IndigoLib (Indigo 1.2.1-dev5-moderna API)

All Superinterfaces:: com.sun.jna.Library

public interface IndigoLib
extends com.sun.jna.Library

Nested Class Summary
- Nested classes/interfaces inherited from interface com.sun.jna.Library
  com.sun.jna.Library.Handler

Field Summary
- Fields inherited from interface com.sun.jna.Library
  OPTION_ALLOW_OBJECTS, OPTION_CALLING_CONVENTION, OPTION_FUNCTION_MAPPER, OPTION_INVOCATION_MAPPER, OPTION_OPEN_FLAGS, OPTION_STRUCTURE_ALIGNMENT, OPTION_TYPE_MAPPER

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`indigoAddAtom(int molecule, String symbol)`
`int`	`indigoAddBond(int source, int destination, int order)`
`int`	`indigoAddCatalyst(int reaction, int molecule)`
`int`	`indigoAddConstraint(int item, String type, String value)`
`int`	`indigoAddConstraintNot(int item, String type, String value)`
`int`	`indigoAddConstraintOr(int item, String type, String value)`
`int`	`indigoAddDataSGroup(int molecule, int natoms, int[] atoms, int nbonds, int[] bonds, String description, String data)`
`int`	`indigoAddDecomposition(int decomp, int q_match)`
`int`	`indigoAddProduct(int reaction, int molecule)`
`int`	`indigoAddReactant(int reaction, int molecule)`
`int`	`indigoAddRSite(int molecule, String name)`
`int`	`indigoAddStereocenter(int atom, int type, int v1, int v2, int v3, int v4)`
`float`	`indigoAlignAtoms(int molecule, int natoms, int[] atom_ids, float[] desired_xyz)`
`long`	`indigoAllocSessionId()`
`int`	`indigoAllScaffolds(int extracted)`
`int`	`indigoAppend(int saver, int object)`
`int`	`indigoAromatize(int item)`
`int`	`indigoArrayAdd(int arr, int object)`
`int`	`indigoAt(int item, int index)`
`int`	`indigoAtomicNumber(int atom)`
`int`	`indigoAutomap(int reaction, String mode)`
`int`	`indigoBond(int nei)`
`int`	`indigoBondOrder(int bond)`
`int`	`indigoBondStereo(int bond)`
`com.sun.jna.Pointer`	`indigoCanonicalSmiles(int molecule)`
`int`	`indigoChangeStereocenterType(int atom, int type)`
`com.sun.jna.Pointer`	`indigoCheckAmbiguousH(int handle)`
`com.sun.jna.Pointer`	`indigoCheckBadValence(int handle)`
`int`	`indigoClear(int arr)`
`int`	`indigoClearAAM(int reaction)`
`int`	`indigoClearAlleneCenters(int handle)`
`int`	`indigoClearAttachmentPoints(int item)`
`int`	`indigoClearCisTrans(int handle)`
`int`	`indigoClearProperties(int handle)`
`int`	`indigoClearStereocenters(int handle)`
`int`	`indigoClearTautomerRules()`
`int`	`indigoClone(int handle)`
`int`	`indigoClose(int handle)`
`com.sun.jna.Pointer`	`indigoCml(int object)`
`int`	`indigoCmlAppend(int output, int item)`
`int`	`indigoCmlFooter(int output)`
`int`	`indigoCmlHeader(int output)`
`int`	`indigoCommonBits(int fingerprint1, int fingerprint2)`
`int`	`indigoComponent(int molecule, int index)`
`int`	`indigoComponentIndex(int atom)`
`int`	`indigoCorrectReactingCenters(int reaction)`
`int`	`indigoCount(int item)`
`int`	`indigoCountAlleneCenters(int molecule)`
`int`	`indigoCountAtoms(int molecule)`
`int`	`indigoCountAttachmentPoints(int rgroup)`
`int`	`indigoCountBits(int fingerprint)`
`int`	`indigoCountBonds(int molecule)`
`int`	`indigoCountCatalysts(int reaction)`
`int`	`indigoCountComponents(int molecule)`
`int`	`indigoCountDataSGroups(int molecule)`
`int`	`indigoCountGenericSGroups(int molecule)`
`int`	`indigoCountHeavyAtoms(int molecule)`
`int`	`indigoCountHydrogens(int atom, com.sun.jna.ptr.IntByReference valence)`
`int`	`indigoCountImplicitHydrogens(int item)`
`int`	`indigoCountMatches(int matcher, int query)`
`int`	`indigoCountMatchesWithLimit(int matcher, int query, int embeddings_limit)`
`int`	`indigoCountMolecules(int reaction)`
`int`	`indigoCountMultipleGroups(int molecule)`
`int`	`indigoCountProducts(int reaction)`
`int`	`indigoCountPseudoatoms(int molecule)`
`int`	`indigoCountReactants(int reaction)`
`int`	`indigoCountReferences()`
`int`	`indigoCountRepeatingUnits(int molecule)`
`int`	`indigoCountRSites(int molecule)`
`int`	`indigoCountSSSR(int molecule)`
`int`	`indigoCountStereocenters(int molecule)`
`int`	`indigoCountSuperatoms(int molecule)`
`int`	`indigoCreateArray()`
`int`	`indigoCreateDecomposer(int scaffold)`
`int`	`indigoCreateEdgeSubmolecule(int molecule, int nvertices, int[] vertices, int nedges, int[] edges)`
`int`	`indigoCreateFileSaver(String filename, String format)`
`int`	`indigoCreateMolecule()`
`int`	`indigoCreateQueryMolecule()`
`int`	`indigoCreateQueryReaction()`
`int`	`indigoCreateReaction()`
`int`	`indigoCreateSaver(int output, String format)`
`int`	`indigoCreateSubmolecule(int molecule, int nvertices, int[] vertices)`
`com.sun.jna.Pointer`	`indigoData(int data_sgroup)`
`int`	`indigoDbgBreakpoint()`
`com.sun.jna.Pointer`	`indigoDbgInternalType(int object)`
`int`	`indigoDearomatize(int item)`
`int`	`indigoDecomposedMoleculeHighlighted(int decomp)`
`int`	`indigoDecomposedMoleculeScaffold(int decomp)`
`int`	`indigoDecomposedMoleculeWithRGroups(int decomp)`
`int`	`indigoDecomposeMolecule(int decomp, int mol)`
`int`	`indigoDecomposeMolecules(int scaffold, int structures)`
`int`	`indigoDegree(int atom)`
`com.sun.jna.Pointer`	`indigoDescription(int data_sgroup)`
`int`	`indigoDestination(int bond)`
`int`	`indigoExactMatch(int item1, int item2, String flags)`
`int`	`indigoExpandAbbreviations(int structure)`
`int`	`indigoExtractCommonScaffold(int structures, String options)`
`int`	`indigoFingerprint(int item, String type)`
`int`	`indigoFoldHydrogens(int item)`
`int`	`indigoFree(int handle)`
`int`	`indigoGetAtom(int molecule, int idx)`
`int`	`indigoGetAtomMappingNumber(int reaction, int reaction_atom)`
`int`	`indigoGetBond(int molecule, int idx)`
`int`	`indigoGetCharge(int atom, com.sun.jna.ptr.IntByReference charge)`
`int`	`indigoGetDataSGroup(int molecule, int index)`
`int`	`indigoGetExplicitValence(int atom, com.sun.jna.ptr.IntByReference valence)`
`int`	`indigoGetGenericSGroup(int molecule, int index)`
`String`	`indigoGetLastError()`
`int`	`indigoGetMolecule(int reaction, int idx)`
`int`	`indigoGetMultipleGroup(int molecule, int index)`
`com.sun.jna.Pointer`	`indigoGetProperty(int handle, String prop)`
`int`	`indigoGetRadical(int atom, com.sun.jna.ptr.IntByReference radical)`
`int`	`indigoGetRadicalElectrons(int atom, com.sun.jna.ptr.IntByReference electrons)`
`int`	`indigoGetReactingCenter(int reaction, int reaction_bond, com.sun.jna.ptr.IntByReference rc)`
`int`	`indigoGetRepeatingUnit(int molecule, int index)`
`int`	`indigoGetSubmolecule(int molecule, int nvertices, int[] vertices)`
`int`	`indigoGetSuperatom(int molecule, int index)`
`int`	`indigoGrossFormula(int molecule)`
`int`	`indigoHasCoord(int molecule)`
`int`	`indigoHasNext(int iter)`
`int`	`indigoHasProperty(int handle, String prop)`
`int`	`indigoHasZCoord(int molecule)`
`int`	`indigoHighlight(int atom)`
`int`	`indigoHighlightedTarget(int match)`
`int`	`indigoIgnoreAtom(int matcher, int atom)`
`int`	`indigoIndex(int item)`
`int`	`indigoInvertStereo(int item)`
`int`	`indigoIsChiral(int molecule)`
`int`	`indigoIsHighlighted(int item)`
`int`	`indigoIsotope(int atom)`
`int`	`indigoIsPseudoatom(int atom)`
`int`	`indigoIsRSite(int atom)`
`int`	`indigoIterateAlleneCenters(int molecule)`
`int`	`indigoIterateArray(int arr)`
`int`	`indigoIterateAtoms(int molecule)`
`int`	`indigoIterateAttachmentPoints(int item, int order)`
`int`	`indigoIterateBonds(int molecule)`
`int`	`indigoIterateCatalysts(int reaction)`
`int`	`indigoIterateCML(int reader)`
`int`	`indigoIterateCMLFile(String filename)`
`int`	`indigoIterateComponents(int molecule)`
`int`	`indigoIterateDataSGroups(int molecule)`
`int`	`indigoIterateDecomposedMolecules(int decomp)`
`int`	`indigoIterateDecompositions(int deco_item)`
`int`	`indigoIterateEdgeSubmolecules(int molecule, int min_bonds, int max_bonds)`
`int`	`indigoIterateGenericSGroups(int molecule)`
`int`	`indigoIterateMatches(int matcher, int query)`
`int`	`indigoIterateMolecules(int reaction)`
`int`	`indigoIterateMultipleGroups(int molecule)`
`int`	`indigoIterateNeighbors(int atom)`
`int`	`indigoIterateProducts(int reaction)`
`int`	`indigoIterateProperties(int handle)`
`int`	`indigoIteratePseudoatoms(int molecule)`
`int`	`indigoIterateRDF(int reader)`
`int`	`indigoIterateRDFile(String filename)`
`int`	`indigoIterateReactants(int reaction)`
`int`	`indigoIterateRepeatingUnits(int molecule)`
`int`	`indigoIterateRGroupFragments(int rgroup)`
`int`	`indigoIterateRGroups(int molecule)`
`int`	`indigoIterateRings(int molecule, int min_atoms, int max_atoms)`
`int`	`indigoIterateRSites(int molecule)`
`int`	`indigoIterateSDF(int reader)`
`int`	`indigoIterateSDFile(String filename)`
`int`	`indigoIterateSmiles(int reader)`
`int`	`indigoIterateSmilesFile(String filename)`
`int`	`indigoIterateSSSR(int molecule)`
`int`	`indigoIterateStereocenters(int molecule)`
`int`	`indigoIterateSubtrees(int molecule, int min_atoms, int max_atoms)`
`int`	`indigoIterateSuperatoms(int molecule)`
`com.sun.jna.Pointer`	`indigoLayeredCode(int molecule)`
`int`	`indigoLayout(int object)`
`int`	`indigoLoadBuffer(byte[] buf, int size)`
`int`	`indigoLoadMolecule(int source)`
`int`	`indigoLoadMoleculeFromBuffer(byte[] buffer, int size)`
`int`	`indigoLoadMoleculeFromFile(String filename)`
`int`	`indigoLoadMoleculeFromString(String str)`
`int`	`indigoLoadQueryMolecule(int source)`
`int`	`indigoLoadQueryMoleculeFromBuffer(byte[] buffer, int size)`
`int`	`indigoLoadQueryMoleculeFromFile(String filename)`
`int`	`indigoLoadQueryMoleculeFromString(String str)`
`int`	`indigoLoadQueryReaction(int source)`
`int`	`indigoLoadQueryReactionFromBuffer(byte[] buf, int size)`
`int`	`indigoLoadQueryReactionFromFile(String filename)`
`int`	`indigoLoadQueryReactionFromString(String str)`
`int`	`indigoLoadReaction(int source)`
`int`	`indigoLoadReactionFromBuffer(byte[] buf, int size)`
`int`	`indigoLoadReactionFromFile(String filename)`
`int`	`indigoLoadReactionFromString(String string)`
`int`	`indigoLoadReactionSmarts(int source)`
`int`	`indigoLoadReactionSmartsFromBuffer(byte[] buf, int size)`
`int`	`indigoLoadReactionSmartsFromFile(String filename)`
`int`	`indigoLoadReactionSmartsFromString(String str)`
`int`	`indigoLoadSmarts(int source)`
`int`	`indigoLoadSmartsFromBuffer(byte[] buffer, int size)`
`int`	`indigoLoadSmartsFromFile(String filename)`
`int`	`indigoLoadSmartsFromString(String str)`
`int`	`indigoLoadString(String str)`
`int`	`indigoMapAtom(int match, int query_atom)`
`int`	`indigoMapBond(int match, int query_bond)`
`int`	`indigoMapMolecule(int match, int query_reaction_molecule)`
`int`	`indigoMarkEitherCisTrans(int handle)`
`int`	`indigoMarkStereobonds(int handle)`
`int`	`indigoMatch(int matcher, int query)`
`int`	`indigoMerge(int where_to, int what)`
`float`	`indigoMolecularWeight(int molecule)`
`com.sun.jna.Pointer`	`indigoMolfile(int molecule)`
`float`	`indigoMonoisotopicMass(int molecule)`
`float`	`indigoMostAbundantMass(int molecule)`
`com.sun.jna.Pointer`	`indigoName(int handle)`
`int`	`indigoNext(int iter)`
`int`	`indigoNormalize(int structure, String options)`
`int`	`indigoOptimize(int query, String options)`
`com.sun.jna.Pointer`	`indigoRawData(int item)`
`int`	`indigoRdfAppend(int output, int item)`
`int`	`indigoRdfHeader(int output)`
`int`	`indigoReactionProductEnumerate(int reaction, int monomers)`
`int`	`indigoReadFile(String filename)`
`void`	`indigoReleaseSessionId(long id)`
`int`	`indigoRemove(int item)`
`int`	`indigoRemoveAtoms(int molecule, int nvertices, int[] vertices)`
`int`	`indigoRemoveBonds(int molecule, int nbonds, int[] bonds)`
`int`	`indigoRemoveConstraints(int item, String type)`
`int`	`indigoRemoveProperty(int item, String prop)`
`int`	`indigoRemoveTautomerRule(int id)`
`int`	`indigoResetAtom(int atom, String symbol)`
`int`	`indigoResetCharge(int atom)`
`int`	`indigoResetExplicitValence(int atom)`
`int`	`indigoResetIsotope(int atom)`
`int`	`indigoResetRadical(int atom)`
`int`	`indigoResetStereo(int item)`
`int`	`indigoResetSymmetricCisTrans(int handle)`
`int`	`indigoResetSymmetricStereocenters(int handle)`
`com.sun.jna.Pointer`	`indigoRxnfile(int reaction)`
`int`	`indigoSaveCml(int object, int output)`
`int`	`indigoSaveCmlToFile(int object, String filename)`
`int`	`indigoSaveMDLCT(int item, int output)`
`int`	`indigoSaveMolfile(int molecule, int output)`
`int`	`indigoSaveMolfileToFile(int molecule, String filename)`
`int`	`indigoSaveRxnfile(int reaction, int output)`
`int`	`indigoSaveRxnfileToFile(int reaction, String filename)`
`int`	`indigoSdfAppend(int output, int item)`
`int`	`indigoSerialize(int handle, com.sun.jna.ptr.PointerByReference buf, com.sun.jna.ptr.IntByReference size)`
`int`	`indigoSetAtomMappingNumber(int reaction, int reaction_atom, int number)`
`int`	`indigoSetAttachmentPoint(int atom, int order)`
`int`	`indigoSetBondOrder(int bond, int order)`
`int`	`indigoSetCharge(int atom, int charge)`
`int`	`indigoSetDataSGroupXY(int sgroup, float x, float y, String options)`
`int`	`indigoSetExplicitValence(int atom, int valence)`
`int`	`indigoSetImplicitHCount(int atom, int impl_h)`
`int`	`indigoSetIsotope(int atom, int isotope)`
`int`	`indigoSetName(int handle, String name)`
`int`	`indigoSetOption(String name, String value)`
`int`	`indigoSetOptionBool(String name, int value)`
`int`	`indigoSetOptionColor(String name, float r, float g, float b)`
`int`	`indigoSetOptionFloat(String name, float value)`
`int`	`indigoSetOptionInt(String name, int value)`
`int`	`indigoSetOptionXY(String name, int x, int y)`
`int`	`indigoSetProperty(int item, String prop, String value)`
`int`	`indigoSetRadical(int atom, int radical)`
`int`	`indigoSetReactingCenter(int reaction, int reaction_bond, int rc)`
`int`	`indigoSetRSite(int atom, String name)`
`void`	`indigoSetSessionId(long id)`
`int`	`indigoSetStereocenterGroup(int atom, int group)`
`int`	`indigoSetTautomerRule(int id, String beg, String end)`
`int`	`indigoSetXYZ(int atom, float x, float y, float z)`
`float`	`indigoSimilarity(int item1, int item2, String metrics)`
`int`	`indigoSingleAllowedRGroup(int rsite)`
`com.sun.jna.Pointer`	`indigoSmiles(int item)`
`int`	`indigoSmilesAppend(int output, int item)`
`int`	`indigoSource(int bond)`
`int`	`indigoStereocenterGroup(int atom)`
`com.sun.jna.Pointer`	`indigoStereocenterPyramid(int atom)`
`int`	`indigoStereocenterType(int atom)`
`int`	`indigoSubstructureMatcher(int target, String mode)`
`com.sun.jna.Pointer`	`indigoSymbol(int atom)`
`com.sun.jna.Pointer`	`indigoSymmetryClasses(int molecule, com.sun.jna.ptr.IntByReference count)`
`int`	`indigoTell(int handle)`
`int`	`indigoToBuffer(int handle, com.sun.jna.ptr.PointerByReference buf, com.sun.jna.ptr.IntByReference size)`
`int`	`indigoTopology(int bond)`
`com.sun.jna.Pointer`	`indigoToString(int handle)`
`int`	`indigoTransform(int reaction, int monomers)`
`int`	`indigoUnfoldHydrogens(int item)`
`int`	`indigoUnhighlight(int item)`
`int`	`indigoUnignoreAllAtoms(int matcher)`
`int`	`indigoUnignoreAtom(int matcher, int atom)`
`int`	`indigoUnserialize(byte[] buf, int size)`
`int`	`indigoValence(int atom)`
`int`	`indigoValidateChirality(int handle)`
`String`	`indigoVersion()`
`int`	`indigoWriteBuffer()`
`int`	`indigoWriteFile(String filename)`
`com.sun.jna.Pointer`	`indigoXYZ(int atom)`

Method Detail

indigoVersion
```
String indigoVersion()
```

indigoAllocSessionId
```
long indigoAllocSessionId()
```

indigoSetSessionId
```
void indigoSetSessionId(long id)
```

indigoReleaseSessionId
```
void indigoReleaseSessionId(long id)
```

indigoGetLastError
```
String indigoGetLastError()
```

indigoFree
```
int indigoFree(int handle)
```

indigoClone
```
int indigoClone(int handle)
```

indigoCountReferences
```
int indigoCountReferences()
```

indigoSetOption

int indigoSetOption(String name,
                  String value)

indigoSetOptionInt

int indigoSetOptionInt(String name,
                     int value)

indigoSetOptionBool

int indigoSetOptionBool(String name,
                      int value)

indigoSetOptionFloat

int indigoSetOptionFloat(String name,
                       float value)

indigoSetOptionColor

int indigoSetOptionColor(String name,
                       float r,
                       float g,
                       float b)

indigoSetOptionXY

int indigoSetOptionXY(String name,
                    int x,
                    int y)

indigoReadFile
```
int indigoReadFile(String filename)
```

indigoLoadString
```
int indigoLoadString(String str)
```

indigoLoadBuffer

int indigoLoadBuffer(byte[] buf,
                   int size)

indigoWriteFile
```
int indigoWriteFile(String filename)
```

indigoWriteBuffer
```
int indigoWriteBuffer()
```

indigoClose
```
int indigoClose(int handle)
```

indigoNext
```
int indigoNext(int iter)
```

indigoHasNext
```
int indigoHasNext(int iter)
```

indigoIndex
```
int indigoIndex(int item)
```

indigoRemove
```
int indigoRemove(int item)
```

indigoCreateMolecule
```
int indigoCreateMolecule()
```

indigoCreateQueryMolecule
```
int indigoCreateQueryMolecule()
```

indigoLoadMolecule
```
int indigoLoadMolecule(int source)
```

indigoLoadMoleculeFromString

int indigoLoadMoleculeFromString(String str)

indigoLoadMoleculeFromFile

int indigoLoadMoleculeFromFile(String filename)

indigoLoadMoleculeFromBuffer

int indigoLoadMoleculeFromBuffer(byte[] buffer,
                               int size)

indigoLoadQueryMolecule

int indigoLoadQueryMolecule(int source)

indigoLoadQueryMoleculeFromString

int indigoLoadQueryMoleculeFromString(String str)

indigoLoadQueryMoleculeFromFile

int indigoLoadQueryMoleculeFromFile(String filename)

indigoLoadQueryMoleculeFromBuffer

int indigoLoadQueryMoleculeFromBuffer(byte[] buffer,
                                    int size)

indigoLoadSmarts
```
int indigoLoadSmarts(int source)
```

indigoLoadSmartsFromString

int indigoLoadSmartsFromString(String str)

indigoLoadSmartsFromFile

int indigoLoadSmartsFromFile(String filename)

indigoLoadSmartsFromBuffer

int indigoLoadSmartsFromBuffer(byte[] buffer,
                             int size)

indigoSaveMolfile

int indigoSaveMolfile(int molecule,
                    int output)

indigoSaveMolfileToFile

int indigoSaveMolfileToFile(int molecule,
                          String filename)

indigoMolfile

com.sun.jna.Pointer indigoMolfile(int molecule)

indigoSaveCml

int indigoSaveCml(int object,
                int output)

indigoSaveCmlToFile

int indigoSaveCmlToFile(int object,
                      String filename)

indigoCml

com.sun.jna.Pointer indigoCml(int object)

indigoSaveMDLCT

int indigoSaveMDLCT(int item,
                  int output)

indigoLoadReaction
```
int indigoLoadReaction(int source)
```

indigoLoadReactionFromString

int indigoLoadReactionFromString(String string)

indigoLoadReactionFromFile

int indigoLoadReactionFromFile(String filename)

indigoLoadReactionFromBuffer

int indigoLoadReactionFromBuffer(byte[] buf,
                               int size)

indigoLoadQueryReaction

int indigoLoadQueryReaction(int source)

indigoLoadQueryReactionFromString

int indigoLoadQueryReactionFromString(String str)

indigoLoadQueryReactionFromFile

int indigoLoadQueryReactionFromFile(String filename)

indigoLoadQueryReactionFromBuffer

int indigoLoadQueryReactionFromBuffer(byte[] buf,
                                    int size)

indigoLoadReactionSmarts

int indigoLoadReactionSmarts(int source)

indigoLoadReactionSmartsFromString

int indigoLoadReactionSmartsFromString(String str)

indigoLoadReactionSmartsFromFile

int indigoLoadReactionSmartsFromFile(String filename)

indigoLoadReactionSmartsFromBuffer

int indigoLoadReactionSmartsFromBuffer(byte[] buf,
                                     int size)

indigoCreateReaction
```
int indigoCreateReaction()
```

indigoCreateQueryReaction
```
int indigoCreateQueryReaction()
```

indigoAddReactant

int indigoAddReactant(int reaction,
                    int molecule)

indigoAddProduct

int indigoAddProduct(int reaction,
                   int molecule)

indigoAddCatalyst

int indigoAddCatalyst(int reaction,
                    int molecule)

indigoCountReactants

int indigoCountReactants(int reaction)

indigoCountProducts
```
int indigoCountProducts(int reaction)
```

indigoCountCatalysts

int indigoCountCatalysts(int reaction)

indigoCountMolecules

int indigoCountMolecules(int reaction)

indigoIterateReactants

int indigoIterateReactants(int reaction)

indigoIterateProducts

int indigoIterateProducts(int reaction)

indigoIterateCatalysts

int indigoIterateCatalysts(int reaction)

indigoIterateMolecules

int indigoIterateMolecules(int reaction)

indigoSaveRxnfile

int indigoSaveRxnfile(int reaction,
                    int output)

indigoSaveRxnfileToFile

int indigoSaveRxnfileToFile(int reaction,
                          String filename)

indigoRxnfile

com.sun.jna.Pointer indigoRxnfile(int reaction)

indigoOptimize

int indigoOptimize(int query,
                 String options)

indigoNormalize

int indigoNormalize(int structure,
                  String options)

indigoAutomap

int indigoAutomap(int reaction,
                String mode)

indigoGetAtomMappingNumber

int indigoGetAtomMappingNumber(int reaction,
                             int reaction_atom)

indigoSetAtomMappingNumber

int indigoSetAtomMappingNumber(int reaction,
                             int reaction_atom,
                             int number)

indigoClearAAM
```
int indigoClearAAM(int reaction)
```

indigoCorrectReactingCenters

int indigoCorrectReactingCenters(int reaction)

indigoIterateAtoms
```
int indigoIterateAtoms(int molecule)
```

indigoIteratePseudoatoms

int indigoIteratePseudoatoms(int molecule)

indigoIterateRSites
```
int indigoIterateRSites(int molecule)
```

indigoIterateStereocenters

int indigoIterateStereocenters(int molecule)

indigoIterateAlleneCenters

int indigoIterateAlleneCenters(int molecule)

indigoIterateRGroups

int indigoIterateRGroups(int molecule)

indigoIsPseudoatom
```
int indigoIsPseudoatom(int atom)
```

indigoIsRSite
```
int indigoIsRSite(int atom)
```

indigoStereocenterType
```
int indigoStereocenterType(int atom)
```

indigoStereocenterGroup
```
int indigoStereocenterGroup(int atom)
```

indigoStereocenterPyramid

com.sun.jna.Pointer indigoStereocenterPyramid(int atom)

indigoSetStereocenterGroup

int indigoSetStereocenterGroup(int atom,
                             int group)

indigoChangeStereocenterType

int indigoChangeStereocenterType(int atom,
                               int type)

indigoSingleAllowedRGroup

int indigoSingleAllowedRGroup(int rsite)

indigoAddStereocenter

int indigoAddStereocenter(int atom,
                        int type,
                        int v1,
                        int v2,
                        int v3,
                        int v4)

indigoIterateRGroupFragments

int indigoIterateRGroupFragments(int rgroup)

indigoCountAttachmentPoints

int indigoCountAttachmentPoints(int rgroup)

indigoSymbol

com.sun.jna.Pointer indigoSymbol(int atom)

indigoDegree
```
int indigoDegree(int atom)
```

indigoGetCharge

int indigoGetCharge(int atom,
                  com.sun.jna.ptr.IntByReference charge)

indigoGetRadical

int indigoGetRadical(int atom,
                   com.sun.jna.ptr.IntByReference radical)

indigoGetExplicitValence

int indigoGetExplicitValence(int atom,
                           com.sun.jna.ptr.IntByReference valence)

indigoGetRadicalElectrons

int indigoGetRadicalElectrons(int atom,
                            com.sun.jna.ptr.IntByReference electrons)

indigoAtomicNumber
```
int indigoAtomicNumber(int atom)
```

indigoIsotope
```
int indigoIsotope(int atom)
```

indigoValence
```
int indigoValence(int atom)
```

indigoCountHydrogens

int indigoCountHydrogens(int atom,
                       com.sun.jna.ptr.IntByReference valence)

indigoCountImplicitHydrogens

int indigoCountImplicitHydrogens(int item)

indigoGetReactingCenter

int indigoGetReactingCenter(int reaction,
                          int reaction_bond,
                          com.sun.jna.ptr.IntByReference rc)

indigoSetReactingCenter

int indigoSetReactingCenter(int reaction,
                          int reaction_bond,
                          int rc)

indigoXYZ

com.sun.jna.Pointer indigoXYZ(int atom)

indigoSetXYZ

int indigoSetXYZ(int atom,
               float x,
               float y,
               float z)

indigoCountSuperatoms

int indigoCountSuperatoms(int molecule)

indigoCountDataSGroups

int indigoCountDataSGroups(int molecule)

indigoCountRepeatingUnits

int indigoCountRepeatingUnits(int molecule)

indigoCountMultipleGroups

int indigoCountMultipleGroups(int molecule)

indigoCountGenericSGroups

int indigoCountGenericSGroups(int molecule)

indigoIterateDataSGroups

int indigoIterateDataSGroups(int molecule)

indigoIterateSuperatoms

int indigoIterateSuperatoms(int molecule)

indigoIterateGenericSGroups

int indigoIterateGenericSGroups(int molecule)

indigoIterateRepeatingUnits

int indigoIterateRepeatingUnits(int molecule)

indigoIterateMultipleGroups

int indigoIterateMultipleGroups(int molecule)

indigoGetSuperatom

int indigoGetSuperatom(int molecule,
                     int index)

indigoGetDataSGroup

int indigoGetDataSGroup(int molecule,
                      int index)

indigoGetGenericSGroup

int indigoGetGenericSGroup(int molecule,
                         int index)

indigoGetMultipleGroup

int indigoGetMultipleGroup(int molecule,
                         int index)

indigoGetRepeatingUnit

int indigoGetRepeatingUnit(int molecule,
                         int index)

indigoDescription

com.sun.jna.Pointer indigoDescription(int data_sgroup)

indigoData

com.sun.jna.Pointer indigoData(int data_sgroup)

indigoAddDataSGroup

int indigoAddDataSGroup(int molecule,
                      int natoms,
                      int[] atoms,
                      int nbonds,
                      int[] bonds,
                      String description,
                      String data)

indigoSetDataSGroupXY

int indigoSetDataSGroupXY(int sgroup,
                        float x,
                        float y,
                        String options)

indigoResetCharge
```
int indigoResetCharge(int atom)
```

indigoResetExplicitValence

int indigoResetExplicitValence(int atom)

indigoResetRadical
```
int indigoResetRadical(int atom)
```

indigoResetIsotope
```
int indigoResetIsotope(int atom)
```

indigoSetAttachmentPoint

int indigoSetAttachmentPoint(int atom,
                           int order)

indigoClearAttachmentPoints

int indigoClearAttachmentPoints(int item)

indigoIterateAttachmentPoints

int indigoIterateAttachmentPoints(int item,
                                int order)

indigoRemoveConstraints

int indigoRemoveConstraints(int item,
                          String type)

indigoAddConstraint

int indigoAddConstraint(int item,
                      String type,
                      String value)

indigoAddConstraintNot

int indigoAddConstraintNot(int item,
                         String type,
                         String value)

indigoAddConstraintOr

int indigoAddConstraintOr(int item,
                        String type,
                        String value)

indigoResetStereo
```
int indigoResetStereo(int item)
```

indigoInvertStereo
```
int indigoInvertStereo(int item)
```

indigoCountAtoms
```
int indigoCountAtoms(int molecule)
```

indigoCountBonds
```
int indigoCountBonds(int molecule)
```

indigoCountPseudoatoms

int indigoCountPseudoatoms(int molecule)

indigoCountRSites
```
int indigoCountRSites(int molecule)
```

indigoIterateBonds
```
int indigoIterateBonds(int molecule)
```

indigoBondOrder
```
int indigoBondOrder(int bond)
```

indigoBondStereo
```
int indigoBondStereo(int bond)
```

indigoTopology
```
int indigoTopology(int bond)
```

indigoIterateNeighbors
```
int indigoIterateNeighbors(int atom)
```

indigoBond
```
int indigoBond(int nei)
```

indigoGetAtom

int indigoGetAtom(int molecule,
                int idx)

indigoGetBond

int indigoGetBond(int molecule,
                int idx)

indigoGetMolecule

int indigoGetMolecule(int reaction,
                    int idx)

indigoSource
```
int indigoSource(int bond)
```

indigoDestination
```
int indigoDestination(int bond)
```

indigoClearCisTrans
```
int indigoClearCisTrans(int handle)
```

indigoClearStereocenters

int indigoClearStereocenters(int handle)

indigoClearAlleneCenters

int indigoClearAlleneCenters(int handle)

indigoCountStereocenters

int indigoCountStereocenters(int molecule)

indigoCountAlleneCenters

int indigoCountAlleneCenters(int molecule)

indigoResetSymmetricCisTrans

int indigoResetSymmetricCisTrans(int handle)

indigoResetSymmetricStereocenters

int indigoResetSymmetricStereocenters(int handle)

indigoMarkEitherCisTrans

int indigoMarkEitherCisTrans(int handle)

indigoMarkStereobonds
```
int indigoMarkStereobonds(int handle)
```

indigoValidateChirality

int indigoValidateChirality(int handle)

indigoAddAtom

int indigoAddAtom(int molecule,
                String symbol)

indigoResetAtom

int indigoResetAtom(int atom,
                  String symbol)

indigoAddRSite

int indigoAddRSite(int molecule,
                 String name)

indigoSetRSite

int indigoSetRSite(int atom,
                 String name)

indigoSetCharge

int indigoSetCharge(int atom,
                  int charge)

indigoSetExplicitValence

int indigoSetExplicitValence(int atom,
                           int valence)

indigoSetIsotope

int indigoSetIsotope(int atom,
                   int isotope)

indigoSetImplicitHCount

int indigoSetImplicitHCount(int atom,
                          int impl_h)

indigoSetRadical

int indigoSetRadical(int atom,
                   int radical)

indigoAddBond

int indigoAddBond(int source,
                int destination,
                int order)

indigoSetBondOrder

int indigoSetBondOrder(int bond,
                     int order)

indigoMerge

int indigoMerge(int where_to,
              int what)

indigoHighlight
```
int indigoHighlight(int atom)
```

indigoUnhighlight
```
int indigoUnhighlight(int item)
```

indigoIsHighlighted
```
int indigoIsHighlighted(int item)
```

indigoCountComponents

int indigoCountComponents(int molecule)

indigoComponentIndex
```
int indigoComponentIndex(int atom)
```

indigoIterateComponents

int indigoIterateComponents(int molecule)

indigoComponent

int indigoComponent(int molecule,
                  int index)

indigoCountSSSR
```
int indigoCountSSSR(int molecule)
```

indigoIterateSSSR
```
int indigoIterateSSSR(int molecule)
```

indigoIterateSubtrees

int indigoIterateSubtrees(int molecule,
                        int min_atoms,
                        int max_atoms)

indigoIterateRings

int indigoIterateRings(int molecule,
                     int min_atoms,
                     int max_atoms)

indigoIterateEdgeSubmolecules

int indigoIterateEdgeSubmolecules(int molecule,
                                int min_bonds,
                                int max_bonds)

indigoCountHeavyAtoms

int indigoCountHeavyAtoms(int molecule)

indigoGrossFormula
```
int indigoGrossFormula(int molecule)
```

indigoMolecularWeight

float indigoMolecularWeight(int molecule)

indigoMostAbundantMass

float indigoMostAbundantMass(int molecule)

indigoMonoisotopicMass

float indigoMonoisotopicMass(int molecule)

indigoCanonicalSmiles

com.sun.jna.Pointer indigoCanonicalSmiles(int molecule)

indigoLayeredCode

com.sun.jna.Pointer indigoLayeredCode(int molecule)

indigoSymmetryClasses

com.sun.jna.Pointer indigoSymmetryClasses(int molecule,
                                        com.sun.jna.ptr.IntByReference count)

indigoHasCoord
```
int indigoHasCoord(int molecule)
```

indigoHasZCoord
```
int indigoHasZCoord(int molecule)
```

indigoIsChiral
```
int indigoIsChiral(int molecule)
```

indigoCreateSubmolecule

int indigoCreateSubmolecule(int molecule,
                          int nvertices,
                          int[] vertices)

indigoGetSubmolecule

int indigoGetSubmolecule(int molecule,
                       int nvertices,
                       int[] vertices)

indigoCreateEdgeSubmolecule

int indigoCreateEdgeSubmolecule(int molecule,
                              int nvertices,
                              int[] vertices,
                              int nedges,
                              int[] edges)

indigoRemoveAtoms

int indigoRemoveAtoms(int molecule,
                    int nvertices,
                    int[] vertices)

indigoRemoveBonds

int indigoRemoveBonds(int molecule,
                    int nbonds,
                    int[] bonds)

indigoAlignAtoms

float indigoAlignAtoms(int molecule,
                     int natoms,
                     int[] atom_ids,
                     float[] desired_xyz)

indigoAromatize
```
int indigoAromatize(int item)
```

indigoDearomatize
```
int indigoDearomatize(int item)
```

indigoFoldHydrogens
```
int indigoFoldHydrogens(int item)
```

indigoUnfoldHydrogens
```
int indigoUnfoldHydrogens(int item)
```

indigoLayout
```
int indigoLayout(int object)
```

indigoSmiles

com.sun.jna.Pointer indigoSmiles(int item)

indigoExactMatch

int indigoExactMatch(int item1,
                   int item2,
                   String flags)

indigoSetTautomerRule

int indigoSetTautomerRule(int id,
                        String beg,
                        String end)

indigoRemoveTautomerRule
```
int indigoRemoveTautomerRule(int id)
```

indigoClearTautomerRules
```
int indigoClearTautomerRules()
```

indigoName

com.sun.jna.Pointer indigoName(int handle)

indigoSetName

int indigoSetName(int handle,
                String name)

indigoSerialize

int indigoSerialize(int handle,
                  com.sun.jna.ptr.PointerByReference buf,
                  com.sun.jna.ptr.IntByReference size)

indigoUnserialize

int indigoUnserialize(byte[] buf,
                    int size)

indigoHasProperty

int indigoHasProperty(int handle,
                    String prop)

indigoGetProperty

com.sun.jna.Pointer indigoGetProperty(int handle,
                                    String prop)

indigoSetProperty

int indigoSetProperty(int item,
                    String prop,
                    String value)

indigoRemoveProperty

int indigoRemoveProperty(int item,
                       String prop)

indigoIterateProperties

int indigoIterateProperties(int handle)

indigoClearProperties
```
int indigoClearProperties(int handle)
```

indigoCheckBadValence

com.sun.jna.Pointer indigoCheckBadValence(int handle)

indigoCheckAmbiguousH

com.sun.jna.Pointer indigoCheckAmbiguousH(int handle)

indigoFingerprint

int indigoFingerprint(int item,
                    String type)

indigoCountBits
```
int indigoCountBits(int fingerprint)
```

indigoCommonBits

int indigoCommonBits(int fingerprint1,
                   int fingerprint2)

indigoSimilarity

float indigoSimilarity(int item1,
                     int item2,
                     String metrics)

indigoIterateSDF
```
int indigoIterateSDF(int reader)
```

indigoIterateRDF
```
int indigoIterateRDF(int reader)
```

indigoIterateSmiles
```
int indigoIterateSmiles(int reader)
```

indigoIterateCML
```
int indigoIterateCML(int reader)
```

indigoIterateSDFile

int indigoIterateSDFile(String filename)

indigoIterateRDFile

int indigoIterateRDFile(String filename)

indigoIterateSmilesFile

int indigoIterateSmilesFile(String filename)

indigoIterateCMLFile

int indigoIterateCMLFile(String filename)

indigoRawData

com.sun.jna.Pointer indigoRawData(int item)

indigoTell
```
int indigoTell(int handle)
```

indigoSdfAppend

int indigoSdfAppend(int output,
                  int item)

indigoSmilesAppend

int indigoSmilesAppend(int output,
                     int item)

indigoRdfHeader
```
int indigoRdfHeader(int output)
```

indigoRdfAppend

int indigoRdfAppend(int output,
                  int item)

indigoCmlHeader
```
int indigoCmlHeader(int output)
```

indigoCmlAppend

int indigoCmlAppend(int output,
                  int item)

indigoCmlFooter
```
int indigoCmlFooter(int output)
```

indigoCreateSaver

int indigoCreateSaver(int output,
                    String format)

indigoCreateFileSaver

int indigoCreateFileSaver(String filename,
                        String format)

indigoAppend

int indigoAppend(int saver,
               int object)

indigoCreateArray
```
int indigoCreateArray()
```

indigoArrayAdd

int indigoArrayAdd(int arr,
                 int object)

indigoAt

int indigoAt(int item,
           int index)

indigoCount
```
int indigoCount(int item)
```

indigoClear
```
int indigoClear(int arr)
```

indigoIterateArray
```
int indigoIterateArray(int arr)
```

indigoSubstructureMatcher

int indigoSubstructureMatcher(int target,
                            String mode)

indigoIgnoreAtom

int indigoIgnoreAtom(int matcher,
                   int atom)

indigoUnignoreAtom

int indigoUnignoreAtom(int matcher,
                     int atom)

indigoUnignoreAllAtoms

int indigoUnignoreAllAtoms(int matcher)

indigoMatch

int indigoMatch(int matcher,
              int query)

indigoCountMatches

int indigoCountMatches(int matcher,
                     int query)

indigoCountMatchesWithLimit

int indigoCountMatchesWithLimit(int matcher,
                              int query,
                              int embeddings_limit)

indigoIterateMatches

int indigoIterateMatches(int matcher,
                       int query)

indigoHighlightedTarget

int indigoHighlightedTarget(int match)

indigoMapAtom

int indigoMapAtom(int match,
                int query_atom)

indigoMapBond

int indigoMapBond(int match,
                int query_bond)

indigoMapMolecule

int indigoMapMolecule(int match,
                    int query_reaction_molecule)

indigoExtractCommonScaffold

int indigoExtractCommonScaffold(int structures,
                              String options)

indigoAllScaffolds
```
int indigoAllScaffolds(int extracted)
```

indigoDecomposeMolecules

int indigoDecomposeMolecules(int scaffold,
                           int structures)

indigoDecomposedMoleculeScaffold

int indigoDecomposedMoleculeScaffold(int decomp)

indigoIterateDecomposedMolecules

int indigoIterateDecomposedMolecules(int decomp)

indigoDecomposedMoleculeHighlighted

int indigoDecomposedMoleculeHighlighted(int decomp)

indigoDecomposedMoleculeWithRGroups

int indigoDecomposedMoleculeWithRGroups(int decomp)

indigoCreateDecomposer

int indigoCreateDecomposer(int scaffold)

indigoDecomposeMolecule

int indigoDecomposeMolecule(int decomp,
                          int mol)

indigoIterateDecompositions

int indigoIterateDecompositions(int deco_item)

indigoAddDecomposition

int indigoAddDecomposition(int decomp,
                         int q_match)

indigoToString

com.sun.jna.Pointer indigoToString(int handle)

indigoToBuffer

int indigoToBuffer(int handle,
                 com.sun.jna.ptr.PointerByReference buf,
                 com.sun.jna.ptr.IntByReference size)

indigoReactionProductEnumerate

int indigoReactionProductEnumerate(int reaction,
                                 int monomers)

indigoTransform

int indigoTransform(int reaction,
                  int monomers)

indigoExpandAbbreviations

int indigoExpandAbbreviations(int structure)

indigoDbgBreakpoint
```
int indigoDbgBreakpoint()
```

indigoDbgInternalType

com.sun.jna.Pointer indigoDbgInternalType(int object)

Interface IndigoLib

Nested Class Summary

Nested classes/interfaces inherited from interface com.sun.jna.Library

Field Summary

Fields inherited from interface com.sun.jna.Library

Method Summary

Method Detail

indigoVersion

indigoAllocSessionId

indigoSetSessionId

indigoReleaseSessionId

indigoGetLastError

indigoFree

indigoClone

indigoCountReferences

indigoSetOption

indigoSetOptionInt

indigoSetOptionBool

indigoSetOptionFloat

indigoSetOptionColor

indigoSetOptionXY

indigoReadFile

indigoLoadString

indigoLoadBuffer

indigoWriteFile

indigoWriteBuffer

indigoClose

indigoNext

indigoHasNext

indigoIndex

indigoRemove

indigoCreateMolecule

indigoCreateQueryMolecule

indigoLoadMolecule

indigoLoadMoleculeFromString

indigoLoadMoleculeFromFile

indigoLoadMoleculeFromBuffer

indigoLoadQueryMolecule

indigoLoadQueryMoleculeFromString

indigoLoadQueryMoleculeFromFile

indigoLoadQueryMoleculeFromBuffer

indigoLoadSmarts

indigoLoadSmartsFromString

indigoLoadSmartsFromFile

indigoLoadSmartsFromBuffer

indigoSaveMolfile

indigoSaveMolfileToFile

indigoMolfile

indigoSaveCml

indigoSaveCmlToFile

indigoCml

indigoSaveMDLCT

indigoLoadReaction

indigoLoadReactionFromString

indigoLoadReactionFromFile

indigoLoadReactionFromBuffer

indigoLoadQueryReaction

indigoLoadQueryReactionFromString

indigoLoadQueryReactionFromFile

indigoLoadQueryReactionFromBuffer

indigoLoadReactionSmarts

indigoLoadReactionSmartsFromString

indigoLoadReactionSmartsFromFile

indigoLoadReactionSmartsFromBuffer

indigoCreateReaction

indigoCreateQueryReaction

indigoAddReactant

indigoAddProduct

indigoAddCatalyst

indigoCountReactants

indigoCountProducts

indigoCountCatalysts

indigoCountMolecules

indigoIterateReactants

indigoIterateProducts

indigoIterateCatalysts

indigoIterateMolecules

indigoSaveRxnfile

indigoSaveRxnfileToFile

indigoRxnfile