Indigo (Indigo 1.2.1-dev5-moderna API)

java.lang.Object
- com.ggasoftware.indigo.Indigo

```
public class Indigo
extends Object
```

Field Summary

Fields
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 int`	`OR`
`static int`	`OS_LINUX`
`static int`	`OS_MACOS`
`static int`	`OS_SOLARIS`
`static int`	`OS_WINDOWS`
`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`	`SINGLET`
`static int`	`TRANS`
`static int`	`TRIPLET`
`static int`	`UP`

Constructor Summary

Constructors
Constructor and Description

Indigo()

Indigo(String path)

Constructors
Constructor and Description
`Indigo()`
`Indigo(String path)`

Method Summary

Methods
Modifier and Type	Method and Description
`static int`	`checkResult(Object obj, int result)`
`static int`	`checkResult(Object obj, Object obj2, int result)`
`static float`	`checkResultFloat(Object obj, float result)`
`static com.sun.jna.Pointer`	`checkResultPointer(Object obj, com.sun.jna.Pointer result)`
`static String`	`checkResultString(Object obj, com.sun.jna.Pointer result)`
`void`	`clearTautomerRules()`
`int`	`commonBits(IndigoObject fingerprint1, IndigoObject fingerprint2)`
`int`	`countReferences()`
`IndigoObject`	`createArray()`
`IndigoObject`	`createDecomposer(IndigoObject scaffold)`
`IndigoObject`	`createFileSaver(String filename, String format)`
`IndigoObject`	`createMolecule()`
`IndigoObject`	`createQueryMolecule()`
`IndigoObject`	`createQueryReaction()`
`IndigoObject`	`createReaction()`
`IndigoObject`	`createSaver(IndigoObject output, String format)`
`void`	`dbgBreakpoint()`
`IndigoObject`	`decomposeMolecules(IndigoObject scaffold, Collection<IndigoObject> structures)` Deprecated.
`IndigoObject`	`decomposeMolecules(IndigoObject scaffold, IndigoObject structures)` Deprecated.
`IndigoObject`	`exactMatch(IndigoObject obj1, IndigoObject obj2)`
`IndigoObject`	`exactMatch(IndigoObject obj1, IndigoObject obj2, String flags)`
`IndigoObject`	`extractCommonScaffold(Collection<IndigoObject> structures, String options)`
`IndigoObject`	`extractCommonScaffold(IndigoObject structures, String options)`
`static String`	`extractFromJar(Class cls, String path, String filename)`
`protected void`	`finalize()`
`static IndigoLib`	`getLibrary()`
`static int`	`getOs()`
`static String`	`getPlatformDependentPath()`
`long`	`getSid()`
`String`	`getUserSpecifiedPath()`
`IndigoObject`	`iterateCML(IndigoObject reader)`
`IndigoObject`	`iterateCMLFile(String filename)`
`IndigoObject`	`iterateRDF(IndigoObject reader)`
`IndigoObject`	`iterateRDFile(String filename)`
`IndigoObject`	`iterateSDF(IndigoObject reader)`
`IndigoObject`	`iterateSDFile(String filename)`
`IndigoObject`	`iterateSmiles(IndigoObject reader)`
`IndigoObject`	`iterateSmilesFile(String filename)`
`IndigoObject`	`loadBuffer(byte[] buf)`
`IndigoObject`	`loadMolecule(byte[] buf)`
`IndigoObject`	`loadMolecule(String str)`
`IndigoObject`	`loadMoleculeFromFile(String path)`
`IndigoObject`	`loadQueryMolecule(byte[] buf)`
`IndigoObject`	`loadQueryMolecule(String str)`
`IndigoObject`	`loadQueryMoleculeFromFile(String path)`
`IndigoObject`	`loadQueryReaction(byte[] buf)`
`IndigoObject`	`loadQueryReaction(String str)`
`IndigoObject`	`loadQueryReactionFromFile(String path)`
`IndigoObject`	`loadReaction(byte[] buf)`
`IndigoObject`	`loadReaction(String str)`
`IndigoObject`	`loadReactionFromFile(String path)`
`IndigoObject`	`loadReactionSmarts(byte[] buf)`
`IndigoObject`	`loadReactionSmarts(String str)`
`IndigoObject`	`loadReactionSmartsFromFile(String path)`
`IndigoObject`	`loadSmarts(byte[] buf)`
`IndigoObject`	`loadSmarts(String str)`
`IndigoObject`	`loadSmartsFromFile(String path)`
`IndigoObject`	`loadString(String string)`
`IndigoObject`	`reactionProductEnumerate(IndigoObject reaction, IndigoObject monomers)`
`IndigoObject`	`reactionProductEnumerate(IndigoObject reaction, Iterable<Iterable> monomers)`
`void`	`removeTautomerRule(int id)`
`boolean`	`sessionReleased()`
`void`	`setOption(String option, boolean value)`
`void`	`setOption(String option, double value)`
`void`	`setOption(String option, float value)`
`void`	`setOption(String option, float r, float g, float b)`
`void`	`setOption(String option, int value)`
`void`	`setOption(String option, int x, int y)`
`void`	`setOption(String option, String value)`
`void`	`setSessionID()`
`void`	`setTautomerRule(int id, String beg, String end)`
`float`	`similarity(IndigoObject obj1, IndigoObject obj2)`
`float`	`similarity(IndigoObject obj1, IndigoObject obj2, String metrics)`
`IndigoObject`	`substructureMatcher(IndigoObject target)`
`IndigoObject`	`substructureMatcher(IndigoObject target, String mode)`
`static float[]`	`toFloatArray(Collection<Float> collection)`
`IndigoObject`	`toIndigoArray(Collection<IndigoObject> coll)`
`static int[]`	`toIntArray(Collection<Integer> collection)`
`void`	`transform(IndigoObject reaction, IndigoObject monomer)`
`IndigoObject`	`unserialize(byte[] data)`
`String`	`version()`
`IndigoObject`	`writeBuffer()`
`IndigoObject`	`writeFile(String filename)`

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

Field Detail
- ABS
```
public static final int ABS
```
  See Also:
  Constant Field Values
- OR
```
public static final int OR
```
  See Also:
  Constant Field Values
- AND
```
public static final int AND
```
  See Also:
  Constant Field Values
- EITHER
```
public static final int EITHER
```
  See Also:
  Constant Field Values
- UP
```
public static final int UP
```
  See Also:
  Constant Field Values
- DOWN
```
public static final int DOWN
```
  See Also:
  Constant Field Values
- CIS
```
public static final int CIS
```
  See Also:
  Constant Field Values
- TRANS
```
public static final int TRANS
```
  See Also:
  Constant Field Values
- CHAIN
```
public static final int CHAIN
```
  See Also:
  Constant Field Values
- RING
```
public static final int RING
```
  See Also:
  Constant Field Values
- ALLENE
```
public static final int ALLENE
```
  See Also:
  Constant Field Values
- SINGLET
```
public static final int SINGLET
```
  See Also:
  Constant Field Values
- DOUBLET
```
public static final int DOUBLET
```
  See Also:
  Constant Field Values
- TRIPLET
```
public static final int TRIPLET
```
  See Also:
  Constant Field Values
- RC_NOT_CENTER
```
public static final int RC_NOT_CENTER
```
  See Also:
  Constant Field Values
- RC_UNMARKED
```
public static final int RC_UNMARKED
```
  See Also:
  Constant Field Values
- RC_CENTER
```
public static final int RC_CENTER
```
  See Also:
  Constant Field Values
- RC_UNCHANGED
```
public static final int RC_UNCHANGED
```
  See Also:
  Constant Field Values
- RC_MADE_OR_BROKEN
```
public static final int RC_MADE_OR_BROKEN
```
  See Also:
  Constant Field Values
- RC_ORDER_CHANGED
```
public static final int RC_ORDER_CHANGED
```
  See Also:
  Constant Field Values
- OS_WINDOWS
```
public static final int OS_WINDOWS
```
  See Also:
  Constant Field Values
- OS_MACOS
```
public static final int OS_MACOS
```
  See Also:
  Constant Field Values
- OS_LINUX
```
public static final int OS_LINUX
```
  See Also:
  Constant Field Values
- OS_SOLARIS
```
public static final int OS_SOLARIS
```
  See Also:
  Constant Field Values

Constructor Detail

Indigo
```
public Indigo(String path)
```

Indigo
```
public Indigo()
```

Method Detail

checkResult

public static int checkResult(Object obj,
              int result)

checkResult

public static int checkResult(Object obj,
              Object obj2,
              int result)

checkResultFloat

public static float checkResultFloat(Object obj,
                     float result)

checkResultString

public static String checkResultString(Object obj,
                       com.sun.jna.Pointer result)

checkResultPointer

public static com.sun.jna.Pointer checkResultPointer(Object obj,
                                     com.sun.jna.Pointer result)

toIntArray

public static int[] toIntArray(Collection<Integer> collection)

toFloatArray

public static float[] toFloatArray(Collection<Float> collection)

extractFromJar

public static String extractFromJar(Class cls,
                    String path,
                    String filename)

getPlatformDependentPath

public static String getPlatformDependentPath()

sessionReleased
```
public boolean sessionReleased()
```

getLibrary
```
public static IndigoLib getLibrary()
```

getOs
```
public static int getOs()
```

version
```
public String version()
```

countReferences
```
public int countReferences()
```

setSessionID
```
public void setSessionID()
```

setOption

public void setOption(String option,
             String value)

setOption

public void setOption(String option,
             int value)

setOption

public void setOption(String option,
             int x,
             int y)

setOption

public void setOption(String option,
             float r,
             float g,
             float b)

setOption

public void setOption(String option,
             boolean value)

setOption

public void setOption(String option,
             float value)

setOption

public void setOption(String option,
             double value)

writeFile

public IndigoObject writeFile(String filename)

writeBuffer
```
public IndigoObject writeBuffer()
```

createMolecule
```
public IndigoObject createMolecule()
```

createQueryMolecule

public IndigoObject createQueryMolecule()

loadMolecule

public IndigoObject loadMolecule(String str)

loadMolecule

public IndigoObject loadMolecule(byte[] buf)

loadMoleculeFromFile

public IndigoObject loadMoleculeFromFile(String path)

loadQueryMolecule

public IndigoObject loadQueryMolecule(String str)

loadQueryMolecule

public IndigoObject loadQueryMolecule(byte[] buf)

loadQueryMoleculeFromFile

public IndigoObject loadQueryMoleculeFromFile(String path)

loadSmarts

public IndigoObject loadSmarts(String str)

loadSmarts

public IndigoObject loadSmarts(byte[] buf)

loadSmartsFromFile

public IndigoObject loadSmartsFromFile(String path)

loadReaction

public IndigoObject loadReaction(String str)

loadReaction

public IndigoObject loadReaction(byte[] buf)

loadReactionFromFile

public IndigoObject loadReactionFromFile(String path)

loadQueryReaction

public IndigoObject loadQueryReaction(String str)

loadQueryReaction

public IndigoObject loadQueryReaction(byte[] buf)

loadQueryReactionFromFile

public IndigoObject loadQueryReactionFromFile(String path)

loadReactionSmarts

public IndigoObject loadReactionSmarts(String str)

loadReactionSmarts

public IndigoObject loadReactionSmarts(byte[] buf)

loadReactionSmartsFromFile

public IndigoObject loadReactionSmartsFromFile(String path)

createReaction
```
public IndigoObject createReaction()
```

createQueryReaction

public IndigoObject createQueryReaction()

exactMatch

public IndigoObject exactMatch(IndigoObject obj1,
                      IndigoObject obj2,
                      String flags)

exactMatch

public IndigoObject exactMatch(IndigoObject obj1,
                      IndigoObject obj2)

setTautomerRule

public void setTautomerRule(int id,
                   String beg,
                   String end)

removeTautomerRule

public void removeTautomerRule(int id)

clearTautomerRules
```
public void clearTautomerRules()
```

similarity

public float similarity(IndigoObject obj1,
               IndigoObject obj2)

similarity

public float similarity(IndigoObject obj1,
               IndigoObject obj2,
               String metrics)

commonBits

public int commonBits(IndigoObject fingerprint1,
             IndigoObject fingerprint2)

unserialize

public IndigoObject unserialize(byte[] data)

createArray
```
public IndigoObject createArray()
```

iterateSDFile

public IndigoObject iterateSDFile(String filename)

iterateRDFile

public IndigoObject iterateRDFile(String filename)

iterateSmilesFile

public IndigoObject iterateSmilesFile(String filename)

iterateCMLFile

public IndigoObject iterateCMLFile(String filename)

substructureMatcher

public IndigoObject substructureMatcher(IndigoObject target,
                               String mode)

substructureMatcher

public IndigoObject substructureMatcher(IndigoObject target)

extractCommonScaffold

public IndigoObject extractCommonScaffold(IndigoObject structures,
                                 String options)

extractCommonScaffold

public IndigoObject extractCommonScaffold(Collection<IndigoObject> structures,
                                 String options)

decomposeMolecules

@Deprecated
public IndigoObject decomposeMolecules(IndigoObject scaffold,
                                         IndigoObject structures)

Deprecated.

Use createDecomposer() and decomposeMolecule()

decomposeMolecules

@Deprecated
public IndigoObject decomposeMolecules(IndigoObject scaffold,
                                         Collection<IndigoObject> structures)

Deprecated.

Use createDecomposer() and decomposeMolecule()

createDecomposer

public IndigoObject createDecomposer(IndigoObject scaffold)

reactionProductEnumerate

public IndigoObject reactionProductEnumerate(IndigoObject reaction,
                                    IndigoObject monomers)

reactionProductEnumerate

public IndigoObject reactionProductEnumerate(IndigoObject reaction,
                                    Iterable<Iterable> monomers)

transform

public void transform(IndigoObject reaction,
             IndigoObject monomer)

createSaver

public IndigoObject createSaver(IndigoObject output,
                       String format)

createFileSaver

public IndigoObject createFileSaver(String filename,
                           String format)

dbgBreakpoint
```
public void dbgBreakpoint()
```

toIndigoArray

public IndigoObject toIndigoArray(Collection<IndigoObject> coll)

getUserSpecifiedPath
```
public String getUserSpecifiedPath()
```

getSid
```
public long getSid()
```

loadBuffer

public IndigoObject loadBuffer(byte[] buf)

loadString

public IndigoObject loadString(String string)

iterateSDF

public IndigoObject iterateSDF(IndigoObject reader)

iterateRDF

public IndigoObject iterateRDF(IndigoObject reader)

iterateCML

public IndigoObject iterateCML(IndigoObject reader)

iterateSmiles

public IndigoObject iterateSmiles(IndigoObject reader)

finalize

protected void finalize()
                 throws Throwable

Overrides:: finalize in class Object
Throws:: Throwable

Class Indigo

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ABS

OR

AND

EITHER

UP

DOWN

CIS

TRANS

CHAIN

RING

ALLENE

SINGLET

DOUBLET

TRIPLET

RC_NOT_CENTER

RC_UNMARKED

RC_CENTER

RC_UNCHANGED

RC_MADE_OR_BROKEN

RC_ORDER_CHANGED

OS_WINDOWS

OS_MACOS

OS_LINUX

OS_SOLARIS

Constructor Detail

Indigo

Indigo

Method Detail

checkResult

checkResult

checkResultFloat

checkResultString

checkResultPointer

toIntArray

toFloatArray

extractFromJar

getPlatformDependentPath

sessionReleased

getLibrary

getOs

version

countReferences

setSessionID

setOption

setOption

setOption

setOption

setOption

setOption

setOption

writeFile

writeBuffer

createMolecule

createQueryMolecule

loadMolecule

loadMolecule

loadMoleculeFromFile

loadQueryMolecule

loadQueryMolecule

loadQueryMoleculeFromFile

loadSmarts

loadSmarts

loadSmartsFromFile

loadReaction

loadReaction

loadReactionFromFile

loadQueryReaction

loadQueryReaction

loadQueryReactionFromFile

loadReactionSmarts

loadReactionSmarts

loadReactionSmartsFromFile

createReaction

createQueryReaction