Package org.jmol.inchi

Class InChIJNA

java.lang.Object
org.jmol.inchi.InchiJmol
org.jmol.inchi.InChIJNA
All Implemented Interfaces:
InChIStructureProvider, JmolInChI
public class InChIJNA extends InchiJmol
Interface with inchi.c via JNA (see JNA-InChI github project). For InChI to SMILES, we use JNA-InChI to read InChI's input structure, via -InChI.

  • Constructor Details

    • InChIJNA

      public InChIJNA()

  • Method Details

    • getInchi

      public String getInchi(Viewer vwr, BS atoms, Object molData, String options)
      Parameters:
      vwr -
      atoms -
      molData - can be String or InputStream
      options -
      Returns:
      InChI or SMILES or InChIKey or internal InChI structure details

    • initializeModelForSmiles

      public void initializeModelForSmiles()

    • getNumAtoms

      public int getNumAtoms()

    • setAtom

      public InChIStructureProvider setAtom(int i)

    • getElementType

      public String getElementType()

    • getX

      public double getX()

    • getY

      public double getY()

    • getZ

      public double getZ()

    • getCharge

      public int getCharge()

    • getIsotopicMass

      public int getIsotopicMass()
      Description copied from interface: InChIStructureProvider
      from inchi_api.h #define ISOTOPIC_SHIFT_FLAG 10000 add to isotopic mass if isotopic_mass = (isotopic mass - average atomic mass) AT_NUM isotopic_mass; 0 => non-isotopic; isotopic mass or ISOTOPIC_SHIFT_FLAG + mass - (average atomic mass)
      Returns:
      inchi's value of average mass

    • getImplicitH

      public int getImplicitH()

    • getNumBonds

      public int getNumBonds()

    • setBond

      public InChIStructureProvider setBond(int i)

    • getIndexOriginAtom

      public int getIndexOriginAtom()

    • getIndexTargetAtom

      public int getIndexTargetAtom()

    • getInchiBondType

      public String getInchiBondType()

    • getNumStereo0D

      public int getNumStereo0D()

    • setStereo0D

      public InChIStructureProvider setStereo0D(int i)

    • getNeighbors

      public int[] getNeighbors()

    • getCenterAtom

      public int getCenterAtom()

    • getStereoType

      public String getStereoType()

    • getParity

      public String getParity()

    • getInternalInchiVersion

      public static String getInternalInchiVersion()
      Get the InChI version directly from the inchi code without an API. To be replaced in the future with a simple inchi IXA call? Future format may change.
      Returns:
      something like "InChI version 1, Software 1.07.2 (API Library)"