A B C D E F G I J K L M N O P R S T U V W X Y Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
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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