Package org.jmol.inchi
Class InChIJNI
java.lang.Object
org.jmol.inchi.InChIJNI
- All Implemented Interfaces:
JmolInChI
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate SmilesAtom
addH
(javajs.util.Lst<SmilesAtom> atoms, SmilesAtom n, int nb) private int
checkFormalCharges
(javajs.util.Lst<SmilesAtom> atoms, int nb, boolean hackImine) protected String
decodeInchiStereo
(SimpleNode[] nodes) private static 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 String
private String
getStructure
(net.sf.jniinchi.JniInchiStructure mol) protected 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, 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, Boolean v) private static String
toString
(net.sf.jniinchi.JniInchiStructure mol)
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Field Details
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mapTet
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mapPlanar
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Constructor Details
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InChIJNI
public InChIJNI()
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Method Details
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getInchi
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getStructure
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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
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newJniInchiStructure
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
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getOrder
private static net.sf.jniinchi.INCHI_BOND_TYPE getOrder(int order) -
toString
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getSmiles
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setPlanarKey
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addH
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checkFormalCharges
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isInchiOpposite
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decodeInchiStereo
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getNodeIndex
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getIntKey
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orderList
private static javajs.util.BS orderList(int[] list) -
isPermutation
private static boolean isPermutation(int[] list, int[] list2) -
getOtherEneAtom
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getJmolBondType
private static int getJmolBondType(net.sf.jniinchi.JniInchiBond b)
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