org.jmol.adapter.smarter

Class Atom

public class Atom extends Point3f implements Cloneable

Field Summary
charalternateLocationID
float[]anisoBorU
intatomIndex
StringatomName
intatomSerial
intatomSetIndex
intatomSite
floatbfactor
BitSetbsSymmetry
charchainID
static int[]elementCharMasks
Bits which indicate whether or not an element symbol is valid.
shortelementNumber
StringelementSymbol
Object[]ellipsoid
intformalCharge
Stringgroup3
charinsertionCode
booleanisHetero
intoccupancy
floatpartialCharge
floatradius
intsequenceNumber
floatvectorX
floatvectorY
floatvectorZ
Constructor Summary
Atom()
Method Summary
voidaddVibrationVector(float vectorX, float vectorY, float vectorZ)
AtomcloneAtom()
StringgetElementSymbol()
static booleanisValidElementSymbol(char ch)
static booleanisValidElementSymbol(char chFirst, char chSecond)
static booleanisValidElementSymbolNoCaseSecondChar(char chFirst, char chSecond)
static booleanisValidElementSymbolNoCaseSecondChar(String str)
static booleanisValidFirstSymbolChar(char ch)

Field Detail

alternateLocationID

public char alternateLocationID

anisoBorU

public float[] anisoBorU

atomIndex

public int atomIndex

atomName

public String atomName

atomSerial

public int atomSerial

atomSetIndex

public int atomSetIndex

atomSite

public int atomSite

bfactor

public float bfactor

bsSymmetry

public BitSet bsSymmetry

chainID

public char chainID

elementCharMasks

static final int[] elementCharMasks
Bits which indicate whether or not an element symbol is valid.

If the high bit is set, then it is valid as a standalone char. otherwise, bits 0-25 say whether or not is valid when followed by the letters a-z.

elementNumber

public short elementNumber

elementSymbol

public String elementSymbol

ellipsoid

public Object[] ellipsoid

formalCharge

public int formalCharge

group3

public String group3

insertionCode

public char insertionCode

isHetero

public boolean isHetero

occupancy

public int occupancy

partialCharge

public float partialCharge

radius

public float radius

sequenceNumber

public int sequenceNumber

vectorX

public float vectorX

vectorY

public float vectorY

vectorZ

public float vectorZ

Constructor Detail

Atom

public Atom()

Method Detail

addVibrationVector

public void addVibrationVector(float vectorX, float vectorY, float vectorZ)

cloneAtom

public Atom cloneAtom()

getElementSymbol

public String getElementSymbol()

isValidElementSymbol

public static boolean isValidElementSymbol(char ch)

isValidElementSymbol

public static boolean isValidElementSymbol(char chFirst, char chSecond)

isValidElementSymbolNoCaseSecondChar

public static boolean isValidElementSymbolNoCaseSecondChar(char chFirst, char chSecond)

isValidElementSymbolNoCaseSecondChar

public static boolean isValidElementSymbolNoCaseSecondChar(String str)

isValidFirstSymbolChar

public static boolean isValidFirstSymbolChar(char ch)