Uses of Class
com.ggasoftware.indigo.IndigoObject

Uses of IndigoObject in com.ggasoftware.indigo

Methods in com.ggasoftware.indigo that return IndigoObject

Modifier and Type	Method and Description
IndigoObject	IndigoObject.addAtom(String symbol)
IndigoObject	IndigoObject.addBond(IndigoObject atom, int order)
IndigoObject	IndigoObject.addDataSGroup(Collection<Integer> atoms, Collection<Integer> bonds, String description, String data)
IndigoObject	IndigoObject.addDataSGroup(int[] atoms, int[] bonds, String description, String data)
IndigoObject	IndigoObject.addRSite(String name)
IndigoObject	IndigoObject.allScaffolds()
IndigoObject	IndigoObject.at(int idx)
IndigoObject	IndigoObject.bond()
IndigoObject	IndigoObject.clone()
IndigoObject	IndigoObject.component(int index)
IndigoObject	Indigo.createArray()
IndigoObject	Indigo.createDecomposer(IndigoObject scaffold)
IndigoObject	IndigoObject.createEdgeSubmolecule(Collection<Integer> vertices, Collection<Integer> edges)
IndigoObject	IndigoObject.createEdgeSubmolecule(int[] vertices, int[] edges)
IndigoObject	Indigo.createFileSaver(String filename, String format)
IndigoObject	Indigo.createMolecule()
IndigoObject	Indigo.createQueryMolecule()
IndigoObject	Indigo.createQueryReaction()
IndigoObject	Indigo.createReaction()
IndigoObject	Indigo.createSaver(IndigoObject output, String format)
IndigoObject	IndigoObject.createSubmolecule(Collection<Integer> vertices)
IndigoObject	IndigoObject.createSubmolecule(int[] vertices)
IndigoObject	IndigoObject.decomposedMoleculeHighlighted()
IndigoObject	IndigoObject.decomposedMoleculeScaffold()
IndigoObject	IndigoObject.decomposedMoleculeWithRGroups()
IndigoObject	IndigoObject.decomposeMolecule(IndigoObject mol)
IndigoObject	Indigo.decomposeMolecules(IndigoObject scaffold, Collection<IndigoObject> structures) Deprecated.
IndigoObject	Indigo.decomposeMolecules(IndigoObject scaffold, IndigoObject structures) Deprecated.
IndigoObject	IndigoObject.destination()
IndigoObject	Indigo.exactMatch(IndigoObject obj1, IndigoObject obj2)
IndigoObject	Indigo.exactMatch(IndigoObject obj1, IndigoObject obj2, String flags)
IndigoObject	Indigo.extractCommonScaffold(Collection<IndigoObject> structures, String options)
IndigoObject	Indigo.extractCommonScaffold(IndigoObject structures, String options)
IndigoObject	IndigoObject.fingerprint()
IndigoObject	IndigoObject.fingerprint(String type)
IndigoObject	IndigoObject.getAtom(int idx)
IndigoObject	IndigoObject.getBond(int idx)
IndigoObject	IndigoObject.getDataSGroup(int index)
IndigoObject	IndigoObject.getGenericSGroup(int index)
IndigoObject	IndigoObject.getMolecule(int idx)
IndigoObject	IndigoObject.getMultipleGroup(int index)
IndigoObject	IndigoObject.getRepeatingUnit(int index)
IndigoObject	IndigoObject.getSubmolecule(Collection<Integer> vertices)
IndigoObject	IndigoObject.getSubmolecule(int[] vertices)
IndigoObject	IndigoObject.getSuperatom(int index)
IndigoObject	IndigoObject.highlightedTarget()
IndigoObject	IndigoObject.iterateAlleneCenters()
IndigoObject	IndigoObject.iterateArray()
IndigoObject	IndigoObject.iterateAtoms()
IndigoObject	IndigoObject.iterateAttachmentPoints(int order)
IndigoObject	IndigoObject.iterateBonds()
IndigoObject	IndigoObject.iterateCatalysts()
IndigoObject	Indigo.iterateCML(IndigoObject reader)
IndigoObject	Indigo.iterateCMLFile(String filename)
IndigoObject	IndigoObject.iterateComponents()
IndigoObject	IndigoObject.iterateDataSGroups()
IndigoObject	IndigoObject.iterateDecomposedMolecules() Deprecated.
IndigoObject	IndigoObject.iterateDecompositions()
IndigoObject	IndigoObject.iterateEdgeSubmolecules(int min_edges, int max_edges)
IndigoObject	IndigoObject.iterateGenericSGroups()
IndigoObject	IndigoObject.iterateMatches(IndigoObject query)
IndigoObject	IndigoObject.iterateMolecules()
IndigoObject	IndigoObject.iterateMultipleGroups()
IndigoObject	IndigoObject.iterateNeighbors()
IndigoObject	IndigoObject.iterateProducts()
IndigoObject	IndigoObject.iterateProperties()
IndigoObject	IndigoObject.iteratePseudoatoms()
IndigoObject	Indigo.iterateRDF(IndigoObject reader)
IndigoObject	Indigo.iterateRDFile(String filename)
IndigoObject	IndigoObject.iterateReactants()
IndigoObject	IndigoObject.iterateRepeatingUnits()
IndigoObject	IndigoObject.iterateRGroupFragments()
IndigoObject	IndigoObject.iterateRGroups()
IndigoObject	IndigoObject.iterateRings(int min_vertices, int max_vertices)
IndigoObject	IndigoObject.iterateRSites()
IndigoObject	Indigo.iterateSDF(IndigoObject reader)
IndigoObject	Indigo.iterateSDFile(String filename)
IndigoObject	Indigo.iterateSmiles(IndigoObject reader)
IndigoObject	Indigo.iterateSmilesFile(String filename)
IndigoObject	IndigoObject.iterateSSSR()
IndigoObject	IndigoObject.iterateStereocenters()
IndigoObject	IndigoObject.iterateSubtrees(int min_vertices, int max_vertices)
IndigoObject	IndigoObject.iterateSuperatoms()
IndigoObject	Indigo.loadBuffer(byte[] buf)
IndigoObject	Indigo.loadMolecule(byte[] buf)
IndigoObject	Indigo.loadMolecule(String str)
IndigoObject	Indigo.loadMoleculeFromFile(String path)
IndigoObject	Indigo.loadQueryMolecule(byte[] buf)
IndigoObject	Indigo.loadQueryMolecule(String str)
IndigoObject	Indigo.loadQueryMoleculeFromFile(String path)
IndigoObject	Indigo.loadQueryReaction(byte[] buf)
IndigoObject	Indigo.loadQueryReaction(String str)
IndigoObject	Indigo.loadQueryReactionFromFile(String path)
IndigoObject	Indigo.loadReaction(byte[] buf)
IndigoObject	Indigo.loadReaction(String str)
IndigoObject	Indigo.loadReactionFromFile(String path)
IndigoObject	Indigo.loadReactionSmarts(byte[] buf)
IndigoObject	Indigo.loadReactionSmarts(String str)
IndigoObject	Indigo.loadReactionSmartsFromFile(String path)
IndigoObject	Indigo.loadSmarts(byte[] buf)
IndigoObject	Indigo.loadSmarts(String str)
IndigoObject	Indigo.loadSmartsFromFile(String path)
IndigoObject	Indigo.loadString(String string)
IndigoObject	IndigoObject.mapAtom(IndigoObject query_atom)
IndigoObject	IndigoObject.mapBond(IndigoObject query_bond)
IndigoObject	IndigoObject.mapMolecule(IndigoObject query_reaction_molecule)
IndigoObject	IndigoObject.match(IndigoObject query)
IndigoObject	IndigoObject.merge(IndigoObject other)
IndigoObject	IndigoObject.next()
IndigoObject	Indigo.reactionProductEnumerate(IndigoObject reaction, IndigoObject monomers)
IndigoObject	Indigo.reactionProductEnumerate(IndigoObject reaction, Iterable<Iterable> monomers)
IndigoObject	IndigoObject.resetAtom(String symbol)
IndigoObject	IndigoObject.setRSite(String name)
IndigoObject	IndigoObject.source()
IndigoObject	Indigo.substructureMatcher(IndigoObject target)
IndigoObject	Indigo.substructureMatcher(IndigoObject target, String mode)
IndigoObject	Indigo.toIndigoArray(Collection<IndigoObject> coll)
IndigoObject	Indigo.unserialize(byte[] data)
IndigoObject	Indigo.writeBuffer()
IndigoObject	Indigo.writeFile(String filename)

Methods in com.ggasoftware.indigo that return types with arguments of type IndigoObject

Modifier and Type	Method and Description
Iterator<IndigoObject>	IndigoObject.iterator()

Methods in com.ggasoftware.indigo with parameters of type IndigoObject

Modifier and Type	Method and Description
IndigoObject	IndigoObject.addBond(IndigoObject atom, int order)
void	IndigoObject.addCatalyst(IndigoObject molecule)
void	IndigoObject.addDecomposition(IndigoObject q_match)
void	IndigoObject.addProduct(IndigoObject molecule)
void	IndigoObject.addReactant(IndigoObject molecule)
void	IndigoObject.append(IndigoObject obj)
int	IndigoObject.arrayAdd(IndigoObject other)
int	IndigoObject.atomMappingNumber(IndigoObject reaction_atom)
void	IndigoObject.cmlAppend(IndigoObject item)
int	Indigo.commonBits(IndigoObject fingerprint1, IndigoObject fingerprint2)
int	IndigoObject.countMatches(IndigoObject query)
int	IndigoObject.countMatchesWithLimit(IndigoObject query, int embeddings_limit)
IndigoObject	Indigo.createDecomposer(IndigoObject scaffold)
IndigoObject	Indigo.createSaver(IndigoObject output, String format)
IndigoObject	IndigoObject.decomposeMolecule(IndigoObject mol)
IndigoObject	Indigo.decomposeMolecules(IndigoObject scaffold, Collection<IndigoObject> structures) Deprecated.
IndigoObject	Indigo.decomposeMolecules(IndigoObject scaffold, IndigoObject structures) Deprecated.
IndigoObject	Indigo.exactMatch(IndigoObject obj1, IndigoObject obj2)
IndigoObject	Indigo.exactMatch(IndigoObject obj1, IndigoObject obj2, String flags)
IndigoObject	Indigo.extractCommonScaffold(IndigoObject structures, String options)
void	IndigoObject.ignoreAtom(IndigoObject atom)
IndigoObject	Indigo.iterateCML(IndigoObject reader)
IndigoObject	IndigoObject.iterateMatches(IndigoObject query)
IndigoObject	Indigo.iterateRDF(IndigoObject reader)
IndigoObject	Indigo.iterateSDF(IndigoObject reader)
IndigoObject	Indigo.iterateSmiles(IndigoObject reader)
IndigoObject	IndigoObject.mapAtom(IndigoObject query_atom)
IndigoObject	IndigoObject.mapBond(IndigoObject query_bond)
IndigoObject	IndigoObject.mapMolecule(IndigoObject query_reaction_molecule)
IndigoObject	IndigoObject.match(IndigoObject query)
IndigoObject	IndigoObject.merge(IndigoObject other)
void	IndigoObject.rdfAppend(IndigoObject item)
int	IndigoObject.reactingCenter(IndigoObject bond)
IndigoObject	Indigo.reactionProductEnumerate(IndigoObject reaction, IndigoObject monomers)
IndigoObject	Indigo.reactionProductEnumerate(IndigoObject reaction, Iterable<Iterable> monomers)
void	IndigoObject.sdfAppend(IndigoObject item)
void	IndigoObject.setAtomMappingNumber(IndigoObject reaction_atom, int number)
void	IndigoObject.setReactingCenter(IndigoObject bond, int type)
float	Indigo.similarity(IndigoObject obj1, IndigoObject obj2)
float	Indigo.similarity(IndigoObject obj1, IndigoObject obj2, String metrics)
void	IndigoObject.smilesAppend(IndigoObject item)
IndigoObject	Indigo.substructureMatcher(IndigoObject target)
IndigoObject	Indigo.substructureMatcher(IndigoObject target, String mode)
void	Indigo.transform(IndigoObject reaction, IndigoObject monomer)
void	IndigoObject.unignoreAtom(IndigoObject atom)

Method parameters in com.ggasoftware.indigo with type arguments of type IndigoObject

Modifier and Type	Method and Description
IndigoObject	Indigo.decomposeMolecules(IndigoObject scaffold, Collection<IndigoObject> structures) Deprecated.
IndigoObject	Indigo.extractCommonScaffold(Collection<IndigoObject> structures, String options)
IndigoObject	Indigo.toIndigoArray(Collection<IndigoObject> coll)