ambit2.smarts

Class AtomEquivalenceInfo

java.lang.Object

ambit2.smarts.AtomEquivalenceInfo

public class AtomEquivalenceInfo
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
List<Integer>	atomLayersCode
List<org.openscience.cdk.interfaces.IAtom>	curLayerAtoms
List<org.openscience.cdk.interfaces.IAtom>	prevLayerAtoms
static int	SHIFT_ATOM_ELEMENT
static int	SHIFT_BOND_TYPE
static int	SHIFT_INNER_BOND_TYPE
static int	SHIFT_ISOTOPE
static int	SHIFT_LAYER_AT1
static int	SHIFT_LAYER_AT2
static int	SHIFT_NEG_CHARGE
static int	SHIFT_POS_CHARGE
static int	SHIFT_TOP_DEGREE
static int	SHIFT_TOP_LAYER

Constructor Summary

Constructors

Constructor and Description
AtomEquivalenceInfo()

Method Summary

Modifier and Type	Method and Description
void	firstLayer(org.openscience.cdk.interfaces.IAtomContainer mol)
static Integer	getAtomCode(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IBond bond, int topDegree, int layerNum)
static Integer	getBondCode(org.openscience.cdk.interfaces.IBond bond, int at1, int at2, int layerNum)
static int[]	getSortedCodesIndices(int[] codes)
static int[]	getSortedCodesIndices(List<Integer> codes)
void	initialize(org.openscience.cdk.interfaces.IAtom at)
void	initialize(org.openscience.cdk.interfaces.IAtom at, int numLayers, org.openscience.cdk.interfaces.IAtomContainer mol)
void	nextLayer(org.openscience.cdk.interfaces.IAtomContainer mol)
void	processAllLayers(org.openscience.cdk.interfaces.IAtomContainer mol)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

SHIFT_ATOM_ELEMENT

public static final int SHIFT_ATOM_ELEMENT

See Also:

Constant Field Values

SHIFT_BOND_TYPE

public static final int SHIFT_BOND_TYPE

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Constant Field Values

SHIFT_TOP_DEGREE

public static final int SHIFT_TOP_DEGREE

See Also:

Constant Field Values

SHIFT_POS_CHARGE

public static final int SHIFT_POS_CHARGE

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Constant Field Values

SHIFT_NEG_CHARGE

public static final int SHIFT_NEG_CHARGE

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Constant Field Values

SHIFT_ISOTOPE

public static final int SHIFT_ISOTOPE

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Constant Field Values

SHIFT_TOP_LAYER

public static final int SHIFT_TOP_LAYER

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Constant Field Values

SHIFT_LAYER_AT1

public static final int SHIFT_LAYER_AT1

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Constant Field Values

SHIFT_LAYER_AT2

public static final int SHIFT_LAYER_AT2

See Also:

Constant Field Values

SHIFT_INNER_BOND_TYPE

public static final int SHIFT_INNER_BOND_TYPE

See Also:

Constant Field Values

atomLayersCode

public List<Integer> atomLayersCode

curLayerAtoms

public List<org.openscience.cdk.interfaces.IAtom> curLayerAtoms

prevLayerAtoms

public List<org.openscience.cdk.interfaces.IAtom> prevLayerAtoms

Constructor Detail

AtomEquivalenceInfo

public AtomEquivalenceInfo()

Method Detail

initialize

public void initialize(org.openscience.cdk.interfaces.IAtom at)

initialize

public void initialize(org.openscience.cdk.interfaces.IAtom at,
                       int numLayers,
                       org.openscience.cdk.interfaces.IAtomContainer mol)

processAllLayers

public void processAllLayers(org.openscience.cdk.interfaces.IAtomContainer mol)

firstLayer

public void firstLayer(org.openscience.cdk.interfaces.IAtomContainer mol)

nextLayer

public void nextLayer(org.openscience.cdk.interfaces.IAtomContainer mol)

getAtomCode

public static Integer getAtomCode(org.openscience.cdk.interfaces.IAtom atom,
                                  org.openscience.cdk.interfaces.IBond bond,
                                  int topDegree,
                                  int layerNum)

getBondCode

public static Integer getBondCode(org.openscience.cdk.interfaces.IBond bond,
                                  int at1,
                                  int at2,
                                  int layerNum)

getSortedCodesIndices

public static int[] getSortedCodesIndices(int[] codes)

getSortedCodesIndices

public static int[] getSortedCodesIndices(List<Integer> codes)

toString

public String toString()

Overrides:

toString in class Object