public class Indigo extends Object
| Modifier and Type | Field and Description |
|---|---|
static int |
ABS |
static int |
ALLENE |
static int |
AND |
static int |
CHAIN |
static int |
CIS |
static int |
DOUBLET |
static int |
DOWN |
static int |
EITHER |
static String |
INDIGO_DLL |
static String |
LIBINDIGO_DYLIB |
static String |
LIBINDIGO_SO |
static int |
OR |
static int |
RC_CENTER |
static int |
RC_MADE_OR_BROKEN |
static int |
RC_NOT_CENTER |
static int |
RC_ORDER_CHANGED |
static int |
RC_UNCHANGED |
static int |
RC_UNMARKED |
static int |
RING |
static int |
SG_TYPE_ANY |
static int |
SG_TYPE_COM |
static int |
SG_TYPE_COP |
static int |
SG_TYPE_CRO |
static int |
SG_TYPE_DAT |
static int |
SG_TYPE_FOR |
static int |
SG_TYPE_GEN |
static int |
SG_TYPE_GRA |
static int |
SG_TYPE_MER |
static int |
SG_TYPE_MIX |
static int |
SG_TYPE_MOD |
static int |
SG_TYPE_MON |
static int |
SG_TYPE_MUL |
static int |
SG_TYPE_SRU |
static int |
SG_TYPE_SUP |
static int |
SINGLET |
static int |
TRANS |
static int |
TRIPLET |
static int |
UP |
static String[] |
WIN_DLLS |
public static final int ABS
public static final int OR
public static final int AND
public static final int EITHER
public static final int UP
public static final int DOWN
public static final int CIS
public static final int TRANS
public static final int CHAIN
public static final int RING
public static final int ALLENE
public static final int SINGLET
public static final int DOUBLET
public static final int TRIPLET
public static final int RC_NOT_CENTER
public static final int RC_UNMARKED
public static final int RC_CENTER
public static final int RC_UNCHANGED
public static final int RC_MADE_OR_BROKEN
public static final int RC_ORDER_CHANGED
public static final int SG_TYPE_GEN
public static final int SG_TYPE_DAT
public static final int SG_TYPE_SUP
public static final int SG_TYPE_SRU
public static final int SG_TYPE_MUL
public static final int SG_TYPE_MON
public static final int SG_TYPE_MER
public static final int SG_TYPE_COP
public static final int SG_TYPE_CRO
public static final int SG_TYPE_MOD
public static final int SG_TYPE_GRA
public static final int SG_TYPE_COM
public static final int SG_TYPE_MIX
public static final int SG_TYPE_FOR
public static final int SG_TYPE_ANY
public static final String INDIGO_DLL
public static final String LIBINDIGO_SO
public static final String LIBINDIGO_DYLIB
public static final String[] WIN_DLLS
public Indigo(String path)
public Indigo()
public static int checkResult(Object obj, int result)
public static long checkResultLong(Object obj, long result)
public static float checkResultFloat(Object obj, float result)
public static double checkResultDouble(Object obj, double result)
public static com.sun.jna.Pointer checkResultPointer(Object obj, com.sun.jna.Pointer result)
public static int[] toIntArray(Collection<Integer> collection)
public static float[] toFloatArray(Collection<Float> collection)
public static String getPlatformDependentPath()
public static IndigoLib getLibrary()
public boolean sessionReleased()
public String version()
public String versionInfo()
public int countReferences()
public void setSessionID()
public void setOption(String option, int value)
public void setOption(String option, int x, int y)
public void setOption(String option, float r, float g, float b)
public void setOption(String option, boolean value)
public void setOption(String option, float value)
public void setOption(String option, double value)
public boolean getOptionBool(String option)
public void resetOptions()
public IndigoObject writeFile(String filename)
public IndigoObject writeBuffer()
public IndigoObject createMolecule()
public IndigoObject createQueryMolecule()
public IndigoObject loadMolecule(String str)
public IndigoObject loadMolecule(byte[] buf)
public IndigoObject loadMoleculeFromFile(String path)
public IndigoObject loadMoleculeFromBuffer(byte[] buf)
public IndigoObject loadQueryMolecule(String str)
public IndigoObject loadQueryMolecule(byte[] buf)
public IndigoObject loadQueryMoleculeFromFile(String path)
public IndigoObject loadSmarts(String str)
public IndigoObject loadSmarts(byte[] buf)
public IndigoObject loadSmartsFromFile(String path)
public IndigoObject loadMonomerLibrary(String str)
public IndigoObject loadMonomerLibraryFromFile(String path)
public IndigoObject loadKetDocument(String str)
public IndigoObject loadKetDocumentFromFile(String path)
public IndigoObject loadSequence(String str, String seq_type, IndigoObject library)
public IndigoObject loadSequenceFromFile(String path, String seq_type, IndigoObject library)
public IndigoObject loadFasta(String str, String seq_type, IndigoObject library)
public IndigoObject loadFastaFromFile(String path, String seq_type, IndigoObject library)
public IndigoObject loadIdt(String str, IndigoObject library)
public IndigoObject loadIdtFromFile(String path, IndigoObject library)
public IndigoObject loadHelm(String str, IndigoObject library)
public IndigoObject loadHelmFromFile(String path, IndigoObject library)
public IndigoObject loadReaction(String str)
public IndigoObject loadReaction(byte[] buf)
public IndigoObject loadReactionFromFile(String path)
public IndigoObject loadQueryReaction(String str)
public IndigoObject loadQueryReaction(byte[] buf)
public IndigoObject loadQueryReactionFromFile(String path)
public IndigoObject loadReactionSmarts(String str)
public IndigoObject loadReactionSmarts(byte[] buf)
public IndigoObject loadReactionSmartsFromFile(String path)
public IndigoObject loadStructure(String str)
public IndigoObject loadStructure(String str, String params)
public IndigoObject loadStructure(byte[] buf)
public IndigoObject loadStructure(byte[] buf, String params)
public IndigoObject loadStructureFromFile(String path)
public IndigoObject loadStructureFromFile(String path, String params)
public IndigoObject loadStructureFromBuffer(byte[] buf)
public IndigoObject loadStructureFromBuffer(byte[] buf, String params)
public IndigoObject loadFingerprintFromBuffer(byte[] buf)
public IndigoObject loadFingerprintFromDescriptors(double[] descriptors, int size, double density)
public IndigoObject createReaction()
public IndigoObject createQueryReaction()
public IndigoObject exactMatch(IndigoObject obj1, IndigoObject obj2, String flags)
public IndigoObject exactMatch(IndigoObject obj1, IndigoObject obj2)
public void removeTautomerRule(int id)
public void clearTautomerRules()
public float similarity(IndigoObject obj1, IndigoObject obj2)
public float similarity(IndigoObject obj1, IndigoObject obj2, String metrics)
public int commonBits(IndigoObject fingerprint1, IndigoObject fingerprint2)
@Deprecated public IndigoObject unserialize(byte[] data)
deserialize(byte[]) insteadpublic IndigoObject deserialize(byte[] data)
public IndigoObject createArray()
public IndigoObject iterateSDFile(String filename)
public IndigoObject iterateRDFile(String filename)
public IndigoObject iterateSmilesFile(String filename)
public IndigoObject iterateCMLFile(String filename)
public IndigoObject iterateCDXFile(String filename)
public IndigoObject substructureMatcher(IndigoObject target, String mode)
public IndigoObject substructureMatcher(IndigoObject target)
public IndigoObject extractCommonScaffold(IndigoObject structures, String options)
public IndigoObject extractCommonScaffold(Collection<IndigoObject> structures, String options)
public IndigoObject rgroupComposition(IndigoObject molecule, String options)
public IndigoObject getFragmentedMolecule(IndigoObject molecule, String options)
@Deprecated public IndigoObject decomposeMolecules(IndigoObject scaffold, IndigoObject structures)
@Deprecated public IndigoObject decomposeMolecules(IndigoObject scaffold, Collection<IndigoObject> structures)
public IndigoObject createDecomposer(IndigoObject scaffold)
public IndigoObject reactionProductEnumerate(IndigoObject reaction, IndigoObject monomers)
public IndigoObject reactionProductEnumerate(IndigoObject reaction, Iterable<Iterable<IndigoObject>> monomers)
public IndigoObject transform(IndigoObject reaction, IndigoObject monomer)
public IndigoObject createSaver(IndigoObject output, String format)
public IndigoObject createFileSaver(String filename, String format)
public void dbgBreakpoint()
public IndigoObject toIndigoArray(Collection<IndigoObject> coll)
public String getUserSpecifiedPath()
public long getSid()
public IndigoObject loadBuffer(byte[] buf)
public IndigoObject loadString(String string)
public IndigoObject iterateSDF(IndigoObject reader)
public IndigoObject iterateRDF(IndigoObject reader)
public IndigoObject iterateCML(IndigoObject reader)
public IndigoObject iterateCDX(IndigoObject reader)
public IndigoObject iterateSmiles(IndigoObject reader)
public IndigoObject iterateTautomers(IndigoObject molecule, String params)
public int buildPkaModel(int level,
float threshold,
String filename)
public IndigoObject nameToStructure(String name)
public IndigoObject nameToStructure(String name, String params)
public IndigoObject transformHELMtoSCSR(IndigoObject item)
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