Package ffx.potential.parameters

Class VDWType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.VDWType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="vdw",clazz=java.lang.String.class,propertyGroup=PotentialFunctionParameter,description="[1 integer and 3 reals]\nProvides values for a single van der Waals parameter. The integer modifier, if positive,\ngives the atom class number for which vdw parameters are to be defined. Note that vdw parameters are given for atom classes, not atom types.\nThe three real number modifiers give the values of the atom size in Angstroms, homoatomic well depth in kcal/mole,\nand an optional reduction factor for univalent atoms.\n") @FFXProperty(name="vdw14",clazz=java.lang.String.class,propertyGroup=PotentialFunctionParameter,description="[1 integer and 2 reals]\nProvides values for a single van der Waals parameter for use in 1-4 nonbonded interactions.\nThe integer modifier, if positive, gives the atom class number for which vdw parameters are to be defined.\nNote that vdw parameters are given for atom classes, not atom types.\nThe two real number modifiers give the values of the atom size in Angstroms and the homoatomic well depth in kcal/mole.\nReduction factors, if used, are carried over from the vdw keyword for the same atom class.\n")
public final class VDWType
extends BaseType
implements Comparator<String>

The VDWType class defines van der Waals type for a normal interaction or a special 1-4 interaction.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	VDWType.VDWMode	Torsion modes include Normal or In-Plane

Field Summary

Fields

Modifier and Type	Field	Description
int	atomClass	The atom class that uses this van der Waals parameter.
final double	radius	The radius of the minimum well depth energy (angstroms).
final double	reductionFactor	Reduction factor for evaluating van der Waals pairs.
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
VDWType(int atomClass, double radius, double wellDepth, double reductionFactor)	van der Waals constructor.
VDWType(int atomClass, double radius, double wellDepth, double reductionFactor, VDWType.VDWMode vdwMode)	van der Waals constructor.

Method Summary

Modifier and Type	Method	Description
static VDWType	average(VDWType vdwType1, VDWType vdwType2, int atomClass)	Average two VDWType objects.
int	compare(String s1, String s2)
boolean	equals(Object o)
int	hashCode()
static VDWType	parse(String input, String[] tokens)	Construct a VDWType from multiple input lines.
static VDWType	parseVDW14(String input, String[] tokens)	Construct a 1-4 VDWType from multiple input lines.
String	toString()

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).

reductionFactor

public final double reductionFactor

Reduction factor for evaluating van der Waals pairs. Valid range: 0.0 .GT. reduction .LE. 1.0 Usually only hydrogen atoms have a reduction factor. Setting the reduction to .LT. 0.0 indicates it is not being used.

atomClass

public int atomClass

The atom class that uses this van der Waals parameter.

Constructor Details

VDWType

public VDWType(int atomClass,
 double radius,
 double wellDepth,
 double reductionFactor)

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

Parameters:

atomClass - The atom class that uses this van der Waals parameter.

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

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

reductionFactor - Reduction factor for evaluating van der Waals pairs.

VDWType

public VDWType(int atomClass,
 double radius,
 double wellDepth,
 double reductionFactor,
 VDWType.VDWMode vdwMode)

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

Parameters:

atomClass - The atom class that uses this van der Waals parameter.

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

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

reductionFactor - Reduction factor for evaluating van der Waals pairs.

vdwMode - The VDWMode to use.

Method Details

average

public static VDWType average(VDWType vdwType1,
 VDWType vdwType2,
 int atomClass)

Average two VDWType objects.

Parameters:

vdwType1 - The first VDWType.

vdwType2 - The second VDWType.

atomClass - The new atom class.

Returns:

The new averaged VDWType.

parse

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

Construct a VDWType from multiple input lines.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a VDWType instance.

parseVDW14

public static VDWType parseVDW14(String input,
 String[] tokens)

Construct a 1-4 VDWType from multiple input lines.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a VDWType instance.

compare

public int compare(String s1,
 String s2)

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