public class Atom
extends javax.vecmath.Point3f
implements java.lang.Cloneable
Modifier and Type | Field and Description |
---|---|
char |
alternateLocationID |
float[] |
anisoBorU |
int |
atomIndex |
java.lang.String |
atomName |
int |
atomSerial |
int |
atomSetIndex |
int |
atomSite |
float |
bfactor |
java.util.BitSet |
bsSymmetry |
char |
chainID |
(package private) static int[] |
elementCharMasks
Bits which indicate whether or not an element symbol is valid.
|
short |
elementNumber |
java.lang.String |
elementSymbol |
Quadric[] |
ellipsoid |
int |
formalCharge |
java.lang.String |
group3 |
boolean |
ignoreSymmetry |
char |
insertionCode |
boolean |
isHetero |
int |
occupancy |
float |
partialCharge |
float |
radius |
int |
sequenceNumber |
(package private) float |
vectorX |
(package private) float |
vectorY |
(package private) float |
vectorZ |
Constructor and Description |
---|
Atom() |
Modifier and Type | Method and Description |
---|---|
Atom |
cloneAtom() |
java.lang.String |
getElementSymbol() |
static boolean |
isValidElementSymbol(char ch) |
static boolean |
isValidElementSymbol(char chFirst,
char chSecond) |
static boolean |
isValidElementSymbolNoCaseSecondChar(char chFirst,
char chSecond) |
static boolean |
isValidElementSymbolNoCaseSecondChar(java.lang.String str) |
static boolean |
isValidFirstSymbolChar(char ch) |
void |
scaleVector(float vibScale) |
void |
setEllipsoid(Quadric e) |
distance, distanceL1, distanceLinf, distanceSquared, project
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
public int atomSetIndex
public int atomIndex
public java.util.BitSet bsSymmetry
public int atomSite
public java.lang.String elementSymbol
public short elementNumber
public java.lang.String atomName
public int formalCharge
public float partialCharge
float vectorX
float vectorY
float vectorZ
public float bfactor
public int occupancy
public float radius
public boolean isHetero
public int atomSerial
public char chainID
public char alternateLocationID
public java.lang.String group3
public int sequenceNumber
public char insertionCode
public float[] anisoBorU
public Quadric[] ellipsoid
public boolean ignoreSymmetry
static final int[] elementCharMasks
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.
public void setEllipsoid(Quadric e)
public Atom cloneAtom() throws java.lang.Exception
java.lang.Exception
public java.lang.String getElementSymbol()
public static boolean isValidElementSymbol(char ch)
public static boolean isValidElementSymbol(char chFirst, char chSecond)
public static boolean isValidElementSymbolNoCaseSecondChar(char chFirst, char chSecond)
public static boolean isValidFirstSymbolChar(char ch)
public static boolean isValidElementSymbolNoCaseSecondChar(java.lang.String str)
public void scaleVector(float vibScale)