public interface IndigoLib
extends com.sun.jna.Library
| 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 |
indigoAddSGroupAttachmentPoint(int sgroup,
int aidx,
int lvidx,
String apid) |
int |
indigoAddStereocenter(int atom,
int type,
int v1,
int v2,
int v3,
int v4) |
int |
indigoAddTemplate(int molecule,
int templates,
String name) |
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) |
int |
indigoBuildPkaModel(int level,
float theshold,
String filename) |
com.sun.jna.Pointer |
indigoCanonicalSmarts(int item) |
com.sun.jna.Pointer |
indigoCanonicalSmiles(int molecule) |
com.sun.jna.Pointer |
indigoCdxBase64(int object) |
com.sun.jna.Pointer |
indigoCdxml(int object) |
int |
indigoChangeStereocenterType(int atom,
int type) |
com.sun.jna.Pointer |
indigoCheck(String item,
String type,
String options) |
int |
indigoCheck3DStereo(int item) |
com.sun.jna.Pointer |
indigoCheckAmbiguousH(int handle) |
com.sun.jna.Pointer |
indigoCheckBadValence(int handle) |
int |
indigoCheckChirality(int item) |
com.sun.jna.Pointer |
indigoCheckObj(int item,
String type) |
int |
indigoCheckQuery(int item) |
int |
indigoCheckRGroups(int item) |
int |
indigoCheckStereo(int item) |
com.sun.jna.Pointer |
indigoCheckStructure(String structure,
String type) |
int |
indigoCheckValence(int atom) |
int |
indigoClean2d(int object) |
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 |
indigoClearXYZ(int item) |
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 |
indigoCopyRGroups(int molecule_from,
int molecule_to) |
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 |
indigoCountRGroups(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 |
indigoCreateSGroup(String type,
int mapping,
String name) |
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) |
int |
indigoDeleteSGroupAttachmentPoint(int sgroup,
int apidx) |
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) |
com.sun.jna.Pointer |
indigoFasta(int molecule,
int library) |
int |
indigoFindSGroups(int molecule,
String property,
String value) |
int |
indigoFindTemplate(int molecule,
String name) |
int |
indigoFingerprint(int item,
String type) |
int |
indigoFoldHydrogens(int item) |
int |
indigoFoldUnfoldHydrogens(int item) |
int |
indigoFree(int handle) |
com.sun.jna.Pointer |
indigoGetAcidPkaValue(int item,
int atom,
int level,
int min_level) |
int |
indigoGetAtom(int molecule,
int idx) |
int |
indigoGetAtomMappingNumber(int reaction,
int reaction_atom) |
com.sun.jna.Pointer |
indigoGetBasicPkaValue(int item,
int atom,
int level,
int min_level) |
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 |
indigoGetFragmentedMolecule(int molecule,
String options) |
int |
indigoGetGenericSGroup(int molecule,
int index) |
int |
indigoGetHybridization(int atom) |
String |
indigoGetLastError() |
int |
indigoGetMolecule(int reaction,
int idx) |
int |
indigoGetMultipleGroup(int molecule,
int index) |
com.sun.jna.Pointer |
indigoGetOption(String name) |
int |
indigoGetOptionBool(String name,
com.sun.jna.ptr.IntByReference value) |
int |
indigoGetOptionFloat(String name,
com.sun.jna.ptr.FloatByReference value) |
int |
indigoGetOptionInt(String name,
com.sun.jna.ptr.IntByReference value) |
com.sun.jna.Pointer |
indigoGetOptionType(String name) |
com.sun.jna.Pointer |
indigoGetOriginalFormat(int item) |
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 |
indigoGetRepeatingUnitConnectivity(int sgroup) |
com.sun.jna.Pointer |
indigoGetRepeatingUnitSubscript(int sgroup) |
com.sun.jna.Pointer |
indigoGetSGroupClass(int sgroup) |
com.sun.jna.Pointer |
indigoGetSGroupCoords(int sgroup) |
int |
indigoGetSGroupDisplayOption(int sgroup) |
int |
indigoGetSGroupIndex(int sgroup) |
int |
indigoGetSGroupMultiplier(int sgroup) |
com.sun.jna.Pointer |
indigoGetSGroupName(int sgroup) |
int |
indigoGetSGroupNumCrossBonds(int sgroup) |
int |
indigoGetSGroupOriginalId(int sgroup) |
int |
indigoGetSGroupParentId(int sgroup) |
int |
indigoGetSGroupSeqId(int sgroup) |
int |
indigoGetSGroupType(int sgroup) |
int |
indigoGetSubmolecule(int molecule,
int nvertices,
int[] vertices) |
int |
indigoGetSuperatom(int molecule,
int index) |
com.sun.jna.Pointer |
indigoGetTemplateAtomClass(int atom) |
com.sun.jna.Pointer |
indigoGetTGroupAlias(int tgroup) |
com.sun.jna.Pointer |
indigoGetTGroupClass(int tgroup) |
com.sun.jna.Pointer |
indigoGetTGroupName(int tgroup) |
int |
indigoGrossFormula(int molecule) |
int |
indigoHasCoord(int molecule) |
long |
indigoHash(int item) |
int |
indigoHasNext(int iter) |
int |
indigoHasProperty(int handle,
String prop) |
int |
indigoHasZCoord(int molecule) |
com.sun.jna.Pointer |
indigoHelm(int molecule,
int library) |
int |
indigoHighlight(int atom) |
int |
indigoHighlightedTarget(int match) |
com.sun.jna.Pointer |
indigoIdt(int molecule,
int library) |
int |
indigoIgnoreAtom(int matcher,
int atom) |
int |
indigoIndex(int item) |
int |
indigoInvertStereo(int item) |
int |
indigoIonize(int item,
float pH,
float pH_toll) |
int |
indigoIsChiral(int molecule) |
int |
indigoIsHighlighted(int item) |
int |
indigoIsotope(int atom) |
int |
indigoIsPossibleFischerProjection(int molecule,
String options) |
int |
indigoIsPseudoatom(int atom) |
int |
indigoIsRSite(int atom) |
int |
indigoIsTemplateAtom(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 |
indigoIterateCDX(int reader) |
int |
indigoIterateCDXFile(String filename) |
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 |
indigoIterateReactions(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 |
indigoIterateSGroups(int molecule) |
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) |
int |
indigoIterateTautomers(int structure,
String params) |
int |
indigoIterateTGroups(int molecule) |
com.sun.jna.Pointer |
indigoJson(int object) |
com.sun.jna.Pointer |
indigoLayeredCode(int molecule) |
int |
indigoLayout(int object) |
int |
indigoLoadBuffer(byte[] buf,
int size) |
int |
indigoLoadFasta(int source,
String seq_type,
int library) |
int |
indigoLoadFastaFromFile(String filename,
String seq_type,
int library) |
int |
indigoLoadFastaFromString(String str,
String seq_type,
int library) |
int |
indigoLoadFingerprintFromBuffer(byte[] buffer,
int size) |
int |
indigoLoadFingerprintFromDescriptors(double[] arr,
int arr_len,
int size,
double density) |
int |
indigoLoadHelm(int source,
int library) |
int |
indigoLoadHelmFromFile(String filename,
int library) |
int |
indigoLoadHelmFromString(String str,
int library) |
int |
indigoLoadIdt(int source,
int library) |
int |
indigoLoadIdtFromFile(String filename,
int library) |
int |
indigoLoadIdtFromString(String str,
int library) |
int |
indigoLoadKetDocument(int source) |
int |
indigoLoadKetDocumentFromFile(String filename) |
int |
indigoLoadKetDocumentFromString(String str) |
int |
indigoLoadMolecule(int source) |
int |
indigoLoadMoleculeFromBuffer(byte[] buffer,
int size) |
int |
indigoLoadMoleculeFromFile(String filename) |
int |
indigoLoadMoleculeFromString(String str) |
int |
indigoLoadMonomerLibrary(int source) |
int |
indigoLoadMonomerLibraryFromFile(String filename) |
int |
indigoLoadMonomerLibraryFromString(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 |
indigoLoadSequence(int source,
String seq_type,
int library) |
int |
indigoLoadSequenceFromFile(String filename,
String seq_type,
int library) |
int |
indigoLoadSequenceFromString(String str,
String seq_type,
int library) |
int |
indigoLoadSmarts(int source) |
int |
indigoLoadSmartsFromBuffer(byte[] buffer,
int size) |
int |
indigoLoadSmartsFromFile(String filename) |
int |
indigoLoadSmartsFromString(String str) |
int |
indigoLoadString(String str) |
int |
indigoLoadStructureFromBuffer(byte[] buffer,
int size,
String params) |
int |
indigoLoadStructureFromFile(String filename,
String params) |
int |
indigoLoadStructureFromString(String str,
String params) |
double |
indigoLogP(int molecule) |
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) |
com.sun.jna.Pointer |
indigoMassComposition(int molecule) |
int |
indigoMatch(int matcher,
int query) |
int |
indigoMerge(int where_to,
int what) |
double |
indigoMolarRefractivity(int molecule) |
double |
indigoMolecularWeight(int molecule) |
com.sun.jna.Pointer |
indigoMolfile(int molecule) |
double |
indigoMonoisotopicMass(int molecule) |
double |
indigoMostAbundantMass(int molecule) |
com.sun.jna.Pointer |
indigoName(int handle) |
int |
indigoNameToStructure(String name,
String params) |
int |
indigoNext(int iter) |
int |
indigoNormalize(int structure,
String options) |
int |
indigoNumHydrogenBondAcceptors(int molecule) |
int |
indigoNumHydrogenBondDonors(int molecule) |
int |
indigoNumRotatableBonds(int molecule) |
com.sun.jna.Pointer |
indigoOneBitsList(int fingerprint) |
int |
indigoOptimize(int query,
String options) |
double |
indigoPka(int molecule) |
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 |
indigoRemoveTemplate(int molecule,
String name) |
int |
indigoResetAtom(int atom,
String symbol) |
int |
indigoResetCharge(int atom) |
int |
indigoResetExplicitValence(int atom) |
int |
indigoResetIsotope(int atom) |
int |
indigoResetOption() |
int |
indigoResetOptions() |
int |
indigoResetRadical(int atom) |
int |
indigoResetStereo(int item) |
int |
indigoResetSymmetricCisTrans(int handle) |
int |
indigoResetSymmetricStereocenters(int handle) |
int |
indigoRGroupComposition(int molecule,
String options) |
com.sun.jna.Pointer |
indigoRxnfile(int reaction) |
int |
indigoSaveCdxml(int object,
int output) |
int |
indigoSaveCdxmlToFile(int object,
String filename) |
int |
indigoSaveCml(int object,
int output) |
int |
indigoSaveCmlToFile(int object,
String filename) |
int |
indigoSaveFastaToFile(int molecule,
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 |
indigoSaveSequence3LetterToFile(int molecule,
String filename,
int library) |
int |
indigoSaveSequenceToFile(int molecule,
String filename,
int library) |
int |
indigoSdfAppend(int output,
int item) |
com.sun.jna.Pointer |
indigoSequence(int molecule,
int library) |
com.sun.jna.Pointer |
indigoSequence3Letter(int molecule,
int library) |
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 |
indigoSetSGroupBrackets(int sgroup,
int brk_style,
float x1,
float y1,
float x2,
float y2,
float x3,
float y3,
float x4,
float y4) |
int |
indigoSetSGroupClass(int sgroup,
String sgclass) |
int |
indigoSetSGroupCoords(int sgroup,
float x,
float y) |
int |
indigoSetSGroupData(int sgroup,
String data) |
int |
indigoSetSGroupDataType(int sgroup,
String type) |
int |
indigoSetSGroupDescription(int sgroup,
String description) |
int |
indigoSetSGroupDisplay(int sgroup,
String option) |
int |
indigoSetSGroupDisplayOption(int sgroup,
int option) |
int |
indigoSetSGroupFieldName(int sgroup,
String name) |
int |
indigoSetSGroupLocation(int sgroup,
String option) |
int |
indigoSetSGroupMultiplier(int sgroup,
int mult) |
int |
indigoSetSGroupName(int sgroup,
String sgname) |
int |
indigoSetSGroupOriginalId(int sgroup,
int original) |
int |
indigoSetSGroupParentId(int sgroup,
int parent) |
int |
indigoSetSGroupQueryCode(int sgroup,
String querycode) |
int |
indigoSetSGroupQueryOper(int sgroup,
String queryoper) |
int |
indigoSetSGroupTag(int sgroup,
String tag) |
int |
indigoSetSGroupTagAlign(int sgroup,
int tag_align) |
int |
indigoSetSGroupXCoord(int sgroup,
float x) |
int |
indigoSetSGroupYCoord(int sgroup,
float y) |
int |
indigoSetStereocenterGroup(int atom,
int group) |
int |
indigoSetTautomerRule(int id,
String beg,
String end) |
int |
indigoSetTemplateAtomClass(int atom,
String name) |
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 |
indigoSmarts(int item) |
com.sun.jna.Pointer |
indigoSmiles(int item) |
int |
indigoSmilesAppend(int output,
int item) |
int |
indigoSource(int bond) |
int |
indigoStandardize(int item) |
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) |
double |
indigoTPSA(int molecule,
boolean includeSP) |
int |
indigoTransform(int reaction,
int monomers) |
int |
indigoTransformCTABtoSCSR(int molecule,
int templates) |
int |
indigoTransformHELMtoSCSR(int item) |
int |
indigoTransformSCSRtoCTAB(int molecule) |
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() |
String |
indigoVersionInfo() |
int |
indigoWriteBuffer() |
int |
indigoWriteFile(String filename) |
com.sun.jna.Pointer |
indigoXYZ(int atom) |
String indigoVersion()
String indigoVersionInfo()
long indigoAllocSessionId()
void indigoSetSessionId(long id)
void indigoReleaseSessionId(long id)
String indigoGetLastError()
int indigoFree(int handle)
int indigoClone(int handle)
int indigoCountReferences()
int indigoSetOptionInt(String name, int value)
int indigoSetOptionBool(String name, int value)
int indigoSetOptionFloat(String name, float value)
int indigoSetOptionColor(String name, float r, float g, float b)
int indigoSetOptionXY(String name, int x, int y)
com.sun.jna.Pointer indigoGetOption(String name)
int indigoGetOptionInt(String name, com.sun.jna.ptr.IntByReference value)
int indigoGetOptionBool(String name, com.sun.jna.ptr.IntByReference value)
int indigoGetOptionFloat(String name, com.sun.jna.ptr.FloatByReference value)
com.sun.jna.Pointer indigoGetOptionType(String name)
int indigoResetOption()
int indigoReadFile(String filename)
int indigoLoadString(String str)
int indigoLoadBuffer(byte[] buf,
int size)
int indigoWriteFile(String filename)
int indigoWriteBuffer()
int indigoClose(int handle)
int indigoNext(int iter)
int indigoHasNext(int iter)
int indigoIndex(int item)
int indigoRemove(int item)
com.sun.jna.Pointer indigoGetOriginalFormat(int item)
int indigoCreateMolecule()
int indigoCreateQueryMolecule()
int indigoLoadMolecule(int source)
int indigoLoadMoleculeFromString(String str)
int indigoLoadMoleculeFromFile(String filename)
int indigoLoadMoleculeFromBuffer(byte[] buffer,
int size)
int indigoLoadQueryMolecule(int source)
int indigoLoadQueryMoleculeFromString(String str)
int indigoLoadQueryMoleculeFromFile(String filename)
int indigoLoadQueryMoleculeFromBuffer(byte[] buffer,
int size)
int indigoLoadSmarts(int source)
int indigoLoadSmartsFromString(String str)
int indigoLoadSmartsFromFile(String filename)
int indigoLoadSmartsFromBuffer(byte[] buffer,
int size)
int indigoLoadMonomerLibrary(int source)
int indigoLoadMonomerLibraryFromString(String str)
int indigoLoadMonomerLibraryFromFile(String filename)
int indigoLoadKetDocument(int source)
int indigoLoadKetDocumentFromString(String str)
int indigoLoadKetDocumentFromFile(String filename)
int indigoLoadSequence(int source,
String seq_type,
int library)
int indigoLoadSequenceFromString(String str, String seq_type, int library)
int indigoLoadSequenceFromFile(String filename, String seq_type, int library)
int indigoLoadFasta(int source,
String seq_type,
int library)
int indigoLoadIdt(int source,
int library)
int indigoLoadIdtFromString(String str, int library)
int indigoLoadIdtFromFile(String filename, int library)
int indigoLoadHelm(int source,
int library)
int indigoLoadHelmFromString(String str, int library)
int indigoLoadHelmFromFile(String filename, int library)
int indigoLoadStructureFromBuffer(byte[] buffer,
int size,
String params)
int indigoSaveMolfile(int molecule,
int output)
int indigoSaveSequenceToFile(int molecule,
String filename,
int library)
int indigoSaveSequence3LetterToFile(int molecule,
String filename,
int library)
int indigoSaveFastaToFile(int molecule,
String filename)
int indigoSaveMolfileToFile(int molecule,
String filename)
com.sun.jna.Pointer indigoMolfile(int molecule)
com.sun.jna.Pointer indigoSequence(int molecule,
int library)
com.sun.jna.Pointer indigoSequence3Letter(int molecule,
int library)
com.sun.jna.Pointer indigoFasta(int molecule,
int library)
com.sun.jna.Pointer indigoIdt(int molecule,
int library)
com.sun.jna.Pointer indigoHelm(int molecule,
int library)
int indigoSaveCml(int object,
int output)
int indigoSaveCmlToFile(int object,
String filename)
com.sun.jna.Pointer indigoCml(int object)
com.sun.jna.Pointer indigoJson(int object)
int indigoSaveCdxml(int object,
int output)
int indigoSaveCdxmlToFile(int object,
String filename)
com.sun.jna.Pointer indigoCdxml(int object)
com.sun.jna.Pointer indigoCdxBase64(int object)
int indigoSaveMDLCT(int item,
int output)
int indigoLoadReaction(int source)
int indigoLoadReactionFromString(String string)
int indigoLoadReactionFromFile(String filename)
int indigoLoadReactionFromBuffer(byte[] buf,
int size)
int indigoLoadQueryReaction(int source)
int indigoLoadQueryReactionFromString(String str)
int indigoLoadQueryReactionFromFile(String filename)
int indigoLoadQueryReactionFromBuffer(byte[] buf,
int size)
int indigoLoadReactionSmarts(int source)
int indigoLoadReactionSmartsFromString(String str)
int indigoLoadReactionSmartsFromFile(String filename)
int indigoLoadReactionSmartsFromBuffer(byte[] buf,
int size)
int indigoCreateReaction()
int indigoCreateQueryReaction()
int indigoAddReactant(int reaction,
int molecule)
int indigoAddProduct(int reaction,
int molecule)
int indigoAddCatalyst(int reaction,
int molecule)
int indigoCountReactants(int reaction)
int indigoCountProducts(int reaction)
int indigoCountCatalysts(int reaction)
int indigoCountMolecules(int reaction)
int indigoIterateReactants(int reaction)
int indigoIterateProducts(int reaction)
int indigoIterateCatalysts(int reaction)
int indigoIterateMolecules(int reaction)
int indigoIterateReactions(int reaction)
int indigoSaveRxnfile(int reaction,
int output)
int indigoSaveRxnfileToFile(int reaction,
String filename)
com.sun.jna.Pointer indigoRxnfile(int reaction)
int indigoOptimize(int query,
String options)
int indigoNormalize(int structure,
String options)
int indigoStandardize(int item)
int indigoIonize(int item,
float pH,
float pH_toll)
com.sun.jna.Pointer indigoGetAcidPkaValue(int item,
int atom,
int level,
int min_level)
com.sun.jna.Pointer indigoGetBasicPkaValue(int item,
int atom,
int level,
int min_level)
int indigoBuildPkaModel(int level,
float theshold,
String filename)
int indigoAutomap(int reaction,
String mode)
int indigoGetAtomMappingNumber(int reaction,
int reaction_atom)
int indigoSetAtomMappingNumber(int reaction,
int reaction_atom,
int number)
int indigoClearAAM(int reaction)
int indigoCorrectReactingCenters(int reaction)
int indigoIterateAtoms(int molecule)
int indigoIteratePseudoatoms(int molecule)
int indigoIterateRSites(int molecule)
int indigoIterateStereocenters(int molecule)
int indigoIterateAlleneCenters(int molecule)
int indigoIterateRGroups(int molecule)
int indigoIsPseudoatom(int atom)
int indigoIsRSite(int atom)
int indigoIsTemplateAtom(int atom)
int indigoStereocenterType(int atom)
int indigoStereocenterGroup(int atom)
com.sun.jna.Pointer indigoStereocenterPyramid(int atom)
int indigoSetStereocenterGroup(int atom,
int group)
int indigoChangeStereocenterType(int atom,
int type)
int indigoSingleAllowedRGroup(int rsite)
int indigoAddStereocenter(int atom,
int type,
int v1,
int v2,
int v3,
int v4)
int indigoIterateRGroupFragments(int rgroup)
int indigoCountRGroups(int molecule)
int indigoCountAttachmentPoints(int rgroup)
com.sun.jna.Pointer indigoSymbol(int atom)
int indigoDegree(int atom)
int indigoGetCharge(int atom,
com.sun.jna.ptr.IntByReference charge)
int indigoGetRadical(int atom,
com.sun.jna.ptr.IntByReference radical)
int indigoGetExplicitValence(int atom,
com.sun.jna.ptr.IntByReference valence)
int indigoGetRadicalElectrons(int atom,
com.sun.jna.ptr.IntByReference electrons)
int indigoAtomicNumber(int atom)
int indigoIsotope(int atom)
int indigoValence(int atom)
int indigoGetHybridization(int atom)
int indigoCheckValence(int atom)
int indigoCheckQuery(int item)
int indigoCheckRGroups(int item)
int indigoCheckChirality(int item)
int indigoCheck3DStereo(int item)
int indigoCheckStereo(int item)
int indigoCountHydrogens(int atom,
com.sun.jna.ptr.IntByReference valence)
int indigoCountImplicitHydrogens(int item)
com.sun.jna.Pointer indigoCheckObj(int item,
String type)
int indigoGetReactingCenter(int reaction,
int reaction_bond,
com.sun.jna.ptr.IntByReference rc)
int indigoSetReactingCenter(int reaction,
int reaction_bond,
int rc)
com.sun.jna.Pointer indigoXYZ(int atom)
int indigoSetXYZ(int atom,
float x,
float y,
float z)
int indigoCountSuperatoms(int molecule)
int indigoCountDataSGroups(int molecule)
int indigoCountRepeatingUnits(int molecule)
int indigoCountMultipleGroups(int molecule)
int indigoCountGenericSGroups(int molecule)
int indigoIterateDataSGroups(int molecule)
int indigoIterateSuperatoms(int molecule)
int indigoIterateGenericSGroups(int molecule)
int indigoIterateRepeatingUnits(int molecule)
int indigoIterateMultipleGroups(int molecule)
int indigoIterateSGroups(int molecule)
int indigoIterateTGroups(int molecule)
int indigoGetSuperatom(int molecule,
int index)
int indigoGetDataSGroup(int molecule,
int index)
int indigoGetGenericSGroup(int molecule,
int index)
int indigoGetMultipleGroup(int molecule,
int index)
int indigoGetRepeatingUnit(int molecule,
int index)
com.sun.jna.Pointer indigoDescription(int data_sgroup)
com.sun.jna.Pointer indigoData(int data_sgroup)
int indigoAddDataSGroup(int molecule,
int natoms,
int[] atoms,
int nbonds,
int[] bonds,
String description,
String data)
int indigoSetDataSGroupXY(int sgroup,
float x,
float y,
String options)
int indigoSetSGroupClass(int sgroup,
String sgclass)
int indigoSetSGroupName(int sgroup,
String sgname)
com.sun.jna.Pointer indigoGetSGroupClass(int sgroup)
com.sun.jna.Pointer indigoGetSGroupName(int sgroup)
int indigoGetSGroupNumCrossBonds(int sgroup)
int indigoAddSGroupAttachmentPoint(int sgroup,
int aidx,
int lvidx,
String apid)
int indigoDeleteSGroupAttachmentPoint(int sgroup,
int apidx)
int indigoGetSGroupDisplayOption(int sgroup)
int indigoSetSGroupDisplayOption(int sgroup,
int option)
int indigoGetSGroupSeqId(int sgroup)
int indigoGetSGroupMultiplier(int sgroup)
com.sun.jna.Pointer indigoGetRepeatingUnitSubscript(int sgroup)
int indigoGetRepeatingUnitConnectivity(int sgroup)
int indigoSetSGroupMultiplier(int sgroup,
int mult)
int indigoSetSGroupBrackets(int sgroup,
int brk_style,
float x1,
float y1,
float x2,
float y2,
float x3,
float y3,
float x4,
float y4)
com.sun.jna.Pointer indigoGetSGroupCoords(int sgroup)
int indigoSetSGroupData(int sgroup,
String data)
int indigoSetSGroupCoords(int sgroup,
float x,
float y)
int indigoSetSGroupDescription(int sgroup,
String description)
int indigoSetSGroupFieldName(int sgroup,
String name)
int indigoSetSGroupQueryCode(int sgroup,
String querycode)
int indigoSetSGroupQueryOper(int sgroup,
String queryoper)
int indigoSetSGroupDisplay(int sgroup,
String option)
int indigoSetSGroupLocation(int sgroup,
String option)
int indigoSetSGroupTag(int sgroup,
String tag)
int indigoSetSGroupTagAlign(int sgroup,
int tag_align)
int indigoSetSGroupDataType(int sgroup,
String type)
int indigoSetSGroupXCoord(int sgroup,
float x)
int indigoSetSGroupYCoord(int sgroup,
float y)
int indigoGetSGroupType(int sgroup)
int indigoGetSGroupIndex(int sgroup)
int indigoGetSGroupOriginalId(int sgroup)
int indigoSetSGroupOriginalId(int sgroup,
int original)
int indigoGetSGroupParentId(int sgroup)
int indigoSetSGroupParentId(int sgroup,
int parent)
int indigoAddTemplate(int molecule,
int templates,
String name)
int indigoRemoveTemplate(int molecule,
String name)
int indigoFindTemplate(int molecule,
String name)
com.sun.jna.Pointer indigoGetTGroupClass(int tgroup)
com.sun.jna.Pointer indigoGetTGroupName(int tgroup)
com.sun.jna.Pointer indigoGetTGroupAlias(int tgroup)
int indigoTransformSCSRtoCTAB(int molecule)
int indigoTransformCTABtoSCSR(int molecule,
int templates)
com.sun.jna.Pointer indigoGetTemplateAtomClass(int atom)
int indigoSetTemplateAtomClass(int atom,
String name)
int indigoResetCharge(int atom)
int indigoResetExplicitValence(int atom)
int indigoResetRadical(int atom)
int indigoResetIsotope(int atom)
int indigoSetAttachmentPoint(int atom,
int order)
int indigoClearAttachmentPoints(int item)
int indigoIterateAttachmentPoints(int item,
int order)
int indigoRemoveConstraints(int item,
String type)
int indigoResetStereo(int item)
int indigoInvertStereo(int item)
int indigoCountAtoms(int molecule)
int indigoCountBonds(int molecule)
int indigoCountPseudoatoms(int molecule)
int indigoCountRSites(int molecule)
int indigoIterateBonds(int molecule)
int indigoBondOrder(int bond)
int indigoBondStereo(int bond)
int indigoTopology(int bond)
int indigoIterateNeighbors(int atom)
int indigoBond(int nei)
int indigoGetAtom(int molecule,
int idx)
int indigoGetBond(int molecule,
int idx)
int indigoGetMolecule(int reaction,
int idx)
int indigoSource(int bond)
int indigoDestination(int bond)
int indigoClearCisTrans(int handle)
int indigoClearStereocenters(int handle)
int indigoClearAlleneCenters(int handle)
int indigoCountStereocenters(int molecule)
int indigoCountAlleneCenters(int molecule)
int indigoResetSymmetricCisTrans(int handle)
int indigoResetSymmetricStereocenters(int handle)
int indigoMarkEitherCisTrans(int handle)
int indigoMarkStereobonds(int handle)
int indigoValidateChirality(int handle)
int indigoAddAtom(int molecule,
String symbol)
int indigoResetAtom(int atom,
String symbol)
int indigoAddRSite(int molecule,
String name)
int indigoSetRSite(int atom,
String name)
int indigoSetCharge(int atom,
int charge)
int indigoSetExplicitValence(int atom,
int valence)
int indigoSetIsotope(int atom,
int isotope)
int indigoSetImplicitHCount(int atom,
int impl_h)
int indigoSetRadical(int atom,
int radical)
int indigoAddBond(int source,
int destination,
int order)
int indigoSetBondOrder(int bond,
int order)
int indigoMerge(int where_to,
int what)
int indigoHighlight(int atom)
int indigoUnhighlight(int item)
int indigoIsHighlighted(int item)
int indigoCountComponents(int molecule)
int indigoComponentIndex(int atom)
int indigoIterateComponents(int molecule)
int indigoComponent(int molecule,
int index)
int indigoCountSSSR(int molecule)
int indigoIterateSSSR(int molecule)
int indigoIterateSubtrees(int molecule,
int min_atoms,
int max_atoms)
int indigoIterateRings(int molecule,
int min_atoms,
int max_atoms)
int indigoIterateEdgeSubmolecules(int molecule,
int min_bonds,
int max_bonds)
int indigoCountHeavyAtoms(int molecule)
int indigoGrossFormula(int molecule)
double indigoMolecularWeight(int molecule)
double indigoMostAbundantMass(int molecule)
double indigoMonoisotopicMass(int molecule)
com.sun.jna.Pointer indigoMassComposition(int molecule)
double indigoTPSA(int molecule,
boolean includeSP)
int indigoNumRotatableBonds(int molecule)
int indigoNumHydrogenBondAcceptors(int molecule)
int indigoNumHydrogenBondDonors(int molecule)
double indigoLogP(int molecule)
double indigoMolarRefractivity(int molecule)
double indigoPka(int molecule)
com.sun.jna.Pointer indigoCanonicalSmiles(int molecule)
long indigoHash(int item)
com.sun.jna.Pointer indigoLayeredCode(int molecule)
com.sun.jna.Pointer indigoSymmetryClasses(int molecule,
com.sun.jna.ptr.IntByReference count)
int indigoHasCoord(int molecule)
int indigoHasZCoord(int molecule)
int indigoIsChiral(int molecule)
int indigoIsPossibleFischerProjection(int molecule,
String options)
int indigoCreateSubmolecule(int molecule,
int nvertices,
int[] vertices)
int indigoGetSubmolecule(int molecule,
int nvertices,
int[] vertices)
int indigoCreateEdgeSubmolecule(int molecule,
int nvertices,
int[] vertices,
int nedges,
int[] edges)
int indigoRemoveAtoms(int molecule,
int nvertices,
int[] vertices)
int indigoRemoveBonds(int molecule,
int nbonds,
int[] bonds)
float indigoAlignAtoms(int molecule,
int natoms,
int[] atom_ids,
float[] desired_xyz)
int indigoAromatize(int item)
int indigoDearomatize(int item)
int indigoFoldHydrogens(int item)
int indigoUnfoldHydrogens(int item)
int indigoFoldUnfoldHydrogens(int item)
int indigoClearXYZ(int item)
int indigoLayout(int object)
int indigoClean2d(int object)
com.sun.jna.Pointer indigoSmiles(int item)
com.sun.jna.Pointer indigoSmarts(int item)
com.sun.jna.Pointer indigoCanonicalSmarts(int item)
int indigoExactMatch(int item1,
int item2,
String flags)
int indigoRemoveTautomerRule(int id)
int indigoClearTautomerRules()
com.sun.jna.Pointer indigoName(int handle)
int indigoSetName(int handle,
String name)
int indigoSerialize(int handle,
com.sun.jna.ptr.PointerByReference buf,
com.sun.jna.ptr.IntByReference size)
int indigoUnserialize(byte[] buf,
int size)
int indigoHasProperty(int handle,
String prop)
com.sun.jna.Pointer indigoGetProperty(int handle,
String prop)
int indigoRemoveProperty(int item,
String prop)
int indigoIterateProperties(int handle)
int indigoClearProperties(int handle)
com.sun.jna.Pointer indigoCheckBadValence(int handle)
com.sun.jna.Pointer indigoCheckAmbiguousH(int handle)
int indigoFingerprint(int item,
String type)
com.sun.jna.Pointer indigoOneBitsList(int fingerprint)
int indigoLoadFingerprintFromBuffer(byte[] buffer,
int size)
int indigoLoadFingerprintFromDescriptors(double[] arr,
int arr_len,
int size,
double density)
int indigoCountBits(int fingerprint)
int indigoCommonBits(int fingerprint1,
int fingerprint2)
float indigoSimilarity(int item1,
int item2,
String metrics)
int indigoIterateSDF(int reader)
int indigoIterateRDF(int reader)
int indigoIterateSmiles(int reader)
int indigoIterateCML(int reader)
int indigoIterateCDX(int reader)
int indigoIterateSDFile(String filename)
int indigoIterateRDFile(String filename)
int indigoIterateSmilesFile(String filename)
int indigoIterateCMLFile(String filename)
int indigoIterateCDXFile(String filename)
com.sun.jna.Pointer indigoRawData(int item)
int indigoTell(int handle)
int indigoSdfAppend(int output,
int item)
int indigoSmilesAppend(int output,
int item)
int indigoRdfHeader(int output)
int indigoRdfAppend(int output,
int item)
int indigoCmlHeader(int output)
int indigoCmlAppend(int output,
int item)
int indigoCmlFooter(int output)
int indigoCreateSaver(int output,
String format)
int indigoAppend(int saver,
int object)
int indigoCreateArray()
int indigoArrayAdd(int arr,
int object)
int indigoAt(int item,
int index)
int indigoCount(int item)
int indigoClear(int arr)
int indigoIterateArray(int arr)
int indigoSubstructureMatcher(int target,
String mode)
int indigoIgnoreAtom(int matcher,
int atom)
int indigoUnignoreAtom(int matcher,
int atom)
int indigoUnignoreAllAtoms(int matcher)
int indigoMatch(int matcher,
int query)
int indigoCountMatches(int matcher,
int query)
int indigoCountMatchesWithLimit(int matcher,
int query,
int embeddings_limit)
int indigoIterateMatches(int matcher,
int query)
int indigoHighlightedTarget(int match)
int indigoMapAtom(int match,
int query_atom)
int indigoMapBond(int match,
int query_bond)
int indigoMapMolecule(int match,
int query_reaction_molecule)
int indigoExtractCommonScaffold(int structures,
String options)
int indigoRGroupComposition(int molecule,
String options)
int indigoGetFragmentedMolecule(int molecule,
String options)
int indigoAllScaffolds(int extracted)
int indigoDecomposeMolecules(int scaffold,
int structures)
int indigoDecomposedMoleculeScaffold(int decomp)
int indigoIterateDecomposedMolecules(int decomp)
int indigoDecomposedMoleculeHighlighted(int decomp)
int indigoDecomposedMoleculeWithRGroups(int decomp)
int indigoCreateDecomposer(int scaffold)
int indigoDecomposeMolecule(int decomp,
int mol)
int indigoIterateDecompositions(int deco_item)
int indigoAddDecomposition(int decomp,
int q_match)
com.sun.jna.Pointer indigoToString(int handle)
int indigoToBuffer(int handle,
com.sun.jna.ptr.PointerByReference buf,
com.sun.jna.ptr.IntByReference size)
int indigoReactionProductEnumerate(int reaction,
int monomers)
int indigoTransform(int reaction,
int monomers)
int indigoExpandAbbreviations(int structure)
int indigoIterateTautomers(int structure,
String params)
int indigoTransformHELMtoSCSR(int item)
int indigoResetOptions()
int indigoDbgBreakpoint()
com.sun.jna.Pointer indigoDbgInternalType(int object)
int indigoCopyRGroups(int molecule_from,
int molecule_to)
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