IndigoObject (Indigo 1.2.1-dev5-moderna API)

java.lang.Object
- com.ggasoftware.indigo.IndigoObject

All Implemented Interfaces:: Iterable<IndigoObject>, Iterator<IndigoObject>

public class IndigoObject
extends Object
implements Iterator<IndigoObject>, Iterable<IndigoObject>

Field Summary

Fields
Modifier and Type Field and Description

protected IndigoLib _lib

protected Indigo dispatcher

int self

Fields
Modifier and Type	Field and Description
`protected IndigoLib`	`_lib`
`protected Indigo`	`dispatcher`
`int`	`self`

Constructor Summary

Constructors
Constructor and Description

IndigoObject(Indigo dispatcher, int id)

IndigoObject(Indigo dispatcher, int id, Object parent)

Constructors
Constructor and Description
`IndigoObject(Indigo dispatcher, int id)`
`IndigoObject(Indigo dispatcher, int id, Object parent)`

Method Summary

Methods
Modifier and Type	Method and Description
`IndigoObject`	`addAtom(String symbol)`
`IndigoObject`	`addBond(IndigoObject atom, int order)`
`void`	`addCatalyst(IndigoObject molecule)`
`void`	`addConstraint(String type, String value)`
`void`	`addConstraintNot(String type, String value)`
`void`	`addConstraintOr(String type, String value)`
`IndigoObject`	`addDataSGroup(Collection<Integer> atoms, Collection<Integer> bonds, String description, String data)`
`IndigoObject`	`addDataSGroup(int[] atoms, int[] bonds, String description, String data)`
`void`	`addDecomposition(IndigoObject q_match)`
`void`	`addProduct(IndigoObject molecule)`
`void`	`addReactant(IndigoObject molecule)`
`IndigoObject`	`addRSite(String name)`
`void`	`addStereocenter(int type, int v1, int v2, int v3)`
`void`	`addStereocenter(int type, int v1, int v2, int v3, int v4)`
`float`	`alignAtoms(Collection<Integer> atom_ids, Collection<Float> desired_xyz)`
`float`	`alignAtoms(int[] atom_ids, float[] desired_xyz)`
`IndigoObject`	`allScaffolds()`
`void`	`append(IndigoObject obj)`
`void`	`aromatize()`
`int`	`arrayAdd(IndigoObject other)`
`IndigoObject`	`at(int idx)`
`int`	`atomicNumber()`
`int`	`atomMappingNumber(IndigoObject reaction_atom)`
`void`	`automap()`
`void`	`automap(String mode)`
`IndigoObject`	`bond()`
`int`	`bondOrder()`
`int`	`bondStereo()`
`String`	`canonicalSmiles()`
`void`	`changeStereocenterType(int type)`
`Integer`	`charge()`
`String`	`checkAmbiguousH()`
`String`	`checkBadValence()`
`void`	`clear()`
`void`	`clearAAM()`
`void`	`clearAlleneCenters()`
`void`	`clearAttachmentPoints()`
`void`	`clearCisTrans()`
`void`	`clearProperties()`
`void`	`clearStereocenters()`
`IndigoObject`	`clone()`
`void`	`close()`
`String`	`cml()`
`void`	`cmlAppend(IndigoObject item)`
`void`	`cmlFooter()`
`void`	`cmlHeader()`
`IndigoObject`	`component(int index)`
`int`	`componentIndex()`
`void`	`correctReactingCenters()`
`int`	`count()`
`int`	`countAlleneCenters()`
`int`	`countAtoms()`
`int`	`countAttachmentPoints()`
`int`	`countBits()`
`int`	`countBonds()`
`int`	`countCatalysts()`
`int`	`countComponents()`
`int`	`countDataSGroups()`
`int`	`countGenericSGroups()`
`int`	`countHeavyAtoms()`
`Integer`	`countHydrogens()`
`int`	`countImplicitHydrogens()`
`int`	`countMatches(IndigoObject query)`
`int`	`countMatchesWithLimit(IndigoObject query, int embeddings_limit)`
`int`	`countMolecules()`
`int`	`countMultipleGroups()`
`int`	`countProducts()`
`int`	`countPseudoatoms()`
`int`	`countReactants()`
`int`	`countRepeatingUnits()`
`int`	`countRSites()`
`int`	`countSSSR()`
`int`	`countStereocenters()`
`int`	`countSuperatoms()`
`IndigoObject`	`createEdgeSubmolecule(Collection<Integer> vertices, Collection<Integer> edges)`
`IndigoObject`	`createEdgeSubmolecule(int[] vertices, int[] edges)`
`IndigoObject`	`createSubmolecule(Collection<Integer> vertices)`
`IndigoObject`	`createSubmolecule(int[] vertices)`
`String`	`data()`
`String`	`dbgInternalType()`
`void`	`dearomatize()`
`IndigoObject`	`decomposedMoleculeHighlighted()`
`IndigoObject`	`decomposedMoleculeScaffold()`
`IndigoObject`	`decomposedMoleculeWithRGroups()`
`IndigoObject`	`decomposeMolecule(IndigoObject mol)`
`int`	`degree()`
`String`	`description()`
`IndigoObject`	`destination()`
`void`	`dispose()`
`int`	`expandAbbreviations()`
`Integer`	`explicitValence()`
`protected void`	`finalize()`
`IndigoObject`	`fingerprint()`
`IndigoObject`	`fingerprint(String type)`
`void`	`foldHydrogens()`
`IndigoObject`	`getAtom(int idx)`
`IndigoObject`	`getBond(int idx)`
`IndigoObject`	`getDataSGroup(int index)`
`IndigoObject`	`getGenericSGroup(int index)`
`Indigo`	`getIndigo()`
`IndigoObject`	`getMolecule(int idx)`
`IndigoObject`	`getMultipleGroup(int index)`
`String`	`getProperty(String prop)`
`IndigoObject`	`getRepeatingUnit(int index)`
`IndigoObject`	`getSubmolecule(Collection<Integer> vertices)`
`IndigoObject`	`getSubmolecule(int[] vertices)`
`IndigoObject`	`getSuperatom(int index)`
`String`	`grossFormula()`
`boolean`	`hasCoord()`
`boolean`	`hasNext()`
`boolean`	`hasProperty(String prop)`
`boolean`	`hasZCoord()`
`void`	`highlight()`
`IndigoObject`	`highlightedTarget()`
`void`	`ignoreAtom(IndigoObject atom)`
`int`	`index()`
`void`	`invertStereo()`
`boolean`	`isChiral()`
`boolean`	`isHighlighted()`
`int`	`isotope()`
`boolean`	`isPseudoatom()`
`boolean`	`isRSite()`
`IndigoObject`	`iterateAlleneCenters()`
`IndigoObject`	`iterateArray()`
`IndigoObject`	`iterateAtoms()`
`IndigoObject`	`iterateAttachmentPoints(int order)`
`IndigoObject`	`iterateBonds()`
`IndigoObject`	`iterateCatalysts()`
`IndigoObject`	`iterateComponents()`
`IndigoObject`	`iterateDataSGroups()`
`IndigoObject`	`iterateDecomposedMolecules()` Deprecated.
`IndigoObject`	`iterateDecompositions()`
`IndigoObject`	`iterateEdgeSubmolecules(int min_edges, int max_edges)`
`IndigoObject`	`iterateGenericSGroups()`
`IndigoObject`	`iterateMatches(IndigoObject query)`
`IndigoObject`	`iterateMolecules()`
`IndigoObject`	`iterateMultipleGroups()`
`IndigoObject`	`iterateNeighbors()`
`IndigoObject`	`iterateProducts()`
`IndigoObject`	`iterateProperties()`
`IndigoObject`	`iteratePseudoatoms()`
`IndigoObject`	`iterateReactants()`
`IndigoObject`	`iterateRepeatingUnits()`
`IndigoObject`	`iterateRGroupFragments()`
`IndigoObject`	`iterateRGroups()`
`IndigoObject`	`iterateRings(int min_vertices, int max_vertices)`
`IndigoObject`	`iterateRSites()`
`IndigoObject`	`iterateSSSR()`
`IndigoObject`	`iterateStereocenters()`
`IndigoObject`	`iterateSubtrees(int min_vertices, int max_vertices)`
`IndigoObject`	`iterateSuperatoms()`
`Iterator<IndigoObject>`	`iterator()`
`String`	`layeredCode()`
`void`	`layout()`
`IndigoObject`	`mapAtom(IndigoObject query_atom)`
`IndigoObject`	`mapBond(IndigoObject query_bond)`
`IndigoObject`	`mapMolecule(IndigoObject query_reaction_molecule)`
`int`	`markEitherCisTrans()`
`int`	`markStereobonds()`
`IndigoObject`	`match(IndigoObject query)`
`byte[]`	`mdlct()`
`IndigoObject`	`merge(IndigoObject other)`
`float`	`molecularWeight()`
`String`	`molfile()`
`float`	`monoisotopicMass()`
`float`	`mostAbundantMass()`
`String`	`name()`
`IndigoObject`	`next()`
`boolean`	`normalize()`
`boolean`	`normalize(String options)`
`void`	`optimize()`
`void`	`optimize(String options)`
`Integer`	`radical()`
`Integer`	`radicalElectrons()`
`String`	`rawData()`
`void`	`rdfAppend(IndigoObject item)`
`void`	`rdfHeader()`
`int`	`reactingCenter(IndigoObject bond)`
`void`	`remove()`
`void`	`removeAtoms(Collection<Integer> vertices)`
`void`	`removeAtoms(int[] vertices)`
`void`	`removeBonds(Collection<Integer> bonds)`
`void`	`removeBonds(int[] bonds)`
`void`	`removeConstraints(String type)`
`void`	`removeProperty(String prop)`
`IndigoObject`	`resetAtom(String symbol)`
`void`	`resetCharge()`
`void`	`resetExplicitValence()`
`void`	`resetIsotope()`
`void`	`resetRadical()`
`void`	`resetStereo()`
`int`	`resetSymmetricCisTrans()`
`int`	`resetSymmetricStereocenters()`
`String`	`rxnfile()`
`void`	`saveCml(String filename)`
`void`	`saveMolfile(String filename)`
`void`	`saveRxnfile(String filename)`
`void`	`sdfAppend(IndigoObject item)`
`byte[]`	`serialize()`
`void`	`setAtomMappingNumber(IndigoObject reaction_atom, int number)`
`void`	`setAttachmentPoint(int order)`
`void`	`setBondOrder(int order)`
`void`	`setCharge(int charge)`
`void`	`setDataSGroupXY(float x, float y)`
`void`	`setDataSGroupXY(float x, float y, String options)`
`void`	`setExplicitValence(int valence)`
`void`	`setImplicitHCount(int hcount)`
`void`	`setIsotope(int isotope)`
`void`	`setName(String name)`
`void`	`setProperty(String prop, String value)`
`void`	`setRadical(int radical)`
`void`	`setReactingCenter(IndigoObject bond, int type)`
`IndigoObject`	`setRSite(String name)`
`void`	`setStereocenterGroup(int group)`
`void`	`setXYZ(float[] xyz)`
`void`	`setXYZ(float x, float y, float z)`
`int`	`singleAllowedRGroup()`
`String`	`smiles()`
`void`	`smilesAppend(IndigoObject item)`
`IndigoObject`	`source()`
`int`	`stereocenterGroup()`
`int[]`	`stereocenterPyramid()`
`int`	`stereocenterType()`
`String`	`symbol()`
`int[]`	`symmetryClasses()`
`int`	`tell()`
`byte[]`	`toBuffer()`
`int`	`topology()`
`String`	`toString()`
`void`	`unfoldHydrogens()`
`void`	`unhighlight()`
`void`	`unignoreAllAtoms()`
`void`	`unignoreAtom(IndigoObject atom)`
`int`	`valence()`
`int`	`validateChirality()`
`float[]`	`xyz()`

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

self
```
public int self
```

dispatcher
```
protected Indigo dispatcher
```

_lib
```
protected IndigoLib _lib
```

Constructor Detail

IndigoObject

public IndigoObject(Indigo dispatcher,
            int id)

IndigoObject

public IndigoObject(Indigo dispatcher,
            int id,
            Object parent)

Method Detail

getIndigo
```
public Indigo getIndigo()
```

dispose
```
public void dispose()
```

finalize

protected void finalize()
                 throws Throwable

Overrides:: finalize in class Object
Throws:: Throwable

clone
```
public IndigoObject clone()
```
Overrides:

clone in class Object

molfile
```
public String molfile()
```

saveMolfile

public void saveMolfile(String filename)

cml
```
public String cml()
```

saveCml
```
public void saveCml(String filename)
```

mdlct
```
public byte[] mdlct()
```

addReactant

public void addReactant(IndigoObject molecule)

addProduct

public void addProduct(IndigoObject molecule)

addCatalyst

public void addCatalyst(IndigoObject molecule)

countReactants
```
public int countReactants()
```

countProducts
```
public int countProducts()
```

countCatalysts
```
public int countCatalysts()
```

countMolecules
```
public int countMolecules()
```

iterateAttachmentPoints

public IndigoObject iterateAttachmentPoints(int order)

iterateReactants

public IndigoObject iterateReactants()

iterateProducts
```
public IndigoObject iterateProducts()
```

iterateCatalysts

public IndigoObject iterateCatalysts()

iterateMolecules

public IndigoObject iterateMolecules()

rxnfile
```
public String rxnfile()
```

saveRxnfile

public void saveRxnfile(String filename)

automap
```
public void automap()
```

automap
```
public void automap(String mode)
```

atomMappingNumber

public int atomMappingNumber(IndigoObject reaction_atom)

setAtomMappingNumber

public void setAtomMappingNumber(IndigoObject reaction_atom,
                        int number)

clearAAM
```
public void clearAAM()
```

correctReactingCenters
```
public void correctReactingCenters()
```

iterateAtoms
```
public IndigoObject iterateAtoms()
```

iteratePseudoatoms

public IndigoObject iteratePseudoatoms()

iterateRSites
```
public IndigoObject iterateRSites()
```

iterateStereocenters

public IndigoObject iterateStereocenters()

iterateAlleneCenters

public IndigoObject iterateAlleneCenters()

iterateRGroups
```
public IndigoObject iterateRGroups()
```

iterateRGroupFragments

public IndigoObject iterateRGroupFragments()

countAttachmentPoints
```
public int countAttachmentPoints()
```

isPseudoatom
```
public boolean isPseudoatom()
```

isRSite
```
public boolean isRSite()
```

stereocenterType
```
public int stereocenterType()
```

stereocenterGroup
```
public int stereocenterGroup()
```

stereocenterPyramid
```
public int[] stereocenterPyramid()
```

changeStereocenterType

public void changeStereocenterType(int type)

setStereocenterGroup

public void setStereocenterGroup(int group)

singleAllowedRGroup
```
public int singleAllowedRGroup()
```

symbol
```
public String symbol()
```

degree
```
public int degree()
```

charge
```
public Integer charge()
```

reactingCenter

public int reactingCenter(IndigoObject bond)

setReactingCenter

public void setReactingCenter(IndigoObject bond,
                     int type)

explicitValence
```
public Integer explicitValence()
```

radicalElectrons
```
public Integer radicalElectrons()
```

radical
```
public Integer radical()
```

atomicNumber
```
public int atomicNumber()
```

isotope
```
public int isotope()
```

valence
```
public int valence()
```

countHydrogens
```
public Integer countHydrogens()
```

countImplicitHydrogens
```
public int countImplicitHydrogens()
```

resetCharge
```
public void resetCharge()
```

resetExplicitValence
```
public void resetExplicitValence()
```

resetRadical
```
public void resetRadical()
```

resetIsotope
```
public void resetIsotope()
```

setAttachmentPoint

public void setAttachmentPoint(int order)

clearAttachmentPoints
```
public void clearAttachmentPoints()
```

removeConstraints

public void removeConstraints(String type)

addConstraint

public void addConstraint(String type,
                 String value)

addConstraintNot

public void addConstraintNot(String type,
                    String value)

addConstraintOr

public void addConstraintOr(String type,
                   String value)

resetStereo
```
public void resetStereo()
```

invertStereo
```
public void invertStereo()
```

countAtoms
```
public int countAtoms()
```

countBonds
```
public int countBonds()
```

countPseudoatoms
```
public int countPseudoatoms()
```

countRSites
```
public int countRSites()
```

iterateBonds
```
public IndigoObject iterateBonds()
```

bondOrder
```
public int bondOrder()
```

bondStereo
```
public int bondStereo()
```

topology
```
public int topology()
```

iterateNeighbors

public IndigoObject iterateNeighbors()

bond
```
public IndigoObject bond()
```

getAtom
```
public IndigoObject getAtom(int idx)
```

getMolecule

public IndigoObject getMolecule(int idx)

getBond
```
public IndigoObject getBond(int idx)
```

source
```
public IndigoObject source()
```

destination
```
public IndigoObject destination()
```

clearCisTrans
```
public void clearCisTrans()
```

clearStereocenters
```
public void clearStereocenters()
```

clearAlleneCenters
```
public void clearAlleneCenters()
```

countStereocenters
```
public int countStereocenters()
```

countAlleneCenters
```
public int countAlleneCenters()
```

resetSymmetricCisTrans
```
public int resetSymmetricCisTrans()
```

resetSymmetricStereocenters

public int resetSymmetricStereocenters()

markEitherCisTrans
```
public int markEitherCisTrans()
```

markStereobonds
```
public int markStereobonds()
```

validateChirality
```
public int validateChirality()
```

addAtom

public IndigoObject addAtom(String symbol)

resetAtom

public IndigoObject resetAtom(String symbol)

addRSite

public IndigoObject addRSite(String name)

setRSite

public IndigoObject setRSite(String name)

setCharge
```
public void setCharge(int charge)
```

setRadical
```
public void setRadical(int radical)
```

setExplicitValence

public void setExplicitValence(int valence)

setIsotope
```
public void setIsotope(int isotope)
```

setImplicitHCount

public void setImplicitHCount(int hcount)

addBond

public IndigoObject addBond(IndigoObject atom,
                   int order)

setBondOrder
```
public void setBondOrder(int order)
```

merge

public IndigoObject merge(IndigoObject other)

highlight
```
public void highlight()
```

unhighlight
```
public void unhighlight()
```

isHighlighted
```
public boolean isHighlighted()
```

countComponents
```
public int countComponents()
```

componentIndex
```
public int componentIndex()
```

iterateComponents

public IndigoObject iterateComponents()

component

public IndigoObject component(int index)

countSSSR
```
public int countSSSR()
```

iterateSSSR
```
public IndigoObject iterateSSSR()
```

iterateSubtrees

public IndigoObject iterateSubtrees(int min_vertices,
                           int max_vertices)

iterateRings

public IndigoObject iterateRings(int min_vertices,
                        int max_vertices)

iterateEdgeSubmolecules

public IndigoObject iterateEdgeSubmolecules(int min_edges,
                                   int max_edges)

countHeavyAtoms
```
public int countHeavyAtoms()
```

grossFormula
```
public String grossFormula()
```

molecularWeight
```
public float molecularWeight()
```

mostAbundantMass
```
public float mostAbundantMass()
```

monoisotopicMass
```
public float monoisotopicMass()
```

canonicalSmiles
```
public String canonicalSmiles()
```

layeredCode
```
public String layeredCode()
```

hasCoord
```
public boolean hasCoord()
```

hasZCoord
```
public boolean hasZCoord()
```

isChiral
```
public boolean isChiral()
```

xyz
```
public float[] xyz()
```

setXYZ

public void setXYZ(float x,
          float y,
          float z)

setXYZ
```
public void setXYZ(float[] xyz)
```

countSuperatoms
```
public int countSuperatoms()
```

countDataSGroups
```
public int countDataSGroups()
```

countRepeatingUnits
```
public int countRepeatingUnits()
```

countMultipleGroups
```
public int countMultipleGroups()
```

countGenericSGroups
```
public int countGenericSGroups()
```

iterateSuperatoms

public IndigoObject iterateSuperatoms()

iterateDataSGroups

public IndigoObject iterateDataSGroups()

iterateRepeatingUnits

public IndigoObject iterateRepeatingUnits()

iterateMultipleGroups

public IndigoObject iterateMultipleGroups()

iterateGenericSGroups

public IndigoObject iterateGenericSGroups()

getDataSGroup

public IndigoObject getDataSGroup(int index)

getSuperatom

public IndigoObject getSuperatom(int index)

getGenericSGroup

public IndigoObject getGenericSGroup(int index)

getMultipleGroup

public IndigoObject getMultipleGroup(int index)

getRepeatingUnit

public IndigoObject getRepeatingUnit(int index)

description
```
public String description()
```

data
```
public String data()
```

addDataSGroup

public IndigoObject addDataSGroup(int[] atoms,
                         int[] bonds,
                         String description,
                         String data)

addDataSGroup

public IndigoObject addDataSGroup(Collection<Integer> atoms,
                         Collection<Integer> bonds,
                         String description,
                         String data)

addStereocenter

public void addStereocenter(int type,
                   int v1,
                   int v2,
                   int v3)

addStereocenter

public void addStereocenter(int type,
                   int v1,
                   int v2,
                   int v3,
                   int v4)

setDataSGroupXY

public void setDataSGroupXY(float x,
                   float y)

setDataSGroupXY

public void setDataSGroupXY(float x,
                   float y,
                   String options)

createSubmolecule

public IndigoObject createSubmolecule(int[] vertices)

createSubmolecule

public IndigoObject createSubmolecule(Collection<Integer> vertices)

getSubmolecule

public IndigoObject getSubmolecule(int[] vertices)

getSubmolecule

public IndigoObject getSubmolecule(Collection<Integer> vertices)

createEdgeSubmolecule

public IndigoObject createEdgeSubmolecule(int[] vertices,
                                 int[] edges)

createEdgeSubmolecule

public IndigoObject createEdgeSubmolecule(Collection<Integer> vertices,
                                 Collection<Integer> edges)

removeAtoms

public void removeAtoms(int[] vertices)

removeAtoms

public void removeAtoms(Collection<Integer> vertices)

removeBonds
```
public void removeBonds(int[] bonds)
```

removeBonds

public void removeBonds(Collection<Integer> bonds)

alignAtoms

public float alignAtoms(int[] atom_ids,
               float[] desired_xyz)

alignAtoms

public float alignAtoms(Collection<Integer> atom_ids,
               Collection<Float> desired_xyz)

aromatize
```
public void aromatize()
```

dearomatize
```
public void dearomatize()
```

foldHydrogens
```
public void foldHydrogens()
```

unfoldHydrogens
```
public void unfoldHydrogens()
```

layout
```
public void layout()
```

smiles
```
public String smiles()
```

name
```
public String name()
```

setName
```
public void setName(String name)
```

serialize
```
public byte[] serialize()
```

hasProperty

public boolean hasProperty(String prop)

getProperty

public String getProperty(String prop)

setProperty

public void setProperty(String prop,
               String value)

removeProperty

public void removeProperty(String prop)

iterateProperties

public IndigoObject iterateProperties()

clearProperties
```
public void clearProperties()
```

checkBadValence
```
public String checkBadValence()
```

checkAmbiguousH
```
public String checkAmbiguousH()
```

fingerprint
```
public IndigoObject fingerprint()
```

fingerprint

public IndigoObject fingerprint(String type)

countBits
```
public int countBits()
```

rawData
```
public String rawData()
```

tell
```
public int tell()
```

sdfAppend

public void sdfAppend(IndigoObject item)

smilesAppend

public void smilesAppend(IndigoObject item)

rdfHeader
```
public void rdfHeader()
```

rdfAppend

public void rdfAppend(IndigoObject item)

cmlHeader
```
public void cmlHeader()
```

cmlAppend

public void cmlAppend(IndigoObject item)

cmlFooter
```
public void cmlFooter()
```

iterateArray
```
public IndigoObject iterateArray()
```

count
```
public int count()
```

clear
```
public void clear()
```

arrayAdd

public int arrayAdd(IndigoObject other)

at
```
public IndigoObject at(int idx)
```

ignoreAtom

public void ignoreAtom(IndigoObject atom)

unignoreAtom

public void unignoreAtom(IndigoObject atom)

unignoreAllAtoms
```
public void unignoreAllAtoms()
```

match

public IndigoObject match(IndigoObject query)

countMatches

public int countMatches(IndigoObject query)

countMatchesWithLimit

public int countMatchesWithLimit(IndigoObject query,
                        int embeddings_limit)

iterateMatches

public IndigoObject iterateMatches(IndigoObject query)

highlightedTarget

public IndigoObject highlightedTarget()

mapAtom

public IndigoObject mapAtom(IndigoObject query_atom)

mapMolecule

public IndigoObject mapMolecule(IndigoObject query_reaction_molecule)

mapBond

public IndigoObject mapBond(IndigoObject query_bond)

allScaffolds
```
public IndigoObject allScaffolds()
```

decomposedMoleculeScaffold

public IndigoObject decomposedMoleculeScaffold()

iterateDecomposedMolecules

@Deprecated
public IndigoObject iterateDecomposedMolecules()

Deprecated.

decomposedMoleculeHighlighted

public IndigoObject decomposedMoleculeHighlighted()

decomposedMoleculeWithRGroups

public IndigoObject decomposedMoleculeWithRGroups()

decomposeMolecule

public IndigoObject decomposeMolecule(IndigoObject mol)

iterateDecompositions

public IndigoObject iterateDecompositions()

addDecomposition

public void addDecomposition(IndigoObject q_match)

iterator
```
public Iterator<IndigoObject> iterator()
```
Specified by:

iterator in interface Iterable<IndigoObject>

remove
```
public void remove()
```
Specified by:

remove in interface Iterator<IndigoObject>

close
```
public void close()
```

next
```
public IndigoObject next()
                  throws NoSuchElementException
```
Specified by:

next in interface Iterator<IndigoObject>

Throws:

NoSuchElementException

hasNext
```
public boolean hasNext()
```
Specified by:

hasNext in interface Iterator<IndigoObject>

index
```
public int index()
```

toString
```
public String toString()
```
Overrides:

toString in class Object

toBuffer
```
public byte[] toBuffer()
```

symmetryClasses
```
public int[] symmetryClasses()
```

append
```
public void append(IndigoObject obj)
```

optimize
```
public void optimize()
```

optimize
```
public void optimize(String options)
```

normalize
```
public boolean normalize()
```

normalize

public boolean normalize(String options)

expandAbbreviations
```
public int expandAbbreviations()
```

dbgInternalType
```
public String dbgInternalType()
```

Class IndigoObject

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

self

dispatcher

_lib

Constructor Detail

IndigoObject

IndigoObject

Method Detail

getIndigo

dispose

finalize

clone

molfile

saveMolfile

cml

saveCml

mdlct

addReactant

addProduct

addCatalyst

countReactants

countProducts

countCatalysts

countMolecules

iterateAttachmentPoints

iterateReactants

iterateProducts

iterateCatalysts

iterateMolecules

rxnfile

saveRxnfile

automap

automap

atomMappingNumber

setAtomMappingNumber

clearAAM

correctReactingCenters

iterateAtoms

iteratePseudoatoms

iterateRSites

iterateStereocenters

iterateAlleneCenters

iterateRGroups

iterateRGroupFragments

countAttachmentPoints

isPseudoatom

isRSite

stereocenterType

stereocenterGroup

stereocenterPyramid

changeStereocenterType

setStereocenterGroup

singleAllowedRGroup

symbol

degree

charge

reactingCenter

setReactingCenter

explicitValence

radicalElectrons

radical

atomicNumber

isotope

valence

countHydrogens

countImplicitHydrogens

resetCharge

resetExplicitValence

resetRadical

resetIsotope

setAttachmentPoint

clearAttachmentPoints

removeConstraints

addConstraint

addConstraintNot