Class Atom

java.lang.Object
javajs.util.T3
javajs.util.P3
org.jmol.adapter.smarter.Atom
All Implemented Interfaces:
Serializable, Cloneable, JSONEncodable

public class Atom extends P3 implements Cloneable
See Also:
  • Field Details

    • atomSetIndex

      public int atomSetIndex
    • index

      public int index
    • bsSymmetry

      public BS bsSymmetry
    • atomSite

      public int atomSite
    • elementSymbol

      public String elementSymbol
    • elementNumber

      public short elementNumber
    • atomName

      public String atomName
    • formalCharge

      public int formalCharge
    • partialCharge

      public float partialCharge
    • vib

      public 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

      public String group3
    • sequenceNumber

      public int sequenceNumber
    • insertionCode

      public char insertionCode
    • anisoBorU

      public float[] anisoBorU
    • tensors

      public Lst<Object> tensors
    • isNegDisorder

      public boolean isNegDisorder
    • typeSymbol

      public String typeSymbol
  • Constructor Details

    • Atom

      public Atom()
  • Method Details

    • addTensor

      public Tensor addTensor(Tensor tensor, String type, boolean reset)
    • getClone

      public Atom getClone()
    • getElementSymbol

      public String getElementSymbol()
    • isValidSym1

      public static boolean isValidSym1(char ch)
      Parameters:
      ch -
      Returns:
      true if matches a one-character symbol X
    • isValidSym2

      public static boolean isValidSym2(char ch1, char ch2)
      Parameters:
      ch1 -
      ch2 -
      Returns:
      true if matches a valid symbol Xy
    • isValidSymNoCase

      public static boolean isValidSymNoCase(char ch1, char ch2)
      Parameters:
      ch1 -
      ch2 -
      Returns:
      true if matches a two-character symbol, XX or Xx
    • copyTo

      public Atom copyTo(P3 pt, AtomSetCollection asc)