Package ffx.potential.parameters

Class SoluteType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.SoluteType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="solute",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[integers and 4 reals]\nProvides values for a single implicit solvation parameter.\nThe integer modifier gives the atom type number for which solvation atom size parameters are to be defined.\nThe first three real number modifiers give the values of the atomic diameter in Angstroms,\nfor use in Poisson-Boltzmann (APBS), ddCOSMO and Generalized Kirkwood (GK) calculations, respectively.\nThe final real number is the Sneck scaling factor for implicit solvent interstitial space corrections.\n")
public final class SoluteType
extends BaseType
implements Comparator<String>

The SoluteType class defines one implicit solvent radius.

Since:

1.0

Author:

Michael J. Schnieders

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SoluteType.SOLUTE_RADII_TYPE

Field Summary

Fields

Modifier and Type	Field	Description
double	cosDiameter	Solute atomic diameter for ddCOSMO.
double	DEFAULT_SNECK
String	description	Optional SMARTS description.
double	gkDiameter	Solute atomic diameter for GK.
double	pbDiameter	Solute atomic diameter for PB.
double	sneck	Sneck scaling factor to use with interstitial space corrections

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
SoluteType(int atomType, double diameter)	Constructor for SoluteType.
SoluteType(int atomType, double pbDiameter, double cosDiameter, double gkDiameter)	Constructor for SoluteType.
SoluteType(int atomType, double pbDiameter, double cosDiameter, double gkDiameter, double sneck)	Constructor for SoluteType.
SoluteType(int atomType, String description, double pbDiameter, double cosDiameter, double gkDiameter)	Constructor for SoluteType.

Method Summary

Modifier and Type	Method	Description
int	compare(String key1, String key2)
boolean	equals(Object o)
static SoluteType	getCensusSoluteType(int atomicNumber)
static SoluteType	getFitSoluteType(ForceField forceField, int type)
static SoluteType	getSoluteType(Atom atom, ForceField forceField, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)
static SoluteType	getVDWSoluteType(VDWType vdwType)
int	hashCode()
static SoluteType	parse(String input, String[] tokens)	Construct a SoluteType from an input string.
static void	setSoluteRadii(ForceField forceField, Atom[] atoms, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)
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

pbDiameter

public double pbDiameter

Solute atomic diameter for PB.

cosDiameter

public double cosDiameter

Solute atomic diameter for ddCOSMO.

gkDiameter

public double gkDiameter

Solute atomic diameter for GK.

sneck

public double sneck

Sneck scaling factor to use with interstitial space corrections

DEFAULT_SNECK

public double DEFAULT_SNECK

description

public String description

Optional SMARTS description.

Constructor Details

SoluteType

public SoluteType(int atomType,
 double diameter)

Constructor for SoluteType.

Parameters:

atomType - Atom type.

diameter - Diameter for all continuum electrostatics models.

SoluteType

public SoluteType(int atomType,
 double pbDiameter,
 double cosDiameter,
 double gkDiameter)

Constructor for SoluteType.

Parameters:

atomType - Atom type.

pbDiameter - Diameter for PB continuum electrostatics.

cosDiameter - Diameter for ddCOSMO continuum electrostatics.

gkDiameter - Diameter for GK continuum electrostatics.

SoluteType

public SoluteType(int atomType,
 double pbDiameter,
 double cosDiameter,
 double gkDiameter,
 double sneck)

Constructor for SoluteType.

Parameters:

atomType - Atom type.

pbDiameter - Diameter for PB continuum electrostatics.

cosDiameter - Diameter for ddCOSMO continuum electrostatics.

gkDiameter - Diameter for GK continuum electrostatics.

sneck - Sneck scaling factor for implicit solvent interstitial space corrections

SoluteType

public SoluteType(int atomType,
 String description,
 double pbDiameter,
 double cosDiameter,
 double gkDiameter)

Constructor for SoluteType.

Parameters:

atomType - Atom type.

description - Smarts description.

pbDiameter - Diameter for PB continuum electrostatics.

cosDiameter - Diameter for ddCOSMO continuum electrostatics.

gkDiameter - Diameter for GK continuum electrostatics.

Method Details

parse

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

Construct a SoluteType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a SoluteType 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 bond stretch string.

Overrides:

toString in class BaseType

getCensusSoluteType

public static SoluteType getCensusSoluteType(int atomicNumber)

getVDWSoluteType

public static SoluteType getVDWSoluteType(VDWType vdwType)

getFitSoluteType

public static SoluteType getFitSoluteType(ForceField forceField,
 int type)

getSoluteType

public static SoluteType getSoluteType(Atom atom,
 ForceField forceField,
 SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)

setSoluteRadii

public static void setSoluteRadii(ForceField forceField,
 Atom[] atoms,
 SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)