Package org.jmol.inchi
Class InChIJNI
- java.lang.Object
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- org.jmol.inchi.InChIJNI
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Constructor Summary
Constructors Constructor Description InChIJNI()
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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)
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Method Detail
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getInchi
public java.lang.String getInchi(Viewer vwr, javajs.util.BS atoms, java.lang.String molData, java.lang.String options)
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getStructure
private java.lang.String getStructure(net.sf.jniinchi.JniInchiStructure mol)
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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
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
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getOrder
private static net.sf.jniinchi.INCHI_BOND_TYPE getOrder(int order)
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toString
private static java.lang.String toString(net.sf.jniinchi.JniInchiStructure mol)
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getSmiles
private java.lang.String getSmiles(Viewer vwr, net.sf.jniinchi.JniInchiOutputStructure struc, java.lang.String smilesOptions)
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setPlanarKey
private void setPlanarKey(int i0, int i3, int iA, int iB, java.lang.Boolean v)
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addH
private SmilesAtom addH(javajs.util.Lst<SmilesAtom> atoms, SmilesAtom n, int nb)
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checkFormalCharges
private int checkFormalCharges(javajs.util.Lst<SmilesAtom> atoms, int nb, boolean hackImine)
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isInchiOpposite
protected java.lang.Boolean isInchiOpposite(int i1, int i2, int iA, int iB)
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decodeInchiStereo
protected java.lang.String decodeInchiStereo(SimpleNode[] nodes)
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getNodeIndex
private static int getNodeIndex(SimpleNode node)
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getIntKey
private static java.lang.Integer getIntKey(int i, int iA, int j)
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orderList
private static javajs.util.BS orderList(int[] list)
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isPermutation
private static boolean isPermutation(int[] list, int[] list2)
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getOtherEneAtom
private static int getOtherEneAtom(SmilesAtom[] atoms, int i0, int i1)
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getJmolBondType
private static int getJmolBondType(net.sf.jniinchi.JniInchiBond b)
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