Index (cdk-inchi 2.1.1 API)

A F G I J M O P S

A

atomContainer - Variable in class org.openscience.cdk.inchi.InChIGenerator: AtomContainer instance refers to.

F

FIVE_SECOND_TIMEOUT - Static variable in class org.openscience.cdk.inchi.JniInChIInputAdapter

G

generateAtomContainerFromInchi(IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
getAtomContainer() - Method in class org.openscience.cdk.inchi.InChIToStructure: Returns generated molecule.
getAuxInfo() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets auxillary information.
getIgnoreAromaticBonds() - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Deprecated.
getInchi() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated InChI string.
getInChIGenerator(IAtomContainer) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets an Standard InChI generator for a IAtomContainer.
getInChIGenerator(IAtomContainer, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets InChI generator for CDK IAtomContainer.
getInChIGenerator(IAtomContainer, List<INCHI_OPTION>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets InChI generator for CDK IAtomContainer.
getInchiKey() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated InChIKey string.
getInChIToStructure(String, IChemObjectBuilder) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, String) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getInChIToStructure(String, IChemObjectBuilder, List<String>) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gets structure generator for an InChI string.
getInstance() - Static method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Gives the one InChIGeneratorFactory instance, if needed also creates it.
getLog() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated log.
getLog() - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets generated log.
getMessage() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets generated (error/warning) messages.
getMessage() - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets generated (error/warning) messages.
getNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Makes an array containing the InChI atom numbers of the non-hydrogen atoms in the atomContainer.
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIGenerator: Gets return status from InChI process.
getReturnStatus() - Method in class org.openscience.cdk.inchi.InChIToStructure: Gets return status from InChI process.
getUSmilesNumbers(IAtomContainer) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Obtain the InChI numbers for the input container to be used to order atoms in Universal SMILES [O'Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22].
getWarningFlags() - Method in class org.openscience.cdk.inchi.InChIToStructure: Returns warning flags, see INCHIDIFF in inchicmp.h.

I

InChIGenerator - Class in org.openscience.cdk.inchi: This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer.
InChIGenerator(IAtomContainer, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Constructor.
InChIGenerator(IAtomContainer, String, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Constructor.
InChIGenerator(IAtomContainer, List<INCHI_OPTION>, boolean) - Constructor for class org.openscience.cdk.inchi.InChIGenerator: Constructor.
InChIGeneratorFactory - Class in org.openscience.cdk.inchi: Factory providing access to InChIGenerator and InChIToStructure.
InChINumbersTools - Class in org.openscience.cdk.graph.invariant: Tool for calculating atom numbers using the InChI algorithm.
InChINumbersTools() - Constructor for class org.openscience.cdk.graph.invariant.InChINumbersTools
InChIToStructure - Class in org.openscience.cdk.inchi: This class generates a CDK IAtomContainer from an InChI string.
InChIToStructure(String, IChemObjectBuilder) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
InChIToStructure(String, IChemObjectBuilder, String) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
InChIToStructure(String, IChemObjectBuilder, List<String>) - Constructor for class org.openscience.cdk.inchi.InChIToStructure: Constructor.
input - Variable in class org.openscience.cdk.inchi.InChIGenerator
input - Variable in class org.openscience.cdk.inchi.InChIToStructure

J

JniInChIInputAdapter - Class in org.openscience.cdk.inchi
JniInChIInputAdapter(String) - Constructor for class org.openscience.cdk.inchi.JniInChIInputAdapter
JniInChIInputAdapter(List<INCHI_OPTION>) - Constructor for class org.openscience.cdk.inchi.JniInChIInputAdapter

M

molecule - Variable in class org.openscience.cdk.inchi.InChIToStructure

O

org.openscience.cdk.graph.invariant - package org.openscience.cdk.graph.invariant
org.openscience.cdk.inchi - package org.openscience.cdk.inchi
output - Variable in class org.openscience.cdk.inchi.InChIGenerator
output - Variable in class org.openscience.cdk.inchi.InChIToStructure

P

parseAuxInfo(String, long[]) - Static method in class org.openscience.cdk.graph.invariant.InChINumbersTools: Parse the atom numbering from the auxinfo.

S

setIgnoreAromaticBonds(boolean) - Method in class org.openscience.cdk.inchi.InChIGeneratorFactory: Deprecated.
"the use of aromatic bonds is strongly discouraged" - InChI FAQ, the InChI will fail for many compounds if ignore aromatic bonds is not enabled and the compound have aromatic flags.

A F G I J M O P S