A C D G I J L M N O R S T V

A

addAtom(JniInchiAtom) - Method in class net.sf.jniinchi.JniInchiStructure

Adds atom to inchi molecule.

addAtoms(JniInchiAtom...) - Method in class net.sf.jniinchi.JniInchiStructure

Convenience method to add multiple atoms to molecule.

addBond(JniInchiBond) - Method in class net.sf.jniinchi.JniInchiStructure

Adds bond to inchi molecule.

addBonds(JniInchiBond...) - Method in class net.sf.jniinchi.JniInchiStructure

Convenience method to add multiple bonds to molecule.

addStereo0D(JniInchiStereo0D) - Method in class net.sf.jniinchi.JniInchiStructure

Adds 0D stereo parity to inchi molecule.

C

checkInchi(String, boolean) - Static method in class net.sf.jniinchi.JniInchiWrapper

Checks if the string represents valid InChI/standard InChI.

checkInchiKey(String) - Static method in class net.sf.jniinchi.JniInchiWrapper

Checks whether a string represents valid InChIKey.

checkOptions(List<INCHI_OPTION>) - Static method in class net.sf.jniinchi.JniInchiWrapper

Checks and canonicalises options.

checkOptions(String) - Static method in class net.sf.jniinchi.JniInchiWrapper

Checks and canonicalises options.

createNewDoublebondStereo0D(JniInchiAtom, JniInchiAtom, JniInchiAtom, JniInchiAtom, INCHI_PARITY) - Static method in class net.sf.jniinchi.JniInchiStereo0D

Convenience method for generating 0D stereo parities at stereogenic double bonds.

createNewTetrahedralStereo0D(JniInchiAtom, JniInchiAtom, JniInchiAtom, JniInchiAtom, JniInchiAtom, INCHI_PARITY) - Static method in class net.sf.jniinchi.JniInchiStereo0D

Convenience method for generating 0D stereo parities at tetrahedral atom centres.

D

debug() - Method in class net.sf.jniinchi.JniInchiAtom

Outputs information on atom, for debugging purposes.

debug() - Method in class net.sf.jniinchi.JniInchiBond

Outputs information on bond, for debugging purposes.

debug() - Method in class net.sf.jniinchi.JniInchiStereo0D

Outputs information on stereo parity, for debugging purposes.

G

getAtom(int) - Method in class net.sf.jniinchi.JniInchiStructure

Returns atom from structure.

getAuxInfo() - Method in class net.sf.jniinchi.JniInchiOutput

Gets generated InChI string.

getBond(int) - Method in class net.sf.jniinchi.JniInchiStructure

Returns bond from structure.

getBondStereo() - Method in class net.sf.jniinchi.JniInchiBond

Returns bond stereochemistry.

getBondType() - Method in class net.sf.jniinchi.JniInchiBond

Returns bond type.

getCentralAtom() - Method in class net.sf.jniinchi.JniInchiStereo0D

Returns central atom of stereo parity.

getCharge() - Method in class net.sf.jniinchi.JniInchiAtom

Returns charge on atom.

getDebugString() - Method in class net.sf.jniinchi.JniInchiAtom

Generates string representation of information on atom, for debugging purposes.

getDebugString() - Method in class net.sf.jniinchi.JniInchiBond

Generates string representation of information on bond, for debugging purposes.

getDebugString() - Method in class net.sf.jniinchi.JniInchiStereo0D

Generates string representation of information on stereo parity, for debugging purposes.

getDisconnectedParity() - Method in class net.sf.jniinchi.JniInchiStereo0D

Returns disconnected parity.

getElementType() - Method in class net.sf.jniinchi.JniInchiAtom

Returns chemical element symbol of atom.

getErrorMessage() - Method in class net.sf.jniinchi.JniInchiInputData

getImplicitDeuterium() - Method in class net.sf.jniinchi.JniInchiAtom

Returns number of implicit deuteriums (2H) on atom.

getImplicitH() - Method in class net.sf.jniinchi.JniInchiAtom

Returns number of implicit hydrogens on atom.

getImplicitProtium() - Method in class net.sf.jniinchi.JniInchiAtom

Returns number of implicit protiums (1H) on atom.

getImplicitTritium() - Method in class net.sf.jniinchi.JniInchiAtom

Returns number of implicit tritiums (3H) on atom.

getInchi() - Method in class net.sf.jniinchi.JniInchiInputInchi

Returns options string.

getInchi() - Method in class net.sf.jniinchi.JniInchiOutput

Gets generated InChI string.

getInchi(JniInchiInput) - Static method in class net.sf.jniinchi.JniInchiWrapper

Generates the InChI for a chemical structure.

getInchiFromInchi(JniInchiInputInchi) - Static method in class net.sf.jniinchi.JniInchiWrapper

Converts an InChI into an InChI for validation purposes (the same as the -InChI2InChI option).

getInchiKey(String) - Static method in class net.sf.jniinchi.JniInchiWrapper

Calculates the InChIKey for an InChI string.

getIndx() - Method in enum net.sf.jniinchi.INCHI_BOND_STEREO

getIndx() - Method in enum net.sf.jniinchi.INCHI_BOND_TYPE

getIndx() - Method in enum net.sf.jniinchi.INCHI_KEY

getIndx() - Method in enum net.sf.jniinchi.INCHI_KEY_STATUS

getIndx() - Method in enum net.sf.jniinchi.INCHI_PARITY

getIndx() - Method in enum net.sf.jniinchi.INCHI_RADICAL

Returns index.

getIndx() - Method in enum net.sf.jniinchi.INCHI_RET

getIndx() - Method in enum net.sf.jniinchi.INCHI_STATUS

getIndx() - Method in enum net.sf.jniinchi.INCHI_STEREOTYPE

getInput() - Method in class net.sf.jniinchi.JniInchiInputData

getInputFromAuxInfo(String) - Static method in class net.sf.jniinchi.JniInchiWrapper

getIsotopicMass() - Method in class net.sf.jniinchi.JniInchiAtom

Returns isotopic mass of atom.

getKey() - Method in class net.sf.jniinchi.JniInchiOutputKey

getLog() - Method in class net.sf.jniinchi.JniInchiOutput

Gets generated log.

getLog() - Method in class net.sf.jniinchi.JniInchiOutputStructure

Gets generated log.

getMessage() - Method in class net.sf.jniinchi.JniInchiOutput

Gets generated (error/warning) messages.

getMessage() - Method in class net.sf.jniinchi.JniInchiOutputStructure

Gets generated (error/warning) messages.

getNeighbor(int) - Method in class net.sf.jniinchi.JniInchiStereo0D

getNeighbors() - Method in class net.sf.jniinchi.JniInchiStereo0D

Returns neighboring atoms of stereo parity.

getNumAtoms() - Method in class net.sf.jniinchi.JniInchiStructure

Returns number of atoms in structure.

getNumBonds() - Method in class net.sf.jniinchi.JniInchiStructure

Returns number of bonds in structure.

getNumStereo0D() - Method in class net.sf.jniinchi.JniInchiStructure

Returns number of stereo parities in strucuture.

getOptions() - Method in class net.sf.jniinchi.JniInchiInput

Returns options string.

getOptions() - Method in class net.sf.jniinchi.JniInchiInputInchi

Returns options string.

getOriginAtom() - Method in class net.sf.jniinchi.JniInchiBond

Returns atom at bond origin.

getParity() - Method in class net.sf.jniinchi.JniInchiStereo0D

Returns parity.

getRadical() - Method in class net.sf.jniinchi.JniInchiAtom

Returns radical state of atom.

getReturnStatus() - Method in class net.sf.jniinchi.JniInchiOutput

Gets return status from InChI process.

getReturnStatus() - Method in class net.sf.jniinchi.JniInchiOutputKey

getReturnStatus() - Method in class net.sf.jniinchi.JniInchiOutputStructure

Gets return status from InChI process.

getReturnValue() - Method in class net.sf.jniinchi.JniInchiInputData

getStdInchi(JniInchiInput) - Static method in class net.sf.jniinchi.JniInchiWrapper

Calculates the Standard InChI string for a chemical structure.

getStereo0D(int) - Method in class net.sf.jniinchi.JniInchiStructure

Returns stereo parity from structure.

getStereoType() - Method in class net.sf.jniinchi.JniInchiStereo0D

Returns type of stereochemistry.

getStructureFromInchi(JniInchiInputInchi) - Static method in class net.sf.jniinchi.JniInchiWrapper

Generated 0D structure from an InChI string.

getTargetAtom() - Method in class net.sf.jniinchi.JniInchiBond

Returns atom at bond target.

getTestMolecule() - Static method in class net.sf.jniinchi.Main

Provide test structure.

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_BOND_STEREO

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_BOND_TYPE

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_KEY

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_KEY_STATUS

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_PARITY

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_RADICAL

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_RET

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_STATUS

getValue(int) - Static method in enum net.sf.jniinchi.INCHI_STEREOTYPE

getWarningFlags() - Method in class net.sf.jniinchi.JniInchiOutputStructure

Returns warning flags, see INCHIDIFF in inchicmp.h.

getX() - Method in class net.sf.jniinchi.JniInchiAtom

Returns atom's X-coordinate.

getY() - Method in class net.sf.jniinchi.JniInchiAtom

Returns atom's Y-coordinate.

getZ() - Method in class net.sf.jniinchi.JniInchiAtom

Returns atom's Z-coordinate.

I

INCHI_BOND_STEREO - Enum in net.sf.jniinchi

Enumeration of InChI 2D stereo definitions.

INCHI_BOND_TYPE - Enum in net.sf.jniinchi

Enumeration of InChI bond type definitions.

INCHI_KEY - Enum in net.sf.jniinchi

Type-safe enumeration of InChI return codes.

INCHI_KEY_STATUS - Enum in net.sf.jniinchi

Type-safe enumeration of InChIKey check return codes.

INCHI_OPTION - Enum in net.sf.jniinchi

Type-safe enumeration of InChI options.

INCHI_PARITY - Enum in net.sf.jniinchi

Enumeration of InChI 0D parities.

INCHI_RADICAL - Enum in net.sf.jniinchi

Enumeration of InChI radical definitions.

INCHI_RET - Enum in net.sf.jniinchi

Type-safe enumeration of InChI return codes.

INCHI_STATUS - Enum in net.sf.jniinchi

INCHI_STEREOTYPE - Enum in net.sf.jniinchi

Enumeration of InChI 0D parity types.

inchiString - Variable in class net.sf.jniinchi.JniInchiInputInchi

InChI ASCIIZ string to be converted to a strucure

ISOTOPIC_SHIFT_FLAG - Static variable in class net.sf.jniinchi.JniInchiAtom

Indicates relative rather than absolute isotopic mass.

J

JniInchiAtom - Class in net.sf.jniinchi

Encapsulates properties of InChI Atom.

JniInchiAtom(double, double, double, String) - Constructor for class net.sf.jniinchi.JniInchiAtom

Create new atom.

JniInchiAtom(String) - Constructor for class net.sf.jniinchi.JniInchiAtom

Convenience method to create a new atom with zero coordinates.

JniInchiBond - Class in net.sf.jniinchi

Encapsulates properties of InChI Bond.

JniInchiBond(JniInchiAtom, JniInchiAtom, INCHI_BOND_TYPE, INCHI_BOND_STEREO) - Constructor for class net.sf.jniinchi.JniInchiBond

Create bond.

JniInchiBond(JniInchiAtom, JniInchiAtom, INCHI_BOND_TYPE) - Constructor for class net.sf.jniinchi.JniInchiBond

Create bond.

JniInchiException - Exception in net.sf.jniinchi

Exception thrown by JniInchi.

JniInchiException() - Constructor for exception net.sf.jniinchi.JniInchiException

Constructor.

JniInchiException(String) - Constructor for exception net.sf.jniinchi.JniInchiException

Constructs a new exception with the specified detail message.

JniInchiException(Throwable) - Constructor for exception net.sf.jniinchi.JniInchiException

Constructs a new exception with the specified cause.

JniInchiInput - Class in net.sf.jniinchi

Encapsulates structure input for InChI generation.

JniInchiInput() - Constructor for class net.sf.jniinchi.JniInchiInput

Constructor.

JniInchiInput(String) - Constructor for class net.sf.jniinchi.JniInchiInput

Constructor.

JniInchiInput(List) - Constructor for class net.sf.jniinchi.JniInchiInput

Constructor.

JniInchiInput(JniInchiStructure) - Constructor for class net.sf.jniinchi.JniInchiInput

Constructor.

JniInchiInput(JniInchiStructure, String) - Constructor for class net.sf.jniinchi.JniInchiInput

Constructor.

JniInchiInputData - Class in net.sf.jniinchi

JniInchiInputData(int, JniInchiInput, int, String) - Constructor for class net.sf.jniinchi.JniInchiInputData

JniInchiInputInchi - Class in net.sf.jniinchi

Encapsulates input for InChI to structure conversion.

JniInchiInputInchi(String) - Constructor for class net.sf.jniinchi.JniInchiInputInchi

Constructor.

JniInchiInputInchi(String, String) - Constructor for class net.sf.jniinchi.JniInchiInputInchi

Constructor.

JniInchiInputInchi(String, List) - Constructor for class net.sf.jniinchi.JniInchiInputInchi

Constructor.

JniInchiOutput - Class in net.sf.jniinchi

Encapsulates output from InChI generation.

JniInchiOutput(int, String, String, String, String) - Constructor for class net.sf.jniinchi.JniInchiOutput

JniInchiOutput(INCHI_RET, String, String, String, String) - Constructor for class net.sf.jniinchi.JniInchiOutput

JniInchiOutputKey - Class in net.sf.jniinchi

JniInchiOutputKey(int, String) - Constructor for class net.sf.jniinchi.JniInchiOutputKey

JniInchiOutputKey(INCHI_KEY, String) - Constructor for class net.sf.jniinchi.JniInchiOutputKey

JniInchiOutputStructure - Class in net.sf.jniinchi

Encapsulates output from InChI to structure conversion.

JniInchiOutputStructure(int, String, String, long, long, long, long) - Constructor for class net.sf.jniinchi.JniInchiOutputStructure

JniInchiOutputStructure(INCHI_RET) - Constructor for class net.sf.jniinchi.JniInchiOutputStructure

JniInchiStereo0D - Class in net.sf.jniinchi

Encapsulates properites of InChI Stereo Parity.

JniInchiStereo0D(JniInchiAtom, JniInchiAtom, JniInchiAtom, JniInchiAtom, JniInchiAtom, INCHI_STEREOTYPE, INCHI_PARITY) - Constructor for class net.sf.jniinchi.JniInchiStereo0D

Constructor.

JniInchiStructure - Class in net.sf.jniinchi

JniInchiStructure() - Constructor for class net.sf.jniinchi.JniInchiStructure

JniInchiWrapper - Class in net.sf.jniinchi

JNI Wrapper for International Chemical Identifier (InChI) C++ library.

L

LibInchiGetVersion() - Static method in class net.sf.jniinchi.JniInchiWrapper

loadLibrary() - Static method in class net.sf.jniinchi.JniInchiWrapper

Loads native library.

LoadNativeLibraryException - Exception in net.sf.jniinchi

LoadNativeLibraryException() - Constructor for exception net.sf.jniinchi.LoadNativeLibraryException

Constructor.

LoadNativeLibraryException(String) - Constructor for exception net.sf.jniinchi.LoadNativeLibraryException

Constructor.

LoadNativeLibraryException(Throwable) - Constructor for exception net.sf.jniinchi.LoadNativeLibraryException

M

Main - Class in net.sf.jniinchi

Simple test class, for debugging purposes.

Main() - Constructor for class net.sf.jniinchi.Main

main(String[]) - Static method in class net.sf.jniinchi.Main

N

net.sf.jniinchi - package net.sf.jniinchi

NO_ATOM - Static variable in class net.sf.jniinchi.JniInchiStereo0D

Indicates non-existent (central) atom.

O

options - Variable in class net.sf.jniinchi.JniInchiInput

Options string,

options - Variable in class net.sf.jniinchi.JniInchiInputInchi

InChI options: space-delimited

R

runChecks() - Static method in class net.sf.jniinchi.Main

S

setAuxInfo(String) - Method in class net.sf.jniinchi.JniInchiOutput

setCharge(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets charge on atom.

setDisconnectedParity(INCHI_PARITY) - Method in class net.sf.jniinchi.JniInchiStereo0D

Set second parity (for disconnected systems)

setImplicitDeuterium(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets number of implicit deuterium (2H) on atom.

setImplicitH(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets number of implicit hydrogens on atom.

setImplicitProtium(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets number of implicit protium (1H) on atom.

setImplicitTritium(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets number of implicit tritium (3H) on atom.

setInchi(String) - Method in class net.sf.jniinchi.JniInchiOutput

setIsotopicMass(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets isotopic mass.

setIsotopicMassShift(int) - Method in class net.sf.jniinchi.JniInchiAtom

Sets isotopic mass, relative to standard mass.

setLog(String) - Method in class net.sf.jniinchi.JniInchiOutput

setLog(String) - Method in class net.sf.jniinchi.JniInchiOutputStructure

setMessage(String) - Method in class net.sf.jniinchi.JniInchiOutput

setMessage(String) - Method in class net.sf.jniinchi.JniInchiOutputStructure

setRadical(INCHI_RADICAL) - Method in class net.sf.jniinchi.JniInchiAtom

Sets radical status of atom.

setRetStatus(INCHI_RET) - Method in class net.sf.jniinchi.JniInchiOutput

setRetStatus(INCHI_RET) - Method in class net.sf.jniinchi.JniInchiOutputStructure

setStereoDefinition(INCHI_BOND_STEREO) - Method in class net.sf.jniinchi.JniInchiBond

Set 2D stereo definition.

setStructure(JniInchiStructure) - Method in class net.sf.jniinchi.JniInchiStructure

setWarningFlags(long[][]) - Method in class net.sf.jniinchi.JniInchiOutputStructure

setWarningFlags(long, long, long, long) - Method in class net.sf.jniinchi.JniInchiOutputStructure

T

toString() - Method in class net.sf.jniinchi.JniInchiOutput

V

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_BOND_STEREO

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_BOND_TYPE

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_KEY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_KEY_STATUS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_OPTION

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_PARITY

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_RADICAL

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_RET

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_STATUS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum net.sf.jniinchi.INCHI_STEREOTYPE

Returns the enum constant of this type with the specified name.

valueOfIgnoreCase(String) - Static method in enum net.sf.jniinchi.INCHI_OPTION

values() - Static method in enum net.sf.jniinchi.INCHI_BOND_STEREO

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_BOND_TYPE

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_KEY

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_KEY_STATUS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_OPTION

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_PARITY

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_RADICAL

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_RET

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_STATUS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum net.sf.jniinchi.INCHI_STEREOTYPE

Returns an array containing the constants of this enum type, in the order they are declared.

A C D G I J L M N O R S T V