Package ffx.potential.parameters

Class TorsionTorsionType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.TorsionTorsionType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="tortors",
             clazz=java.lang.String[][].class,
             propertyGroup=PotentialFunctionParameter,
             description="[7 integers, then multiple lines of 2 integers and 1 real]\nProvides the values for a single torsion-torsion parameter.\nThe first five integer modifiers give the atom class numbers for the atoms involved in the two adjacent torsional angles to be defined.\nThe last two integer modifiers contain the number of data grid points that lie along each axis of the torsion-torsion map.\nFor example, this value will be 13 for a 30 degree torsional angle spacing, i.e., 360/30 = 12, but 13\nvalues are required since data values for -180 and +180 degrees must both be supplied.\nThe subsequent lines contain the torsion-torsion map data as the integer values in degrees of each\ntorsional angle and the target energy value in kcal/mole.\n")
public final class TorsionTorsionType
extends BaseType
implements Comparator<String>

The TorsionTorsionType class defines a Torsion-Torsion spline.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final int[]	atomClasses	Atom classes that form this Torsion-Torsion type.
static final double	DEFAULT_TORTOR_UNIT	Default units to convert Torsion-Torsion energy to kcal/mole.
final double[]	dx	First derivative along x.
final double[]	dxy	Second derivatives.
final double[]	dy	First derivative along y.
final double[]	energy	Energy values.
final int	nx	Number of points along x.
final int	ny	Number of point along y.
double	torTorUnit	Convert Torsion-Torsion energy to kcal/mole.
final double[]	tx	Torsion values along x.
final double[]	ty	Torsion values along y.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
TorsionTorsionType(int[] atomClasses, int[] gridPoints, double[] torsion1, double[] torsion2, double[] energy)	Constructor for TorsionTorsionType.

Method Summary

Modifier and Type	Method	Description
static TorsionTorsionType	average(TorsionTorsionType torsionTorsionType1, TorsionTorsionType torsionTorsionType2, int[] atomClasses)	average.
int	compare(String key1, String key2)
boolean	equals(Object o)
static Element	getXMLForce(Document doc, ForceField forceField)	Create an AmoebaTorsionTorsionForce Element.
int	hashCode()
void	incrementClasses(int increment)	Increment the atom classes by a value.
static TorsionTorsionType	parse(String input, String[] tokens)	Construct a TorsionTorsionType from a single input line.
static TorsionTorsionType	parse(String input, String[] tokens, BufferedReader br)	Construct a TorsionTorsionType from multiple input lines.
void	patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
static String	reverseKey(int[] c)	Reversed key for the Torsion-Torsion lookup.
static String	sortKey(int[] c)	No sorting is done for the Torsion-Torsion lookup.
String	toString()
void	toXML(Document doc, Element torTorNode, int label)	Write TorsionTorsionType 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_TORTOR_UNIT

public static final double DEFAULT_TORTOR_UNIT

Default units to convert Torsion-Torsion energy to kcal/mole.

See Also:

• Constant Field Values

torTorUnit

@FFXProperty(name="tortorunit",
             propertyGroup=EnergyUnitConversion,
             defaultValue="1.0",
             description="Sets the scale factor needed to convert the energy value computed by the torsion-torsion 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 torTorUnit

Convert Torsion-Torsion energy to kcal/mole.

atomClasses

public final int[] atomClasses

Atom classes that form this Torsion-Torsion type.

energy

public final double[] energy

Energy values.

nx

public final int nx

Number of points along x.

ny

public final int ny

Number of point along y.

tx

public final double[] tx

Torsion values along x.

ty

public final double[] ty

Torsion values along y.

dx

public final double[] dx

First derivative along x.

dy

public final double[] dy

First derivative along y.

dxy

public final double[] dxy

Second derivatives.

Constructor Details

TorsionTorsionType

public TorsionTorsionType(int[] atomClasses,
 int[] gridPoints,
 double[] torsion1,
 double[] torsion2,
 double[] energy)

Constructor for TorsionTorsionType.

Parameters:

atomClasses - an array of int.

gridPoints - an array of int.

torsion1 - an array of double.

torsion2 - an array of double.

energy - an array of double.

Method Details

average

public static TorsionTorsionType average(TorsionTorsionType torsionTorsionType1,
 TorsionTorsionType torsionTorsionType2,
 int[] atomClasses)

average.

Parameters:

torsionTorsionType1 - a TorsionTorsionType object.

torsionTorsionType2 - a TorsionTorsionType object.

atomClasses - an array of

invalid reference

int

objects.

Returns:

a TorsionTorsionType object.

parse

public static TorsionTorsionType parse(String input,
 String[] tokens,
 BufferedReader br)

Construct a TorsionTorsionType from multiple input lines.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

br - a BufferedReader instance.

Returns:

a TorsionTorsionType instance.

parse

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

Construct a TorsionTorsionType from a single input line.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a TorsionTorsionType instance.

reverseKey

public static String reverseKey(int[] c)

Reversed key for the Torsion-Torsion lookup.

Parameters:

c - atomClasses

Returns:

lookup key

sortKey

public static String sortKey(int[] c)

No sorting is done for the Torsion-Torsion lookup.

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 value.

Parameters:

increment - The increment to add to the atom classes.

patchClasses

public void 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.

toString

public String toString()

Basic toString method.

Nicely formatted torsion-torsion type.

Overrides:

toString in class BaseType

getXMLForce

public static Element getXMLForce(Document doc,
 ForceField forceField)

Create an AmoebaTorsionTorsionForce Element.

Parameters:

doc - the Document instance.

forceField - the ForceField instance to grab constants from.

Returns:

the AmoebaTorsionTorsionForce Element.

toXML

public void toXML(Document doc,
 Element torTorNode,
 int label)

Write TorsionTorsionType to OpenMM XML format.

Parameters:

doc - the Document instance.

torTorNode - the Element to attach TorsionTorsion and TorsionTorsionGrid to.

label - the label used to match TorsionTorsion and TorsionTorsionGrid.