Package org.jmol.inchi

Class InChIJNI

  • All Implemented Interfaces:
    JmolInChI
    public class InChIJNI
extends java.lang.Object
implements JmolInChI

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private java.util.Map<java.lang.Integer,​java.lang.Boolean> mapPlanar  
      private java.util.Map<javajs.util.BS,​int[]> mapTet  

    • Constructor Summary

      Constructors 
      Constructor Description
      InChIJNI()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private SmilesAtom addH​(javajs.util.Lst<SmilesAtom> atoms, SmilesAtom n, int nb)  
      private int checkFormalCharges​(javajs.util.Lst<SmilesAtom> atoms, int nb, boolean hackImine)  
      protected java.lang.String decodeInchiStereo​(SimpleNode[] nodes)  
      java.lang.String getInchi​(Viewer vwr, javajs.util.BS atoms, java.lang.String molData, java.lang.String options)  
      private static java.lang.Integer getIntKey​(int i, int iA, int j)  
      private static int getJmolBondType​(net.sf.jniinchi.JniInchiBond b)  
      private static int getNodeIndex​(SimpleNode node)  
      private static net.sf.jniinchi.INCHI_BOND_TYPE getOrder​(int order)  
      private static int getOtherEneAtom​(SmilesAtom[] atoms, int i0, int i1)  
      private java.lang.String getSmiles​(Viewer vwr, net.sf.jniinchi.JniInchiOutputStructure struc, java.lang.String smilesOptions)  
      private java.lang.String getStructure​(net.sf.jniinchi.JniInchiStructure mol)  
      protected java.lang.Boolean isInchiOpposite​(int i1, int i2, int iA, int iB)  
      private static boolean isPermutation​(int[] list, int[] list2)  
      private static net.sf.jniinchi.JniInchiStructure newJniInchiStructure​(Viewer vwr, java.lang.String molData)
      Jmol addition to create a JniInchiStructure from MOL data.
      private static net.sf.jniinchi.JniInchiStructure newJniInchiStructure​(Viewer vwr, javajs.util.BS bsAtoms)
      Jmol addition to create a JniInchiStructure from Jmol atoms.
      private static javajs.util.BS orderList​(int[] list)  
      private void setPlanarKey​(int i0, int i3, int iA, int iB, java.lang.Boolean v)  
      private static java.lang.String toString​(net.sf.jniinchi.JniInchiStructure mol)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • mapTet

        private java.util.Map<javajs.util.BS,​int[]> mapTet

      • mapPlanar

        private java.util.Map<java.lang.Integer,​java.lang.Boolean> mapPlanar

    • Constructor Detail

      • InChIJNI

        public InChIJNI()

    • Method Detail

      • getInchi

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

      • getStructure

        private java.lang.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,
                                                                      java.lang.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 java.lang.String toString​(net.sf.jniinchi.JniInchiStructure mol)

      • getSmiles

        private java.lang.String getSmiles​(Viewer vwr,
                                   net.sf.jniinchi.JniInchiOutputStructure struc,
                                   java.lang.String smilesOptions)

      • setPlanarKey

        private void setPlanarKey​(int i0,
                          int i3,
                          int iA,
                          int iB,
                          java.lang.Boolean v)

      • checkFormalCharges

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

      • isInchiOpposite

        protected java.lang.Boolean isInchiOpposite​(int i1,
                                            int i2,
                                            int iA,
                                            int iB)

      • decodeInchiStereo

        protected java.lang.String decodeInchiStereo​(SimpleNode[] nodes)

      • getNodeIndex

        private static int getNodeIndex​(SimpleNode node)

      • getIntKey

        private static java.lang.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)