org.jmol.adapter.smarter
Class Atom
java.lang.Object
javax.vecmath.Tuple3f
javax.vecmath.Point3f
org.jmol.adapter.smarter.Atom
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable
public class Atom
- extends javax.vecmath.Point3f
- implements java.lang.Cloneable
- See Also:
- Serialized Form
Fields inherited from class javax.vecmath.Tuple3f |
x, y, z |
Constructor Summary |
Atom()
|
Methods inherited from class javax.vecmath.Point3f |
distance, distanceL1, distanceLinf, distanceSquared, project |
Methods inherited from class javax.vecmath.Tuple3f |
absolute, absolute, add, add, clamp, clamp, clampMax, clampMax, clampMin, clampMin, clone, epsilonEquals, equals, equals, get, get, getX, getY, getZ, hashCode, interpolate, interpolate, negate, negate, scale, scale, scaleAdd, scaleAdd, set, set, set, set, setX, setY, setZ, sub, sub, toString |
Methods inherited from class java.lang.Object |
finalize, getClass, notify, notifyAll, wait, wait, wait |
atomSetIndex
public int atomSetIndex
atomIndex
public int atomIndex
bsSymmetry
public java.util.BitSet bsSymmetry
atomSite
public int atomSite
elementSymbol
public java.lang.String elementSymbol
elementNumber
public short elementNumber
atomName
public java.lang.String atomName
formalCharge
public int formalCharge
partialCharge
public float partialCharge
vectorX
public float vectorX
vectorY
public float vectorY
vectorZ
public float vectorZ
bfactor
public float bfactor
occupancy
public int occupancy
radius
public float radius
isHetero
public boolean isHetero
atomSerial
public int atomSerial
chainID
public char chainID
alternateLocationID
public char alternateLocationID
group3
public java.lang.String group3
sequenceNumber
public int sequenceNumber
insertionCode
public char insertionCode
anisoBorU
public float[] anisoBorU
ellipsoid
public java.lang.Object[] ellipsoid
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.
Atom
public Atom()
cloneAtom
public Atom cloneAtom()
throws java.lang.Exception
- Throws:
java.lang.Exception
getElementSymbol
public java.lang.String getElementSymbol()
addVibrationVector
public void addVibrationVector(float vectorX,
float vectorY,
float vectorZ)
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)
isValidFirstSymbolChar
public static boolean isValidFirstSymbolChar(char ch)
isValidElementSymbolNoCaseSecondChar
public static boolean isValidElementSymbolNoCaseSecondChar(java.lang.String str)