Package net.sf.jniinchi

Class JniInchiAtom

java.lang.Object
net.sf.jniinchi.JniInchiAtom
public class JniInchiAtom extends Object
Encapsulates properties of InChI Atom. See inchi_api.h.

  • Field Details

    • ISOTOPIC_SHIFT_FLAG

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

    • x

      private double x
      Atom x-coordinate.

    • y

      private double y
      Atom y-coordinate.

    • z

      private double z
      Atom z-coordinate.

    • elname

      private 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).

    • radical

      private INCHI_RADICAL radical
      Radical status of atom.

    • charge

      private int charge
      Charge on atom.

  • Constructor Details

    • JniInchiAtom

      public JniInchiAtom(double x, double y, double z, 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:
      NullPointerException - - if the element symbol is null.

    • JniInchiAtom

      public JniInchiAtom(String el)
      Convenience method to create a new atom with zero coordinates.
      Parameters:
      el -

  • Method Details

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

    • debug

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