Class Atom

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, javajs.api.JSONEncodable

    public class Atom
    extends javajs.util.P3
    implements java.lang.Cloneable
    See Also:
    Serialized Form
    • Field Detail

      • atomSetIndex

        public int atomSetIndex
      • index

        public int index
      • bsSymmetry

        public javajs.util.BS 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
      • 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
      • altLoc

        public char altLoc
      • group3

        public java.lang.String group3
      • sequenceNumber

        public int sequenceNumber
      • insertionCode

        public char insertionCode
      • anisoBorU

        public float[] anisoBorU
      • tensors

        public javajs.util.Lst<java.lang.Object> tensors
      • ignoreSymmetry

        public boolean ignoreSymmetry
      • elementCharMasks

        private static final int[] elementCharMasks
    • Constructor Detail

      • Atom

        public Atom()
    • Method Detail

      • addTensor

        public Tensor addTensor​(Tensor tensor,
                                java.lang.String type,
                                boolean reset)
      • getClone

        public Atom getClone()
                      throws java.lang.CloneNotSupportedException
        Throws:
        java.lang.CloneNotSupportedException
      • getElementSymbol

        public java.lang.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
      • isValidSymChar1

        private static boolean isValidSymChar1​(char ch)
        Parameters:
        ch -
        Returns:
        true if matches FIRST character of some symbol Xx