Package ffx.potential.parameters

Class StretchTorsionType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.StretchTorsionType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="strtors",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[2 integers and 1 real]\nProvides the values for a single stretch-torsion cross term potential parameter.\nThe two integer modifiers give the atom class numbers for the atoms involved in the central bond of the torsional angles to be parameterized.\nThe real modifier gives the value of the stretch-torsion force constant for all torsional angles with the defined atom classes for the central bond.\nThe default units for the stretch-torsion force constant can be controlled via the strtorunit keyword.\n")
public final class StretchTorsionType
extends BaseType
implements Comparator<String>

The StretchTorsionType class defines one stretch-torsion energy type.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final int[]	atomClasses	Atom classes for this stretch-torsion type.
static final double	DEFAULT_STRTOR_UNIT
final double[]	forceConstants	Force constants.
double	strTorUnit	Unit conversion.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static StretchTorsionType	average(StretchTorsionType stretchTorsionType1, StretchTorsionType stretchTorsionType2, int[] atomClasses)	average.
int	compare(String s1, String s2)
boolean	equals(Object o)
static Element	getXMLForce(Document doc, ForceField forceField)	Create an AmoebaStretchTorsionForce Element.
int	hashCode()
void	incrementClasses(int increment)	Increment the atom classes by a specified amount.
static StretchTorsionType	parse(String input, String[] tokens)	Construct an StretchTorsionType from an input string.
StretchTorsionType	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 torsion.
String	toString()
Element	toXML(Document doc)	Write StretchTorsionType 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_STRTOR_UNIT

public static final double DEFAULT_STRTOR_UNIT

See Also:

• Constant Field Values

strTorUnit

@FFXProperty(name="strtorunit",
             propertyGroup=EnergyUnitConversion,
             defaultValue="1.0",
             description="Sets the scale factor needed to convert the energy value computed by the bond stretching-torsional\nangle cross term potential into units of kcal/mole. The correct value is force field dependent and typically\nprovided in the header of the master force field parameter file.\n")
public double strTorUnit

Unit conversion.

atomClasses

public final int[] atomClasses

Atom classes for this stretch-torsion type.

forceConstants

public final double[] forceConstants

Force constants.

Constructor Details

StretchTorsionType

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

StretchTorsionType Constructor.

Parameters:

atomClasses - Atom classes.

forceConstants - Force constant.

Method Details

average

public static StretchTorsionType average(StretchTorsionType stretchTorsionType1,
 StretchTorsionType stretchTorsionType2,
 int[] atomClasses)

average.

Parameters:

stretchTorsionType1 - a StretchTorsionType object.

stretchTorsionType2 - a StretchTorsionType object.

atomClasses - an array of

invalid reference

int

objects.

Returns:

a StretchTorsionType object.

parse

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

Construct an StretchTorsionType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

an StretchTorsionType instance.

sortKey

public static String sortKey(int[] c)

This method sorts the atom classes for the 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)

Increment the atom classes by a specified amount.

Parameters:

increment - The increment to add to the atom classes.

patchClasses

public StretchTorsionType 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 StretchTorsionType object.

toString

public String toString()

Basic toString method.

Nicely formatted Stretch-Torsion string.

Overrides:

toString in class BaseType

getXMLForce

public static Element getXMLForce(Document doc,
 ForceField forceField)

Create an AmoebaStretchTorsionForce Element.

Parameters:

doc - the Document instance.

forceField - the ForceField instance to grab constants from.

Returns:

the AmoebaStretchTorsionForce Element.

toXML

public Element toXML(Document doc)

Write StretchTorsionType to OpenMM XML format.

Parameters:

doc - the Document instance.

Returns:

the Torsion element.