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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.
ALLENE - net.sf.jniinchi.INCHI_STEREOTYPE
Allene.
ALTERN - net.sf.jniinchi.INCHI_BOND_TYPE
Alternating (single-double) bond.
atomList - Variable in class net.sf.jniinchi.JniInchiStructure
List of atoms.
atomOrigin - Variable in class net.sf.jniinchi.JniInchiBond
Origin atom in bond.
atomTarget - Variable in class net.sf.jniinchi.JniInchiBond
Target atom in bond.
AuxNone - net.sf.jniinchi.INCHI_OPTION
Omit auxiliary information (default: Include).

B

bondList - Variable in class net.sf.jniinchi.JniInchiStructure
List of bonds.
BREAK - net.sf.jniinchi.INCHI_RET
 
BUSY - net.sf.jniinchi.INCHI_RET
Previuos call to InChI has not returned yet.

C

centralAtom - Variable in class net.sf.jniinchi.JniInchiStereo0D
Central atom.
charge - Variable in class net.sf.jniinchi.JniInchiAtom
Charge on atom.
checkInchi(String, boolean) - Static method in class net.sf.jniinchi.JniInchiWrapper
Checks if the string represents valid InChI/standard InChI.
CheckINCHI(String, boolean) - Method in class net.sf.jniinchi.JniInchiWrapper
 
checkInchiKey(String) - Static method in class net.sf.jniinchi.JniInchiWrapper
Checks whether a string represents valid InChIKey.
CheckINCHIKey(String) - Method in class net.sf.jniinchi.JniInchiWrapper
 
checkNativeCodeVersion() - Static method in class net.sf.jniinchi.JniInchiWrapper
Checks the expected native code version has been loaded.
checkOptions(String) - Static method in class net.sf.jniinchi.JniInchiWrapper
Checks and canonicalises options.
checkOptions(List<INCHI_OPTION>) - Static method in class net.sf.jniinchi.JniInchiWrapper
Checks and canonicalises options.
ChiralFlagOFF - net.sf.jniinchi.INCHI_OPTION
Set Not-Chiral Flag.
ChiralFlagON - net.sf.jniinchi.INCHI_OPTION
Set Chiral Flag.
Compress - net.sf.jniinchi.INCHI_OPTION
Compressed output.
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.
disconParity - Variable in class net.sf.jniinchi.JniInchiStereo0D
Second parity (for disconnected systems).
DoNotAddH - net.sf.jniinchi.INCHI_OPTION
Overrides inchi_Atom::num_iso_H[0] == -1.
DOUBLE - net.sf.jniinchi.INCHI_BOND_TYPE
Double bond.
DOUBLE_EITHER - net.sf.jniinchi.INCHI_BOND_STEREO
Unknown stereobond geometry.
DOUBLEBOND - net.sf.jniinchi.INCHI_STEREOTYPE
Stereogenic bond >A=B< or cumulene >A=C=C=B<.
DOUBLET - net.sf.jniinchi.INCHI_RADICAL
Doublet.

E

elname - Variable in class net.sf.jniinchi.JniInchiAtom
Chemical element symbol eg C, O, Fe, Hg.
EMPTY_INPUT - net.sf.jniinchi.INCHI_KEY
 
EOF - net.sf.jniinchi.INCHI_RET
No structural data has been provided.
ERROR - net.sf.jniinchi.INCHI_RET
Error: no InChI has been created.
errorMessage - Variable in class net.sf.jniinchi.JniInchiInputData
 
EVEN - net.sf.jniinchi.INCHI_PARITY
Even.

F

FAIL_I2I - net.sf.jniinchi.INCHI_STATUS
 
FATAL - net.sf.jniinchi.INCHI_RET
Severe error: no InChI has been created (typically, memory allocation failure).
FB - net.sf.jniinchi.INCHI_OPTION
Same as FixSp3Bug.
FixedH - net.sf.jniinchi.INCHI_OPTION
Mobile H Perception Off (Default: On).
FixSp3Bug - net.sf.jniinchi.INCHI_OPTION
Fix bug leading to missing or undefined sp3 parity.
flagChar - Static variable in class net.sf.jniinchi.JniInchiWrapper
Switch character for passing options.

G

getAtom(int) - Method in class net.sf.jniinchi.JniInchiStructure
Returns atom from structure.
getAtomIndex(JniInchiAtom) - Method in class net.sf.jniinchi.JniInchiStructure
 
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.
GetINCHI(JniInchiInput) - Method in class net.sf.jniinchi.JniInchiWrapper
 
getInchiBondStereo() - Method in class net.sf.jniinchi.JniInchiBond
 
getInchiBondType() - Method in class net.sf.jniinchi.JniInchiBond
 
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).
GetINCHIfromINCHI(String, String) - Method in class net.sf.jniinchi.JniInchiWrapper
 
GetINCHIInputFromAuxInfo(String, boolean, boolean) - Method in class net.sf.jniinchi.JniInchiWrapper
 
getInchiKey(String) - Static method in class net.sf.jniinchi.JniInchiWrapper
Calculates the InChIKey for an InChI string.
GetINCHIKeyFromINCHI(String) - Method in class net.sf.jniinchi.JniInchiWrapper
 
getInchiParity() - Method in class net.sf.jniinchi.JniInchiStereo0D
 
getInchiRadical() - Method in class net.sf.jniinchi.JniInchiAtom
 
getInchiStereoType() - Method in class net.sf.jniinchi.JniInchiStereo0D
 
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_STATUS
 
getIndx() - Method in enum net.sf.jniinchi.INCHI_KEY
 
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
 
getLock() - Static method in class net.sf.jniinchi.JniInchiWrapper
 
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.
GetStdINCHI(JniInchiInput) - Method in class net.sf.jniinchi.JniInchiWrapper
 
GetStdINCHIKeyFromStdINCHI(String) - Method in class net.sf.jniinchi.JniInchiWrapper
 
getStereo0D(int) - Method in class net.sf.jniinchi.JniInchiStructure
Returns stereo parity from structure.
getStereo0DIndex(JniInchiStereo0D) - Method in class net.sf.jniinchi.JniInchiStructure
 
getStereoType() - Method in class net.sf.jniinchi.JniInchiStereo0D
Returns type of stereochemistry.
GetStructFromINCHI(String, String) - Method in class net.sf.jniinchi.JniInchiWrapper
 
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.
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_STATUS
 
getValue(int) - Static method in enum net.sf.jniinchi.INCHI_KEY
 
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.
getWrapper() - Static method in class net.sf.jniinchi.JniInchiWrapper
 
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

ID - Static variable in class net.sf.jniinchi.JniInchiWrapper
 
implicitD - Variable in class net.sf.jniinchi.JniInchiAtom
Number of implicit deuteriums (isotopic 2-H) on atom.
implicitH - Variable in class net.sf.jniinchi.JniInchiAtom
Number of implicit hydrogens on atom.
implicitP - Variable in class net.sf.jniinchi.JniInchiAtom
Number of implicit protiums (isotopic 1-H) on atom.
implicitT - Variable in class net.sf.jniinchi.JniInchiAtom
Number of implicit tritiums (isotopic 3-H) on atom.
INCHI_BOND_STEREO - Enum in net.sf.jniinchi
Enumeration of InChI 2D stereo definitions.
INCHI_BOND_STEREO(int) - Constructor for enum net.sf.jniinchi.INCHI_BOND_STEREO
Constructor.
INCHI_BOND_TYPE - Enum in net.sf.jniinchi
Enumeration of InChI bond type definitions.
INCHI_BOND_TYPE(int) - Constructor for enum net.sf.jniinchi.INCHI_BOND_TYPE
Constructor.
INCHI_KEY - Enum in net.sf.jniinchi
Type-safe enumeration of InChI return codes.
INCHI_KEY(int) - Constructor for enum net.sf.jniinchi.INCHI_KEY
Constructor.
INCHI_KEY_STATUS - Enum in net.sf.jniinchi
Type-safe enumeration of InChIKey check return codes.
INCHI_KEY_STATUS(int) - Constructor for enum net.sf.jniinchi.INCHI_KEY_STATUS
Constructor.
INCHI_OPTION - Enum in net.sf.jniinchi
Type-safe enumeration of InChI options.
INCHI_OPTION() - Constructor for enum net.sf.jniinchi.INCHI_OPTION
 
INCHI_PARITY - Enum in net.sf.jniinchi
Enumeration of InChI 0D parities.
INCHI_PARITY(int) - Constructor for enum net.sf.jniinchi.INCHI_PARITY
Constructor.
INCHI_RADICAL - Enum in net.sf.jniinchi
Enumeration of InChI radical definitions.
INCHI_RADICAL(int) - Constructor for enum net.sf.jniinchi.INCHI_RADICAL
Constructor.
INCHI_RET - Enum in net.sf.jniinchi
Type-safe enumeration of InChI return codes.
INCHI_RET(int) - Constructor for enum net.sf.jniinchi.INCHI_RET
Constructor.
INCHI_STATUS - Enum in net.sf.jniinchi
 
INCHI_STATUS(int) - Constructor for enum net.sf.jniinchi.INCHI_STATUS
Constructor.
INCHI_STEREOTYPE - Enum in net.sf.jniinchi
Enumeration of InChI 0D parity types.
INCHI_STEREOTYPE(int) - Constructor for enum net.sf.jniinchi.INCHI_STEREOTYPE
Constructor.
inchiString - Variable in class net.sf.jniinchi.JniInchiInputInchi
InChI ASCIIZ string to be converted to a strucure
inchiWrapper - Static variable in class net.sf.jniinchi.JniInchiWrapper
 
indx - Variable in enum net.sf.jniinchi.INCHI_BOND_STEREO
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_BOND_TYPE
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_KEY_STATUS
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_KEY
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_PARITY
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_RADICAL
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_RET
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_STATUS
Internal InChI index (from inchi_api.h).
indx - Variable in enum net.sf.jniinchi.INCHI_STEREOTYPE
Internal InChI index (from inchi_api.h).
init() - Static method in class net.sf.jniinchi.JniInchiWrapper
 
input - Variable in class net.sf.jniinchi.JniInchiInputData
 
INVALID_INCHI - net.sf.jniinchi.INCHI_KEY
 
INVALID_INCHI_PREFIX - net.sf.jniinchi.INCHI_KEY
 
INVALID_LAYOUT - net.sf.jniinchi.INCHI_KEY_STATUS
 
INVALID_LAYOUT - net.sf.jniinchi.INCHI_STATUS
 
INVALID_LENGTH - net.sf.jniinchi.INCHI_KEY_STATUS
 
INVALID_PREFIX - net.sf.jniinchi.INCHI_STATUS
 
INVALID_STD_INCHI - net.sf.jniinchi.INCHI_KEY
 
INVALID_VERSION - net.sf.jniinchi.INCHI_KEY_STATUS
 
INVALID_VERSION - net.sf.jniinchi.INCHI_STATUS
 
IS_WINDOWS - Static variable in class net.sf.jniinchi.JniInchiWrapper
Flag indicating windows or linux.
isotopic_mass - Variable in class net.sf.jniinchi.JniInchiAtom
Mass of isotope.
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, int, int) - Constructor for class net.sf.jniinchi.JniInchiBond
 
JniInchiBond(JniInchiAtom, JniInchiAtom, INCHI_BOND_TYPE) - Constructor for class net.sf.jniinchi.JniInchiBond
Create bond.
JniInchiBond(JniInchiAtom, JniInchiAtom, INCHI_BOND_TYPE, INCHI_BOND_STEREO) - 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<INCHI_OPTION>) - 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<INCHI_OPTION>) - 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, int, int) - Constructor for class net.sf.jniinchi.JniInchiStereo0D
 
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.
JniInchiWrapper() - Constructor for class net.sf.jniinchi.JniInchiWrapper
Constructor

K

key - Variable in class net.sf.jniinchi.JniInchiOutputKey
 

L

LibInchiGetVersion() - Static method in class net.sf.jniinchi.JniInchiWrapper
 
libraryLoaded - Static variable in class net.sf.jniinchi.JniInchiWrapper
Records whether native library has been loaded by system.
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
 
lock - Static variable in class net.sf.jniinchi.JniInchiWrapper
 
log - Variable in class net.sf.jniinchi.JniInchiOutputStructure
Log generated.

M

MAX_LOCK_TIMEOUT - Static variable in class net.sf.jniinchi.JniInchiWrapper
Maximum time to wait for a lock (in seconds).
message - Variable in class net.sf.jniinchi.JniInchiOutputStructure
Error/warning messages generated.

N

neighbors - Variable in class net.sf.jniinchi.JniInchiStereo0D
Neighbouring atoms.
net.sf.jniinchi - package net.sf.jniinchi
 
NEWPS - net.sf.jniinchi.INCHI_OPTION
Narrow end of wedge points to stereocentre (default: both).
NO_ATOM - Static variable in class net.sf.jniinchi.JniInchiStereo0D
Indicates non-existent (central) atom.
NoADP - net.sf.jniinchi.INCHI_OPTION
Disable Aggressive Deprotonation (for testing only).
NONE - net.sf.jniinchi.INCHI_BOND_STEREO
No 2D stereo definition recorded.
NONE - net.sf.jniinchi.INCHI_BOND_TYPE
 
NONE - net.sf.jniinchi.INCHI_PARITY
None.
NONE - net.sf.jniinchi.INCHI_RADICAL
No radical status recorded.
NONE - net.sf.jniinchi.INCHI_STEREOTYPE
None.
NOT_ENOUGH_MEMORY - net.sf.jniinchi.INCHI_KEY
 

O

ODD - net.sf.jniinchi.INCHI_PARITY
Odd.
OK - net.sf.jniinchi.INCHI_KEY
 
OKAY - net.sf.jniinchi.INCHI_RET
Success; no errors or warnings.
options - Variable in class net.sf.jniinchi.JniInchiInput
Options string,
options - Variable in class net.sf.jniinchi.JniInchiInputInchi
InChI options: space-delimited
OutputSDF - net.sf.jniinchi.INCHI_OPTION
Output SDfile instead of InChI.

P

parity - Variable in class net.sf.jniinchi.JniInchiStereo0D
Parity.

R

radical - Variable in class net.sf.jniinchi.JniInchiAtom
Radical status of atom.
RecMet - net.sf.jniinchi.INCHI_OPTION
Include reconnected bond to metal results.
retStatus - Variable in class net.sf.jniinchi.JniInchiOutput
InChI return status
retStatus - Variable in class net.sf.jniinchi.JniInchiOutputKey
 
retStatus - Variable in class net.sf.jniinchi.JniInchiOutputStructure
Return status from conversion.
returnValue - Variable in class net.sf.jniinchi.JniInchiInputData
 

S

SAbs - net.sf.jniinchi.INCHI_OPTION
Absolute stereo.
SAsXYZ - net.sf.jniinchi.INCHI_OPTION
Include Arsines Stereochemistry
sAuxInfo - Variable in class net.sf.jniinchi.JniInchiOutput
Aux info ASCIIZ string
serialVersionUID - Static variable in exception net.sf.jniinchi.JniInchiException
 
serialVersionUID - Static variable in exception net.sf.jniinchi.LoadNativeLibraryException
 
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
 
setInchiRadical(int) - Method in class net.sf.jniinchi.JniInchiAtom
 
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
 
sInchi - Variable in class net.sf.jniinchi.JniInchiOutput
InChI ASCIIZ string
SINGLE - net.sf.jniinchi.INCHI_BOND_TYPE
Single bond.
SINGLE_1DOWN - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; positive: the sharp end points to this atom.
SINGLE_1EITHER - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; positive: the sharp end points to this atom.
SINGLE_1UP - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; positive: the sharp end points to this atom.
SINGLE_2DOWN - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; negative: the sharp end points to the opposite atom.
SINGLE_2EITHER - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; negative: the sharp end points to the opposite atom.
SINGLE_2UP - net.sf.jniinchi.INCHI_BOND_STEREO
Stereocenter-related; negative: the sharp end points to the opposite atom.
SINGLET - net.sf.jniinchi.INCHI_RADICAL
Singlet.
SKIP - net.sf.jniinchi.INCHI_RET
Not used in InChI library.
sLog - Variable in class net.sf.jniinchi.JniInchiOutput
log-file ASCIIZ string, contains a human-readable list of recognized options and possibly an Error/warning message
sMessage - Variable in class net.sf.jniinchi.JniInchiOutput
Error/warning ASCIIZ message
SNon - net.sf.jniinchi.INCHI_OPTION
Exclude stereo (Default: Include Absolute stereo).
SPXYZ - net.sf.jniinchi.INCHI_OPTION
Include Phosphines Stereochemistry.
SRac - net.sf.jniinchi.INCHI_OPTION
Racemic stereo.
SRel - net.sf.jniinchi.INCHI_OPTION
Relative stereo.
stereo - Variable in class net.sf.jniinchi.JniInchiBond
Bond 2D stereo definition.
stereoList - Variable in class net.sf.jniinchi.JniInchiStructure
List of stero parities.
SUCF - net.sf.jniinchi.INCHI_OPTION
Use Chiral Flag.
SUU - net.sf.jniinchi.INCHI_OPTION
Include omitted unknown/undefined stereo.

T

TETRAHEDRAL - net.sf.jniinchi.INCHI_STEREOTYPE
Tetrahedral atom.
toString() - Method in class net.sf.jniinchi.JniInchiOutput
 
TRIPLE - net.sf.jniinchi.INCHI_BOND_TYPE
Triple bond.
TRIPLET - net.sf.jniinchi.INCHI_RADICAL
Triplet.
type - Variable in class net.sf.jniinchi.JniInchiBond
Bond type.
type - Variable in class net.sf.jniinchi.JniInchiStereo0D
Stereo parity type.

U

UNDEFINED - net.sf.jniinchi.INCHI_PARITY
Undefined.
UNKNOWN - net.sf.jniinchi.INCHI_PARITY
Unknown.
UNKNOWN - net.sf.jniinchi.INCHI_RET
Unknown program error.
UNKNOWN_ERROR - net.sf.jniinchi.INCHI_KEY
 

V

VALID_BETA - net.sf.jniinchi.INCHI_STATUS
 
VALID_NON_STANDARD - net.sf.jniinchi.INCHI_KEY_STATUS
 
VALID_NON_STANDARD - net.sf.jniinchi.INCHI_STATUS
 
VALID_STANDARD - net.sf.jniinchi.INCHI_KEY_STATUS
 
VALID_STANDARD - net.sf.jniinchi.INCHI_STATUS
 
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_STATUS
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_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_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_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_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.
VERSION - Static variable in class net.sf.jniinchi.JniInchiWrapper
 

W

WARNING - net.sf.jniinchi.INCHI_RET
Success; warning(s) issued.
warningFlags - Variable in class net.sf.jniinchi.JniInchiOutputStructure
Warning flags, see INCHIDIFF in inchicmp.h.
WarnOnEmptyStructure - net.sf.jniinchi.INCHI_OPTION
Warn and produce empty InChI for empty structure.
Wnumber - net.sf.jniinchi.INCHI_OPTION
Set time-out per structure in seconds; W0 means unlimited.

X

x - Variable in class net.sf.jniinchi.JniInchiAtom
Atom x-coordinate.

Y

y - Variable in class net.sf.jniinchi.JniInchiAtom
Atom y-coordinate.

Z

z - Variable in class net.sf.jniinchi.JniInchiAtom
Atom z-coordinate.
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