IndigoObject (Indigo 1.46.0 API)

java.lang.Object
- com.epam.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 Indigo dispatcher

protected IndigoLib lib

int self

Fields
Modifier and Type	Field and Description
`protected Indigo`	`dispatcher`
`protected IndigoLib`	`lib`
`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

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`IndigoObject`	`addAtom(String symbol)`
`IndigoObject`	`addBond(IndigoObject atom, int order)`
`void`	`addCatalyst(IndigoObject molecule)`
`int`	`addCIPStereoDescriptors()`
`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)`
`IndigoObject`	`addSGroup(String type)`
`IndigoObject`	`addSGroup(String type, int extindex)`
`int`	`addSGroupAttachmentPoint(int aidx, int lvidx, String apid)`
`void`	`addStereocenter(int type, int v1, int v2, int v3)`
`void`	`addStereocenter(int type, int v1, int v2, int v3, int v4)`
`IndigoObject`	`addSuperatom(Collection<Integer> atoms, String name)`
`IndigoObject`	`addSuperatom(int[] atoms, String name)`
`int`	`addTemplate(IndigoObject templates, String name)`
`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`	`atomIndex()`
`int`	`atomMappingNumber(IndigoObject reaction_atom)`
`void`	`automap()`
`void`	`automap(String mode)`
`String`	`axolabs(IndigoObject library)`
`String`	`b64cdx()`
`String`	`biln(IndigoObject library)`
`IndigoObject`	`bond()`
`int`	`bondBegin()`
`int`	`bondEnd()`
`int`	`bondIndex()`
`int`	`bondOrder()`
`int`	`bondStereo()`
`String`	`canonicalSmarts()`
`String`	`canonicalSmiles()`
`String`	`cdxml()`
`void`	`changeStereocenterType(int type)`
`Integer`	`charge()`
`String`	`check()`
`String`	`check(String type)`
`int`	`check3DStereo()`
`String`	`checkAmbiguousH()`
`String`	`checkBadValence()`
`int`	`checkChirality()`
`int`	`checkQuery()`
`int`	`checkRGroups()`
`boolean`	`checkSalt()` Verifies whether the structure contains a disconnected inorganic component ("salt").
`int`	`checkStereo()`
`int`	`checkValence()`
`void`	`clean2d()`
`void`	`clear()`
`void`	`clearAAM()`
`void`	`clearAlleneCenters()`
`void`	`clearAttachmentPoints()`
`void`	`clearCisTrans()`
`void`	`clearProperties()`
`int`	`clearSGroupCrossBonds()`
`void`	`clearStereocenters()`
`void`	`clearXYZ()`
`IndigoObject`	`clone()`
`void`	`close()`
`String`	`cml()`
`void`	`cmlAppend(IndigoObject item)`
`void`	`cmlFooter()`
`void`	`cmlHeader()`
`IndigoObject`	`component(int index)`
`int`	`componentIndex()`
`int`	`copyRGroups(IndigoObject other)`
`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`	`countRGroups()`
`int`	`countRSites()`
`int`	`countSSSR()`
`int`	`countStereocenters()`
`int`	`countSuperatoms()`
`int`	`createCrossBonds()`
`IndigoObject`	`createEdgeSubmolecule(Collection<Integer> vertices, Collection<Integer> edges)`
`IndigoObject`	`createEdgeSubmolecule(int[] vertices, int[] edges)`
`IndigoObject`	`createSGroup(String type, IndigoObject mapping, String name)`
`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()`
`int`	`deleteSGroupAttachmentPoint(int apidx)`
`String`	`description()`
`IndigoObject`	`destination()`
`void`	`dispose()`
`int`	`expandAbbreviations()`
`IndigoObject`	`expandedMonomersToAtoms()` Converts expanded template atoms (monomers) to regular atoms.
`void`	`expandMonomers()`
`Integer`	`explicitValence()`
`String`	`fasta(IndigoObject library)`
`protected void`	`finalize()`
`IndigoObject`	`findSGroups(String property, String value)`
`int`	`findTemplate(String name)`
`IndigoObject`	`fingerprint()`
`IndigoObject`	`fingerprint(String type)`
`void`	`foldHydrogens()`
`void`	`foldUnfoldHydrogens()`
`float`	`getAcidPkaValue(IndigoObject atom, int level, int min_level)`
`IndigoObject`	`getAtom(int idx)`
`float`	`getBasicPkaValue(IndigoObject atom, int level, int min_level)`
`IndigoObject`	`getBond(int idx)`
`IndigoObject`	`getDataSGroup(int index)`
`IndigoObject`	`getGenericSGroup(int index)`
`Hybridization`	`getHybridization()`
`String`	`getHybridizationStr()`
`Indigo`	`getIndigo()`
`IndigoObject`	`getMolecule(int idx)`
`IndigoObject`	`getMultipleGroup(int index)`
`String`	`getOriginalFormat()`
`String`	`getProperty(String prop)`
`IndigoObject`	`getRepeatingUnit(int index)`
`int`	`getRepeatingUnitConnectivity()`
`String`	`getRepeatingUnitSubscript()`
`int`	`getSGroupAttachmentPointAtomIdx()`
`String`	`getSGroupAttachmentPointLabel()`
`Integer`	`getSGroupAttachmentPointLeaveAtom()`
`String`	`getSGroupClass()`
`float[]`	`getSGroupCoords()`
`int`	`getSGroupDisplayOption()`
`int`	`getSGroupIndex()`
`int`	`getSGroupMultiplier()`
`String`	`getSGroupName()`
`int`	`getSGroupNumCrossBonds()`
`int`	`getSGroupOriginalId()`
`int`	`getSGroupParentId()`
`int`	`getSGroupSeqId()`
`int`	`getSGroupType()`
`IndigoObject`	`getSubmolecule(Collection<Integer> vertices)`
`IndigoObject`	`getSubmolecule(int[] vertices)`
`IndigoObject`	`getSuperatom(int index)`
`String`	`getTemplateAtomClass()`
`String`	`getTGroupAlias()`
`String`	`getTGroupClass()`
`String`	`getTGroupName()`
`String`	`grossFormula()`
`boolean`	`hasCoord()`
`long`	`hash()`
`boolean`	`hasNext()`
`boolean`	`hasProperty(String prop)`
`boolean`	`hasSelection()`
`boolean`	`hasZCoord()`
`String`	`helm(IndigoObject library)`
`void`	`highlight()`
`IndigoObject`	`highlightedTarget()`
`String`	`idt(IndigoObject library)`
`void`	`ignoreAtom(IndigoObject atom)`
`int`	`index()`
`void`	`invertStereo()`
`void`	`ionize(float pH, float pHToll)`
`boolean`	`isChiral()`
`boolean`	`isHighlighted()`
`int`	`isotope()`
`boolean`	`isPossibleFischerProjection(String options)`
`boolean`	`isPseudoatom()`
`boolean`	`isRSite()`
`boolean`	`isSelected()`
`boolean`	`isTemplateAtom()`
`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`	`iterateReactions()`
`IndigoObject`	`iterateRepeatingUnits()`
`IndigoObject`	`iterateRGroupFragments()`
`IndigoObject`	`iterateRGroups()`
`IndigoObject`	`iterateRings(int min_vertices, int max_vertices)`
`IndigoObject`	`iterateRSites()`
`IndigoObject`	`iterateSGroupAttachmentPoints()`
`IndigoObject`	`iterateSGroupCrossBonds()`
`IndigoObject`	`iterateSGroups()`
`IndigoObject`	`iterateSSSR()`
`IndigoObject`	`iterateStereocenters()`
`IndigoObject`	`iterateSubtrees(int min_vertices, int max_vertices)`
`IndigoObject`	`iterateSuperatoms()`
`IndigoObject`	`iterateTGroups()`
`Iterator<IndigoObject>`	`iterator()`
`String`	`json()`
`String`	`layeredCode()`
`void`	`layout()`
`double`	`logP()`
`String`	`macroProperties(float upc, float nac)`
`IndigoObject`	`mapAtom(IndigoObject query_atom)`
`IndigoObject`	`mapBond(IndigoObject query_bond)`
`IndigoObject`	`mapMolecule(IndigoObject query_reaction_molecule)`
`int`	`markEitherCisTrans()`
`int`	`markStereobonds()`
`String`	`massComposition()`
`IndigoObject`	`match(IndigoObject query)`
`byte[]`	`mdlct()`
`IndigoObject`	`merge(IndigoObject other)`
`double`	`molarRefractivity()`
`String`	`molecularFormula()`
`double`	`molecularWeight()`
`String`	`molfile()`
`double`	`monoisotopicMass()`
`String`	`monomerLibrary()`
`double`	`mostAbundantMass()`
`String`	`name()`
`IndigoObject`	`next()`
`boolean`	`normalize()`
`boolean`	`normalize(String options)`
`int`	`numHydrogenBondAcceptors()`
`int`	`numHydrogenBondDonors()`
`int`	`numRotatableBonds()`
`String`	`oneBitsList()`
`void`	`optimize()`
`void`	`optimize(String options)`
`double`	`pKa()`
`String`	`pKaValues()`
`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)`
`int`	`removeTemplate(String name)`
`IndigoObject`	`resetAtom(String symbol)`
`void`	`resetCharge()`
`void`	`resetExplicitValence()`
`void`	`resetIsotope()`
`void`	`resetRadical()`
`void`	`resetStereo()`
`int`	`resetSymmetricCisTrans()`
`int`	`resetSymmetricStereocenters()`
`String`	`rxnfile()`
`void`	`saveCdxml(String filename)`
`void`	`saveCml(String filename)`
`void`	`saveFastaToFile(String filename)`
`void`	`saveMolfile(String filename)`
`void`	`saveRxnfile(String filename)`
`void`	`saveSequence3LetterToFile(String filename, IndigoObject library)`
`void`	`saveSequenceToFile(String filename, IndigoObject library)`
`void`	`sdfAppend(IndigoObject item)`
`void`	`select()`
`String`	`sequence(IndigoObject library)`
`String`	`sequence3Letter(IndigoObject library)`
`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)`
`int`	`setSGroupAtoms(Collection<Integer> atoms)`
`int`	`setSGroupAtoms(int[] atoms)`
`int`	`setSGroupBonds(Collection<Integer> bonds)`
`int`	`setSGroupBonds(int[] bonds)`
`int`	`setSGroupBrackets(int brk_style, float x1, float y1, float x2, float y2, float x3, float y3, float x4, float y4)`
`void`	`setSGroupClass(String sgclass)`
`int`	`setSGroupCoords(float x, float y)`
`int`	`setSGroupData(String data)`
`int`	`setSGroupDataType(String data_type)`
`int`	`setSGroupDescription(String description)`
`int`	`setSGroupDisplay(String option)`
`int`	`setSGroupDisplayOption(int option)`
`int`	`setSGroupFieldName(String name)`
`int`	`setSGroupLocation(String option)`
`int`	`setSGroupMultiplier(int mult)`
`void`	`setSGroupName(String sgname)`
`int`	`setSGroupOriginalId(int original)`
`int`	`setSGroupParentId(int parent)`
`int`	`setSGroupQueryCode(String querycode)`
`int`	`setSGroupQueryOper(String queryoper)`
`int`	`setSGroupTag(String tag)`
`int`	`setSGroupTagAlign(int tag_align)`
`int`	`setSGroupXCoord(float x)`
`int`	`setSGroupYCoord(float y)`
`void`	`setStereocenterGroup(int group)`
`int`	`setTemplateAtomClass(String name)`
`void`	`setXYZ(float[] xyz)`
`void`	`setXYZ(float x, float y, float z)`
`int`	`singleAllowedRGroup()`
`String`	`smarts()`
`String`	`smiles()`
`void`	`smilesAppend(IndigoObject item)`
`IndigoObject`	`source()`
`void`	`standardize()`
`int`	`stereocenterCIPDescriptor()`
`int`	`stereocenterGroup()`
`int[]`	`stereocenterPyramid()`
`int`	`stereocenterType()`
`IndigoObject`	`stripSalt()` Strips all disconnected inorganic components ("salts") from the molecule.
`IndigoObject`	`stripSalt(boolean inplace)` Strips all disconnected inorganic components ("salts") from the molecule.
`String`	`symbol()`
`int[]`	`symmetryClasses()`
`int`	`tell()`
`byte[]`	`toBuffer()`
`int`	`topology()`
`String`	`toString()`
`double`	`tpsa()`
`double`	`tpsa(boolean includeSP)`
`int`	`transformCTABtoSCSR(IndigoObject templates)`
`int`	`transformSCSRtoCTAB()`
`void`	`unfoldHydrogens()`
`void`	`unhighlight()`
`void`	`unignoreAllAtoms()`
`void`	`unignoreAtom(IndigoObject atom)`
`void`	`unselect()`
`int`	`valence()`
`int`	`validateChirality()`
`float[]`	`xyz()`

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

Methods inherited from interface java.util.Iterator
forEachRemaining

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Field Detail

dispatcher
```
protected final Indigo dispatcher
```

lib
```
protected final IndigoLib lib
```

self
```
public int self
```

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()
```

sequence

public String sequence(IndigoObject library)

sequence3Letter

public String sequence3Letter(IndigoObject library)

fasta

public String fasta(IndigoObject library)

idt

public String idt(IndigoObject library)

helm

public String helm(IndigoObject library)

biln

public String biln(IndigoObject library)

axolabs

public String axolabs(IndigoObject library)

macroProperties

public String macroProperties(float upc,
                              float nac)

getOriginalFormat
```
public String getOriginalFormat()
```

saveMolfile

public void saveMolfile(String filename)

saveSequenceToFile

public void saveSequenceToFile(String filename,
                               IndigoObject library)

saveSequence3LetterToFile

public void saveSequence3LetterToFile(String filename,
                                      IndigoObject library)

saveFastaToFile

public void saveFastaToFile(String filename)

cml
```
public String cml()
```

json
```
public String json()
```

monomerLibrary
```
public String monomerLibrary()
```

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

cdxml
```
public String cdxml()
```

b64cdx
```
public String b64cdx()
```

saveCdxml

public void saveCdxml(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()

iterateReactions

public IndigoObject iterateReactions()

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()

countRGroups
```
public int countRGroups()
```

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

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

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

setRSite

public IndigoObject setRSite(String name)

isTemplateAtom
```
public boolean isTemplateAtom()
```

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()
```

getHybridization

public Hybridization getHybridization()

getHybridizationStr
```
public String getHybridizationStr()
```

checkValence
```
public int checkValence()
```

checkQuery
```
public int checkQuery()
```

checkRGroups
```
public int checkRGroups()
```

atomIndex
```
public int atomIndex()
```

bondIndex
```
public int bondIndex()
```

bondBegin
```
public int bondBegin()
```

bondEnd
```
public int bondEnd()
```

checkChirality
```
public int checkChirality()
```

check3DStereo
```
public int check3DStereo()
```

checkStereo
```
public int checkStereo()
```

check
```
public String check()
```

check
```
public String check(String type)
```

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()
```

stereocenterCIPDescriptor

public int stereocenterCIPDescriptor()

addCIPStereoDescriptors
```
public int addCIPStereoDescriptors()
```

addAtom

public IndigoObject addAtom(String symbol)

resetAtom

public IndigoObject resetAtom(String symbol)

addRSite

public IndigoObject addRSite(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()
```

select
```
public void select()
```

unselect
```
public void unselect()
```

isSelected
```
public boolean isSelected()
```

hasSelection
```
public boolean hasSelection()
```

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

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

iterateComponents

public IndigoObject iterateComponents()

component

public IndigoObject component(int index)

checkSalt
```
public boolean checkSalt()
```
Verifies whether the structure contains a disconnected inorganic component ("salt").

Returns:

true if the structure contains a salt

stripSalt
```
public IndigoObject stripSalt()
```
Strips all disconnected inorganic components ("salts") from the molecule.
Returns a copy of the molecule without its inorganic components.

Returns:

a new molecule without inorganic components

stripSalt
```
public IndigoObject stripSalt(boolean inplace)
```
Strips all disconnected inorganic components ("salts") from the molecule.

Parameters:

inplace - if false - returns a copy of the molecule without inorganic components; if true - strips inorganic components from the molecule itself

Returns:

if inplace is false - a new molecule without inorganic components; if inplace is true - this molecule, without inorganic components

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()
```

molecularFormula
```
public String molecularFormula()
```

molecularWeight
```
public double molecularWeight()
```

mostAbundantMass
```
public double mostAbundantMass()
```

monoisotopicMass
```
public double monoisotopicMass()
```

massComposition
```
public String massComposition()
```

tpsa
```
public double tpsa()
```

tpsa

public double tpsa(boolean includeSP)

numRotatableBonds
```
public int numRotatableBonds()
```

numHydrogenBondAcceptors
```
public int numHydrogenBondAcceptors()
```

numHydrogenBondDonors
```
public int numHydrogenBondDonors()
```

logP
```
public double logP()
```

molarRefractivity
```
public double molarRefractivity()
```

pKa
```
public double pKa()
```

pKaValues
```
public String pKaValues()
```

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

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

hash
```
public long hash()
```

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

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

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

isPossibleFischerProjection

public boolean isPossibleFischerProjection(String options)

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()

iterateSGroups
```
public IndigoObject iterateSGroups()
```

iterateTGroups
```
public IndigoObject iterateTGroups()
```

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)

addSuperatom

public IndigoObject addSuperatom(int[] atoms,
                                 String name)

addSuperatom

public IndigoObject addSuperatom(Collection<Integer> atoms,
                                 String name)

createSGroup

public IndigoObject createSGroup(String type,
                                 IndigoObject mapping,
                                 String name)

getSGroupClass
```
public String getSGroupClass()
```

setSGroupClass

public void setSGroupClass(String sgclass)

getSGroupName
```
public String getSGroupName()
```

setSGroupName

public void setSGroupName(String sgname)

getSGroupNumCrossBonds
```
public int getSGroupNumCrossBonds()
```

createCrossBonds
```
public int createCrossBonds()
```

clearSGroupCrossBonds
```
public int clearSGroupCrossBonds()
```

addSGroup

public IndigoObject addSGroup(String type)

addSGroup

public IndigoObject addSGroup(String type,
                              int extindex)

setSGroupAtoms

public int setSGroupAtoms(int[] atoms)

setSGroupAtoms

public int setSGroupAtoms(Collection<Integer> atoms)

setSGroupBonds

public int setSGroupBonds(int[] bonds)

setSGroupBonds

public int setSGroupBonds(Collection<Integer> bonds)

iterateSGroupCrossBonds

public IndigoObject iterateSGroupCrossBonds()

addSGroupAttachmentPoint

public int addSGroupAttachmentPoint(int aidx,
                                    int lvidx,
                                    String apid)

deleteSGroupAttachmentPoint

public int deleteSGroupAttachmentPoint(int apidx)

iterateSGroupAttachmentPoints

public IndigoObject iterateSGroupAttachmentPoints()

getSGroupAttachmentPointAtomIdx

public int getSGroupAttachmentPointAtomIdx()

getSGroupAttachmentPointLeaveAtom

public Integer getSGroupAttachmentPointLeaveAtom()

getSGroupAttachmentPointLabel

public String getSGroupAttachmentPointLabel()

getSGroupDisplayOption
```
public int getSGroupDisplayOption()
```

getSGroupSeqId
```
public int getSGroupSeqId()
```

getSGroupCoords
```
public float[] getSGroupCoords()
```

setSGroupDisplayOption

public int setSGroupDisplayOption(int option)

getRepeatingUnitSubscript

public String getRepeatingUnitSubscript()

getRepeatingUnitConnectivity

public int getRepeatingUnitConnectivity()

getSGroupMultiplier
```
public int getSGroupMultiplier()
```

setSGroupMultiplier

public int setSGroupMultiplier(int mult)

setSGroupData

public int setSGroupData(String data)

setSGroupCoords

public int setSGroupCoords(float x,
                           float y)

setSGroupDescription

public int setSGroupDescription(String description)

setSGroupFieldName

public int setSGroupFieldName(String name)

setSGroupQueryCode

public int setSGroupQueryCode(String querycode)

setSGroupQueryOper

public int setSGroupQueryOper(String queryoper)

setSGroupDisplay

public int setSGroupDisplay(String option)

setSGroupLocation

public int setSGroupLocation(String option)

setSGroupTag
```
public int setSGroupTag(String tag)
```

setSGroupTagAlign

public int setSGroupTagAlign(int tag_align)

setSGroupDataType

public int setSGroupDataType(String data_type)

setSGroupXCoord
```
public int setSGroupXCoord(float x)
```

setSGroupYCoord
```
public int setSGroupYCoord(float y)
```

findSGroups

public IndigoObject findSGroups(String property,
                                String value)

getSGroupType
```
public int getSGroupType()
```

getSGroupIndex
```
public int getSGroupIndex()
```

getSGroupOriginalId
```
public int getSGroupOriginalId()
```

setSGroupOriginalId

public int setSGroupOriginalId(int original)

getSGroupParentId
```
public int getSGroupParentId()
```

setSGroupParentId

public int setSGroupParentId(int parent)

addTemplate

public int addTemplate(IndigoObject templates,
                       String name)

removeTemplate

public int removeTemplate(String name)

findTemplate
```
public int findTemplate(String name)
```

getTGroupClass
```
public String getTGroupClass()
```

getTGroupName
```
public String getTGroupName()
```

getTGroupAlias
```
public String getTGroupAlias()
```

transformSCSRtoCTAB
```
public int transformSCSRtoCTAB()
```

transformCTABtoSCSR

public int transformCTABtoSCSR(IndigoObject templates)

getTemplateAtomClass
```
public String getTemplateAtomClass()
```

setTemplateAtomClass

public int setTemplateAtomClass(String name)

setSGroupBrackets

public int setSGroupBrackets(int brk_style,
                             float x1,
                             float y1,
                             float x2,
                             float y2,
                             float x3,
                             float y3,
                             float x4,
                             float y4)

setDataSGroupXY

public void setDataSGroupXY(float x,
                            float y)

setDataSGroupXY

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

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)

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()
```

foldUnfoldHydrogens
```
public void foldUnfoldHydrogens()
```

expandMonomers
```
public void expandMonomers()
```

clearXYZ
```
public void clearXYZ()
```

layout
```
public void layout()
```

clean2d
```
public void clean2d()
```

smiles
```
public String smiles()
```

smarts
```
public String smarts()
```

canonicalSmarts
```
public String canonicalSmarts()
```

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)

oneBitsList
```
public String oneBitsList()
```

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)

standardize
```
public void standardize()
```

ionize

public void ionize(float pH,
                   float pHToll)

getAcidPkaValue

public float getAcidPkaValue(IndigoObject atom,
                             int level,
                             int min_level)

getBasicPkaValue

public float getBasicPkaValue(IndigoObject atom,
                              int level,
                              int min_level)

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

expandedMonomersToAtoms
```
public IndigoObject expandedMonomersToAtoms()
```
Converts expanded template atoms (monomers) to regular atoms. Returns a new molecule; the original is not modified.

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

copyRGroups

public int copyRGroups(IndigoObject other)

Class IndigoObject

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Iterator

Methods inherited from interface java.lang.Iterable

Field Detail

dispatcher

lib

self

Constructor Detail

IndigoObject

IndigoObject

Method Detail

getIndigo

dispose

finalize

clone

molfile

sequence

sequence3Letter

fasta

idt

helm

biln

axolabs

macroProperties

getOriginalFormat

saveMolfile

saveSequenceToFile

saveSequence3LetterToFile

saveFastaToFile

cml

json

monomerLibrary

saveCml

cdxml

b64cdx

saveCdxml

mdlct

addReactant

addProduct

addCatalyst

countReactants

countProducts

countCatalysts

countMolecules

iterateAttachmentPoints

iterateReactants

iterateProducts

iterateCatalysts

iterateMolecules

iterateReactions

rxnfile

saveRxnfile

automap

automap

atomMappingNumber

setAtomMappingNumber

clearAAM

correctReactingCenters

iterateAtoms

iteratePseudoatoms

iterateRSites

iterateStereocenters

iterateAlleneCenters

iterateRGroups

iterateRGroupFragments

countRGroups

countAttachmentPoints

isPseudoatom

isRSite

setRSite

isTemplateAtom

stereocenterType

stereocenterGroup

stereocenterPyramid

changeStereocenterType

setStereocenterGroup