Package org.jmol.adapter.smarter

Class Atom

java.lang.Object

javajs.util.T3

javajs.util.P3

org.jmol.adapter.smarter.Atom

All Implemented Interfaces:

Serializable, Cloneable, javajs.api.JSONEncodable

public class Atom
extends javajs.util.P3
implements Cloneable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
char	altLoc
float[]	anisoBorU
String	atomName
int	atomSerial
int	atomSetIndex
int	atomSite
float	bfactor
javajs.util.BS	bsSymmetry
int	chainID
private static int[]	elementCharMasks
short	elementNumber
String	elementSymbol
float	foccupancy
int	formalCharge
String	group3
boolean	ignoreSymmetry
int	index
char	insertionCode
boolean	isHetero
float	partialCharge
float	radius
int	sequenceNumber
javajs.util.Lst<Object>	tensors
javajs.util.V3	vib

Fields inherited from class javajs.util.T3

x, y, z

Constructor Summary

Constructors

Constructor	Description
Atom()

Method Summary

Modifier and Type	Method	Description
Tensor	addTensor(Tensor tensor, String type, boolean reset)
Atom	getClone()
String	getElementSymbol()
static boolean	isValidSym1(char ch)
static boolean	isValidSym2(char ch1, char ch2)
private static boolean	isValidSymChar1(char ch)
static boolean	isValidSymNoCase(char ch1, char ch2)

Methods inherited from class javajs.util.P3

getUnlikely, new3, newP

Methods inherited from class javajs.util.T3

add, add2, add3, ave, cross, distance, distanceSquared, dot, equals, floatToIntBits, hashCode, length, lengthSquared, normalize, scale, scaleAdd2, scaleT, set, setA, setT, sub, sub2, toJSON, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

atomSetIndex

public int atomSetIndex

index

public int index

bsSymmetry

public javajs.util.BS bsSymmetry

atomSite

public int atomSite

elementSymbol

public String elementSymbol

elementNumber

public short elementNumber

atomName

public String atomName

formalCharge

public int formalCharge

partialCharge

public float partialCharge

vib

public javajs.util.V3 vib

bfactor

public float bfactor

foccupancy

public float foccupancy

radius

public float radius

isHetero

public boolean isHetero

atomSerial

public int atomSerial

chainID

public int chainID

altLoc

public char altLoc

group3

public String group3

sequenceNumber

public int sequenceNumber

insertionCode

public char insertionCode

anisoBorU

public float[] anisoBorU

tensors

public javajs.util.Lst<Object> tensors

ignoreSymmetry

public boolean ignoreSymmetry

elementCharMasks

private static final int[] elementCharMasks

Constructor Detail

Atom

public Atom()

Method Detail

addTensor

public Tensor addTensor(Tensor tensor,
                        String type,
                        boolean reset)

getClone

public Atom getClone()
              throws CloneNotSupportedException

Throws:

CloneNotSupportedException

getElementSymbol

public String getElementSymbol()

isValidSym1

public static boolean isValidSym1(char ch)

Parameters:

ch -

Returns:

true if matches a one-character symbol X

isValidSym2

public static boolean isValidSym2(char ch1,
                                  char ch2)

Parameters:

ch1 -

ch2 -

Returns:

true if matches a valid symbol Xy

isValidSymNoCase

public static boolean isValidSymNoCase(char ch1,
                                       char ch2)

Parameters:

ch1 -

ch2 -

Returns:

true if matches a two-character symbol, XX or Xx

isValidSymChar1

private static boolean isValidSymChar1(char ch)

Parameters:

ch -

Returns:

true if matches FIRST character of some symbol Xx