\nThe integer modifiers give the atom class numbers for the four kinds of atoms involved in the torsion and its contained angles.\nThe real number modifiers give the force constant values for both angles coupled with 1-, 2- and 3-fold torsional terms.\nThe default units for the force constants are kcal/mole/radian, but this can be controlled via the angtorunit keyword.\n")
public final class AngleTorsionType
extends BaseType
implements Comparator<String>

The AngleTorsionType class defines one angle-torsion energy type.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
double	angtorunit	Convert angle-torsion to kcal/mole.
final int[]	atomClasses	Atom classes for this stretch-torsion type.
static final double	DEFAULT_ANGTOR_UNIT
final double[]	forceConstants	Force constants.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
AngleTorsionType(int[] atomClasses, double[] forceConstants)	AngleTorsionType Constructor.

Method Summary

Modifier and Type	Method	Description
static AngleTorsionType	average(AngleTorsionType angleTorsionType1, AngleTorsionType angleTorsionType2, int[] atomClasses)	Average two AngleTorsionType instances.
int	compare(String s1, String s2)
boolean	equals(Object o)
static Element	getXMLForce(Document doc, ForceField forceField)	Create an AmoebaAngleTorsionForce Element.
int	hashCode()
void	incrementClasses(int increment)	incrementClasses
static AngleTorsionType	parse(String input, String[] tokens)	Construct an AngleTorsionType from an input string.
AngleTorsionType	patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
static String	sortKey(int[] c)	This method sorts the atom classes for the angle-torsion.
String	toString()
Element	toXML(Document doc)	Write AngleTorsionType 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_ANGTOR_UNIT

public static final double DEFAULT_ANGTOR_UNIT

See Also:

• Constant Field Values

angtorunit

@FFXProperty(name="angtorunit",
             propertyGroup=EnergyUnitConversion,
             defaultValue="Pi/180",
             description="Sets the scale factor needed to convert the energy value computed by the angle bending-torsional angle\ncross term into units of kcal/mole. The correct value is force field dependent and typically provided in the\nheader of the master force field parameter file.\n")
public double angtorunit

Convert angle-torsion to kcal/mole.

atomClasses

public final int[] atomClasses

Atom classes for this stretch-torsion type.

forceConstants

public final double[] forceConstants

Force constants.

Constructor Details

AngleTorsionType

public AngleTorsionType(int[] atomClasses,
 double[] forceConstants)

AngleTorsionType Constructor.

Parameters:

atomClasses - Atomic classes.

forceConstants - Force constants.

Method Details

average

public static AngleTorsionType average(@Nullable
 AngleTorsionType angleTorsionType1,
 @Nullable
 AngleTorsionType angleTorsionType2,
 @Nullable
 int[] atomClasses)

Average two AngleTorsionType instances.

Parameters:

angleTorsionType1 - First AngleTorsionType.

angleTorsionType2 - Second AngleTorsionType.

atomClasses - Atom classes for the averaged type.

Returns:

A new AngleTorsionType with averaged force constants, or null if inputs are invalid.

parse

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

Construct an AngleTorsionType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

an AngleTorsionType instance.

sortKey

public static String sortKey(int[] c)

This method sorts the atom classes for the angle-torsion.

Parameters:

c - atomClasses

Returns:

lookup key

Since:

1.0

compare

public int compare(String s1,
 String s2)

Specified by:

compare in interface Comparator<String>

Since:

1.0

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 value to increment the atom classes by.

patchClasses

public AngleTorsionType 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 AngleTorsionType object.

toString

public String toString()

Basic toString method.

Nicely formatted Angle-Torsion string.

Overrides:

toString in class BaseType

getXMLForce

public static Element getXMLForce(Document doc,
 ForceField forceField)

Create an AmoebaAngleTorsionForce Element.

Parameters:

doc - the Document instance.

forceField - the ForceField instance to grab constants from.

Returns:

the AmoebaAngleTorsionForce Element.

toXML

public Element toXML(Document doc)

Write AngleTorsionType to OpenMM XML format.

Parameters:

doc - the Document instance.

Returns:

the Torsion element.