Package org.jmol.adapter.smarter

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 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