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
- Direct Known Subclasses:
TopoCifParser.TAtom
,TopoCifParser.TNode
,XmlChemDrawReader.CDNode
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionchar
float[]
int
int
int
float
float
javajs.util.BS
int
private static final int[]
short
float
int
int
char
boolean
boolean
float
float
int
javajs.util.Lst
<Object> javajs.util.V3
Fields inherited from class javajs.util.T3
x, y, z
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncopyTo
(javajs.util.P3 pt, AtomSetCollection asc) getClone()
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, newA, 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
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Field Details
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atomSetIndex
public int atomSetIndex -
index
public int index -
bsSymmetry
public javajs.util.BS bsSymmetry -
atomSite
public int atomSite -
elementSymbol
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elementNumber
public short elementNumber -
atomName
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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 -
bondingRadius
public float bondingRadius -
altLoc
public char altLoc -
group3
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sequenceNumber
public int sequenceNumber -
insertionCode
public char insertionCode -
anisoBorU
public float[] anisoBorU -
tensors
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isNegDisorder
public boolean isNegDisorder -
typeSymbol
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elementCharMasks
private static final int[] elementCharMasks
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Constructor Details
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Atom
public Atom()
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Method Details
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addTensor
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getClone
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getElementSymbol
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isValidSym1
public static boolean isValidSym1(char ch) - Parameters:
ch
-- Returns:
- true if matches a one-character symbol X
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isValidSym2
public static boolean isValidSym2(char ch1, char ch2) - Parameters:
ch1
-ch2
-- Returns:
- true if matches a valid symbol Xy
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isValidSymNoCase
public static boolean isValidSymNoCase(char ch1, char ch2) - Parameters:
ch1
-ch2
-- Returns:
- true if matches a two-character symbol, XX or Xx
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isValidSymChar1
private static boolean isValidSymChar1(char ch) - Parameters:
ch
-- Returns:
- true if matches FIRST character of some symbol Xx
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copyTo
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