Class JniInchiAtom


  • public class JniInchiAtom
    extends java.lang.Object
    Encapsulates properties of InChI Atom. See inchi_api.h.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      private int charge
      Charge on atom.
      private java.lang.String elname
      Chemical element symbol eg C, O, Fe, Hg.
      private int implicitD
      Number of implicit deuteriums (isotopic 2-H) on atom.
      private int implicitH
      Number of implicit hydrogens on atom.
      private int implicitP
      Number of implicit protiums (isotopic 1-H) on atom.
      private int implicitT
      Number of implicit tritiums (isotopic 3-H) on atom.
      private int isotopic_mass
      Mass of isotope.
      protected static int ISOTOPIC_SHIFT_FLAG
      Indicates relative rather than absolute isotopic mass.
      private INCHI_RADICAL radical
      Radical status of atom.
      private double x
      Atom x-coordinate.
      private double y
      Atom y-coordinate.
      private double z
      Atom z-coordinate.
    • Constructor Summary

      Constructors 
      Constructor Description
      JniInchiAtom​(double x, double y, double z, java.lang.String el)
      Create new atom.
      JniInchiAtom​(java.lang.String el)
      Convenience method to create a new atom with zero coordinates.
    • Field Detail

      • ISOTOPIC_SHIFT_FLAG

        protected static final int ISOTOPIC_SHIFT_FLAG
        Indicates relative rather than absolute isotopic mass. Value from inchi_api.h.
        See Also:
        Constant Field Values
      • x

        private double x
        Atom x-coordinate.
      • y

        private double y
        Atom y-coordinate.
      • z

        private double z
        Atom z-coordinate.
      • elname

        private java.lang.String elname
        Chemical element symbol eg C, O, Fe, Hg.
      • implicitH

        private int implicitH
        Number of implicit hydrogens on atom. If set to -1, InChI will add implicit H automatically.
      • implicitP

        private int implicitP
        Number of implicit protiums (isotopic 1-H) on atom.
      • implicitD

        private int implicitD
        Number of implicit deuteriums (isotopic 2-H) on atom.
      • implicitT

        private int implicitT
        Number of implicit tritiums (isotopic 3-H) on atom.
      • isotopic_mass

        private int isotopic_mass
        Mass of isotope. If set to 0, no isotopic mass set; otherwise, isotopic mass, or ISOTOPIC_SHIFT_FLAG + (mass - average atomic mass).
      • charge

        private int charge
        Charge on atom.
    • Constructor Detail

      • JniInchiAtom

        public JniInchiAtom​(double x,
                            double y,
                            double z,
                            java.lang.String el)

        Create new atom.

        Coordinates and element symbol must be set (unknown coordinates/dimensions should be set to zero). All other parameters are initialised to default values:

        Num Implicit H = 0
        Num Implicit 1H = 0
        Num Implicit 2H = 0
        Num Implicit 3H = 0
        Isotopic mass = 0 (non isotopic)
        Radical status = NONE (radical status not defined)

        Parameters:
        x - x-coordinate
        y - y-coordinate
        z - z-coordinate
        el - Chemical element symbol
        Throws:
        java.lang.NullPointerException - - if the element symbol is null.
      • JniInchiAtom

        public JniInchiAtom​(java.lang.String el)
        Convenience method to create a new atom with zero coordinates.
        Parameters:
        el -
    • Method Detail

      • setCharge

        public void setCharge​(int charge)
        Sets charge on atom.
        Parameters:
        charge -
      • setRadical

        public void setRadical​(INCHI_RADICAL radical)
        Sets radical status of atom.
        Parameters:
        radical -
      • setIsotopicMass

        public void setIsotopicMass​(int mass)
        Sets isotopic mass. If set to 0, non-isotopic.
        Parameters:
        mass - Isotopic mass
      • setIsotopicMassShift

        public void setIsotopicMassShift​(int shift)
        Sets isotopic mass, relative to standard mass.
        Parameters:
        shift - Isotopic mass minus average atomic mass
      • setImplicitH

        public void setImplicitH​(int n)
        Sets number of implicit hydrogens on atom. If set to -1, InChI will add implicit H automatically.
        Parameters:
        n - Number of implicit hydrogen
      • setImplicitProtium

        public void setImplicitProtium​(int n)
        Sets number of implicit protium (1H) on atom.
        Parameters:
        n - Number of implicit protium
      • setImplicitDeuterium

        public void setImplicitDeuterium​(int n)
        Sets number of implicit deuterium (2H) on atom.
        Parameters:
        n - Number of implicit deuterium
      • setImplicitTritium

        public void setImplicitTritium​(int n)
        Sets number of implicit tritium (3H) on atom.
        Parameters:
        n - Number of implicit tritium
      • getElementType

        public java.lang.String getElementType()
        Returns chemical element symbol of atom.
        Returns:
      • getCharge

        public int getCharge()
        Returns charge on atom.
        Returns:
      • getRadical

        public INCHI_RADICAL getRadical()
        Returns radical state of atom.
        Returns:
      • getX

        public double getX()
        Returns atom's X-coordinate.
        Returns:
      • getY

        public double getY()
        Returns atom's Y-coordinate.
        Returns:
      • getZ

        public double getZ()
        Returns atom's Z-coordinate.
        Returns:
      • getImplicitH

        public int getImplicitH()
        Returns number of implicit hydrogens on atom.
        Returns:
      • getImplicitProtium

        public int getImplicitProtium()
        Returns number of implicit protiums (1H) on atom.
        Returns:
      • getImplicitDeuterium

        public int getImplicitDeuterium()
        Returns number of implicit deuteriums (2H) on atom.
        Returns:
      • getImplicitTritium

        public int getImplicitTritium()
        Returns number of implicit tritiums (3H) on atom.
        Returns:
      • getIsotopicMass

        public int getIsotopicMass()
        Returns isotopic mass of atom.
        Returns:
      • getInchiRadical

        int getInchiRadical()
      • setInchiRadical

        void setInchiRadical​(int radical)
      • getDebugString

        public java.lang.String getDebugString()
        Generates string representation of information on atom, for debugging purposes.
      • debug

        public void debug()
        Outputs information on atom, for debugging purposes.