Class InChIJNI

java.lang.Object
org.jmol.inchi.InChIJNI
All Implemented Interfaces:
JmolInChI

public class InChIJNI extends Object implements JmolInChI
  • Field Details

    • mapTet

      private Map<javajs.util.BS,int[]> mapTet
    • mapPlanar

      private Map<Integer,Boolean> mapPlanar
  • Constructor Details

    • InChIJNI

      public InChIJNI()
  • Method Details

    • getInchi

      public String getInchi(Viewer vwr, javajs.util.BS atoms, String molData, String options)
      Specified by:
      getInchi in interface JmolInChI
    • getStructure

      private String getStructure(net.sf.jniinchi.JniInchiStructure mol)
    • newJniInchiStructure

      private static net.sf.jniinchi.JniInchiStructure newJniInchiStructure(Viewer vwr, javajs.util.BS bsAtoms)
      Jmol addition to create a JniInchiStructure from Jmol atoms. Currently only supports single, double, aromatic_single and aromatic_double.
      Parameters:
      vwr -
      bsAtoms -
      Returns:
      a structure for JniInput
    • newJniInchiStructure

      private static net.sf.jniinchi.JniInchiStructure newJniInchiStructure(Viewer vwr, String molData)
      Jmol addition to create a JniInchiStructure from MOL data. Currently only supports single, double, aromatic_single and aromatic_double.
      Parameters:
      vwr -
      molData -
      Returns:
      a structure for JniInput
    • getOrder

      private static net.sf.jniinchi.INCHI_BOND_TYPE getOrder(int order)
    • toString

      private static String toString(net.sf.jniinchi.JniInchiStructure mol)
    • getSmiles

      private String getSmiles(Viewer vwr, net.sf.jniinchi.JniInchiOutputStructure struc, String smilesOptions)
    • setPlanarKey

      private void setPlanarKey(int i0, int i3, int iA, int iB, Boolean v)
    • addH

      private SmilesAtom addH(javajs.util.Lst<SmilesAtom> atoms, SmilesAtom n, int nb)
    • checkFormalCharges

      private int checkFormalCharges(javajs.util.Lst<SmilesAtom> atoms, int nb, boolean hackImine)
    • isInchiOpposite

      protected Boolean isInchiOpposite(int i1, int i2, int iA, int iB)
    • decodeInchiStereo

      protected String decodeInchiStereo(SimpleNode[] nodes)
    • getNodeIndex

      private static int getNodeIndex(SimpleNode node)
    • getIntKey

      private static Integer getIntKey(int i, int iA, int j)
    • orderList

      private static javajs.util.BS orderList(int[] list)
    • isPermutation

      private static boolean isPermutation(int[] list, int[] list2)
    • getOtherEneAtom

      private static int getOtherEneAtom(SmilesAtom[] atoms, int i0, int i1)
    • getJmolBondType

      private static int getJmolBondType(net.sf.jniinchi.JniInchiBond b)