Package ffx.potential.parameters

Class VDWPairType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.VDWPairType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="vdwpr",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[2 integers and 2 reals]\nProvides the values for the vdw parameters for a single special heteroatomic pair of atoms.\nThe integer modifiers give the pair of atom class numbers for which special vdw parameters are to be defined.\nThe two real number modifiers give the values of the minimum energy contact distance in Angstroms and the well depth at the minimum distance in kcal/mole.\n")
public final class VDWPairType
extends BaseType
implements Comparator<String>

The VDWPairType class defines a van der Waals Pair type.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final int[]	atomClasses	Atom classes that form this bond stretch.
final double	radius	The radius of the minimum well depth energy (angstroms).
final double	wellDepth	The minimum energy of the vdw function (kcal/mol).

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
VDWPairType(int[] atomClasses, double radius, double wellDepth)	van der Waals constructor.

Method Summary

Modifier and Type	Method	Description
static VDWPairType	average(VDWPairType vdwType1, VDWPairType vdwType2, int[] atomClasses)	Average.
int	compare(String key1, String key2)
boolean	equals(Object o)
int	hashCode()
void	incrementClasses(int increment)	Increment the atom classes by a specified amount.
static VDWPairType	parse(String input, String[] tokens)	Construct a VDWPairType from multiple input lines.
static String	sortKey(int[] c)	This method sorts the atom classes as: min, max
String	toString()
Element	toXML(Document doc)	Write VDWPairType 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

radius

public final double radius

The radius of the minimum well depth energy (angstroms).

wellDepth

public final double wellDepth

The minimum energy of the vdw function (kcal/mol).

atomClasses

public final int[] atomClasses

Atom classes that form this bond stretch.

Constructor Details

VDWPairType

public VDWPairType(int[] atomClasses,
 double radius,
 double wellDepth)

van der Waals constructor. If the reduction factor is .LE. 0.0, no reduction is used for this atom type.

Parameters:

atomClasses - The atom class that uses this van der Waals Pair.

radius - The radius of the minimum well depth energy (angstroms).

wellDepth - The minimum energy of the vdw function (kcal/mol).

Method Details

average

public static VDWPairType average(VDWPairType vdwType1,
 VDWPairType vdwType2,
 int[] atomClasses)

Average.

Parameters:

vdwType1 - a VDWPairType object.

vdwType2 - a VDWPairType object.

atomClasses - The atom classes that uses this van der Waals Pair.

Returns:

a VDWPairType object.

parse

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

Construct a VDWPairType from multiple input lines.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a VDWType instance.

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

toString

public String toString()

Basic toString method.

Nicely formatted van der Waals type.

Overrides:

toString in class BaseType

toXML

public Element toXML(Document doc)

Write VDWPairType to OpenMM XML format.

sortKey

public static String sortKey(int[] c)

This method sorts the atom classes as: min, max

Parameters:

c - atomClasses

Returns:

lookup key

incrementClasses

public void incrementClasses(int increment)

Increment the atom classes by a specified amount.

Parameters:

increment - The increment to add to the atom classes.