Package ffx.potential.parameters

Class BioType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.BioType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="biotype",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[integer, name, quoted string and integer]\nProvides the values to define the correspondence between a single bio-polymer atom type and its force field atom type.\n")
public final class BioType
extends BaseType
implements Comparator<String>

The BioType class maps PDB identifiers to atom types.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final String	atomName	The PDB atom name for this BioType.
int	atomType	The force field atom type to be used for the molecule / atom name combination.
final String[]	bonds	Bonds are required to listed atom names.
int	index	The index of this BioType.
final String	moleculeName	The PDB molecule name for this BioType.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
BioType(int index, String atomName, String moleculeName, int atomType, String[] bonds)	BioType Constructor.

Method Summary

Modifier and Type	Method	Description
int	compare(String s1, String s2)
boolean	equals(Object o)
int	hashCode()
static BioType	parse(String input, String[] tokens)	Construct an BioType from an input string.
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

atomName

public final String atomName

The PDB atom name for this BioType.

moleculeName

public final String moleculeName

The PDB molecule name for this BioType.

bonds

public final String[] bonds

Bonds are required to listed atom names.

index

public int index

The index of this BioType.

atomType

public int atomType

The force field atom type to be used for the molecule / atom name combination.

Constructor Details

BioType

public BioType(int index,
 String atomName,
 String moleculeName,
 int atomType,
 String[] bonds)

BioType Constructor.

Parameters:

index - int

atomName - String

moleculeName - String

atomType - int

bonds - an array of String objects.

Method Details

parse

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

Construct an BioType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

an BioType 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 biotype.

Overrides:

toString in class BaseType