Package ffx.potential.parameters

Class StretchBendType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.StretchBendType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="strbnd",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[3 integers and 2 reals]\nProvides the values for a single stretch-bend cross term potential parameter.\nThe integer modifiers give the atom class numbers for the three kinds of atoms involved in the angle which is to be defined.\nThe real number modifiers give the force constant values for the first bond (first two atom classes) with the angle, and the second bond with the angle, respectively.\nThe default units for the stretch-bend force constant are kcal/mole/Ang-radian, but this can be controlled via the strbndunit keyword.\n")
public final class StretchBendType
extends BaseType
implements Comparator<String>

The StretchBendType class defines one out-of-plane angle bending energy type.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final int[]	atomClasses	Atom class for this stretch-bend type.
static final double	DEFAULT_STRBND_UNIT	Constant units=PI / 180.0
final double[]	forceConstants	Force constants (Kcal/mole/Angstrom-Degrees).
double	strbndunit

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static StretchBendType	average(StretchBendType stretchBendType1, StretchBendType stretchBendType2, int[] atomClasses)	average.
int	compare(String key1, String key2)
boolean	equals(Object o)
static Element	getXMLForce(Document doc, ForceField forceField)	Create an AmoebaStretchBendForce element.
int	hashCode()
void	incrementClasses(int increment)	Increment the atom classes by a given value.
static StretchBendType	parse(String input, String[] tokens)	Construct a StretchBendType from an input string.
StretchBendType	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, c[1], max
String	toString()
Element	toXML(Document doc)	Write StretchBendType 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_STRBND_UNIT

public static final double DEFAULT_STRBND_UNIT

Constant units=PI / 180.0

See Also:

• Constant Field Values

strbndunit

@FFXProperty(name="strbndunit",
             propertyGroup=EnergyUnitConversion,
             defaultValue="(Pi/180)",
             description="Sets the scale factor needed to convert the energy value computed by the bond stretching-angle bending cross\nterm potential into units of kcal/mole. The correct value is force field dependent and typically provided\nin the header of the master force field parameter file.\n")
public double strbndunit

atomClasses

public final int[] atomClasses

Atom class for this stretch-bend type.

forceConstants

public final double[] forceConstants

Force constants (Kcal/mole/Angstrom-Degrees).

Constructor Details

StretchBendType

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

StretchBendType Constructor.

Parameters:

atomClasses - int[]

forceConstants - double[]

Method Details

average

public static StretchBendType average(StretchBendType stretchBendType1,
 StretchBendType stretchBendType2,
 int[] atomClasses)

average.

Parameters:

stretchBendType1 - a StretchBendType object.

stretchBendType2 - a StretchBendType object.

atomClasses - an array of

invalid reference

int

objects.

Returns:

a StretchBendType object.

parse

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

Construct a StretchBendType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a StretchBendType instance.

sortKey

public static String sortKey(int[] c)

This method sorts the atom classes as: min, c[1], max

Parameters:

c - atomClasses

Returns:

lookup key

compare

public int compare(String key1,
 String key2)

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)

Increment the atom classes by a given value.

Parameters:

increment - The increment to apply to the atom classes.

patchClasses

public StretchBendType 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 StretchBendType object.

toString

public String toString()

Basic toString method.

Nicely formatted Stretch-Bend string.

Overrides:

toString in class BaseType

getXMLForce

public static Element getXMLForce(Document doc,
 ForceField forceField)

Create an AmoebaStretchBendForce element.

Parameters:

doc - the Document instance.

forceField - the ForceField to grab constants from.

Returns:

the AmoebaStretchBendForce element.

toXML

public Element toXML(Document doc)

Write StretchBendType to OpenMM XML format.