Package org.jmol.adapter.smarter
Class Atom
- java.lang.Object
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- javajs.util.T3
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- javajs.util.P3
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- org.jmol.adapter.smarter.Atom
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,javajs.api.JSONEncodable
- Direct Known Subclasses:
TopoCifParser.TAtom
,TopoCifParser.TNode
public class Atom extends javajs.util.P3 implements java.lang.Cloneable
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description char
altLoc
float[]
anisoBorU
java.lang.String
atomName
int
atomSerial
int
atomSetIndex
int
atomSite
float
bfactor
float
bondingRadius
javajs.util.BS
bsSymmetry
int
chainID
private static int[]
elementCharMasks
short
elementNumber
java.lang.String
elementSymbol
float
foccupancy
int
formalCharge
java.lang.String
group3
boolean
ignoreSymmetry
int
index
char
insertionCode
boolean
isHetero
float
partialCharge
float
radius
int
sequenceNumber
javajs.util.Lst<java.lang.Object>
tensors
java.lang.String
typeSymbol
javajs.util.V3
vib
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Constructor Summary
Constructors Constructor Description Atom()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description Tensor
addTensor(Tensor tensor, java.lang.String type, boolean reset)
Atom
copyTo(javajs.util.P3 pt, AtomSetCollection asc)
Atom
getClone()
java.lang.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)
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Field Detail
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atomSetIndex
public int atomSetIndex
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index
public int index
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bsSymmetry
public javajs.util.BS bsSymmetry
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atomSite
public int atomSite
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elementSymbol
public java.lang.String elementSymbol
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elementNumber
public short elementNumber
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atomName
public java.lang.String atomName
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formalCharge
public int formalCharge
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partialCharge
public float partialCharge
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vib
public javajs.util.V3 vib
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bfactor
public float bfactor
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foccupancy
public float foccupancy
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radius
public float radius
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isHetero
public boolean isHetero
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atomSerial
public int atomSerial
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chainID
public int chainID
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bondingRadius
public float bondingRadius
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altLoc
public char altLoc
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group3
public java.lang.String group3
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sequenceNumber
public int sequenceNumber
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insertionCode
public char insertionCode
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anisoBorU
public float[] anisoBorU
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tensors
public javajs.util.Lst<java.lang.Object> tensors
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ignoreSymmetry
public boolean ignoreSymmetry
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typeSymbol
public java.lang.String typeSymbol
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elementCharMasks
private static final int[] elementCharMasks
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Method Detail
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getClone
public Atom getClone()
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getElementSymbol
public java.lang.String 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
public Atom copyTo(javajs.util.P3 pt, AtomSetCollection asc)
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