Package org.openscience.cdk.inchi

Class InChIGenerator

  • public class InChIGenerator
extends Object

    This class generates the IUPAC International Chemical Identifier (InChI) for a CDK IAtomContainer. It places calls to a JNI wrapper for the InChI C++ library.

    If the atom container has 3D coordinates for all of its atoms then they will be used, otherwise 2D coordinates will be used if available.

    Spin multiplicities and some aspects of stereochemistry are not currently handled completely. Example usage
    // Generate factory - throws CDKException if native code does not load
    InChIGeneratorFactory factory = new InChIGeneratorFactory();
    // Get InChIGenerator
    InChIGenerator gen = factory.getInChIGenerator(container);

    INCHI_RET ret = gen.getReturnStatus();
    if (ret == INCHI_RET.WARNING) {
    // InChI generated, but with warning message
    System.out.println("InChI warning: " + gen.getMessage());
    } else if (ret != INCHI_RET.OKAY) {
    // InChI generation failed
    throw new CDKException("InChI failed: " + ret.toString()
    + " [" + gen.getMessage() + "]");
    }

    String inchi = gen.getInchi();
    String auxinfo = gen.getAuxInfo();

    TODO: distinguish between singlet and undefined spin multiplicity
    TODO: double bond and allene parities
    TODO: problem recognising bond stereochemistry

    Author:
    Sam Adams
    Source code:
    main
    Belongs to CDK module:
    inchi

    • Field Detail

      • options

        protected io.github.dan2097.jnainchi.InchiOptions options

      • input

        protected final io.github.dan2097.jnainchi.InchiInput input

      • output

        protected io.github.dan2097.jnainchi.InchiOutput output

      • atomContainer

        protected IAtomContainer atomContainer
        AtomContainer instance refers to.

    • Constructor Detail

      • InChIGenerator

        protected InChIGenerator​(IAtomContainer atomContainer,
                         io.github.dan2097.jnainchi.InchiOptions options,
                         boolean ignoreAromaticBonds)
                  throws CDKException
        Throws:
        CDKException

      • InChIGenerator

        protected InChIGenerator​(IAtomContainer atomContainer,
                         boolean ignoreAromaticBonds)
                  throws CDKException

        Constructor. Generates InChI from CDK AtomContainer.

        Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

        Parameters:
        atomContainer - AtomContainer to generate InChI for.
        ignoreAromaticBonds - if aromatic bonds should be treated as bonds of type single and double
        Throws:
        CDKException - if there is an error during InChI generation

      • InChIGenerator

        protected InChIGenerator​(IAtomContainer atomContainer,
                         String optStr,
                         boolean ignoreAromaticBonds)
                  throws CDKException

        Constructor. Generates InChI from CDK AtomContainer.

        Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

        Parameters:
        atomContainer - AtomContainer to generate InChI for.
        optStr - Space or comma delimited string of options to pass to InChI library. Each option may optionally be preceded by a command line switch (/ or -).
        ignoreAromaticBonds - if aromatic bonds should be treated as bonds of type single and double
        Throws:
        CDKException

      • InChIGenerator

        @Deprecated
protected InChIGenerator​(IAtomContainer atomContainer,
                         List<INCHI_OPTION> opts,
                         boolean ignoreAromaticBonds)
                  throws CDKException
        Deprecated.

        Constructor. Generates InChI from CDK AtomContainer.

        Reads atoms, bonds etc from atom container and converts to format InChI library requires, then calls the library.

        Parameters:
        atomContainer - AtomContainer to generate InChI for.
        opts - List of INCHI_OPTION.
        ignoreAromaticBonds - if aromatic bonds should be treated as bonds of type single and double
        Throws:
        CDKException

    • Method Detail

      • getReturnStatus

        @Deprecated
public INCHI_RET getReturnStatus()
        Deprecated.
        use getStatus
        Gets return status from InChI process. OKAY and WARNING indicate InChI has been generated, in all other cases InChI generation has failed. This returns the JNI INCHI enum and requires the optional "cdk-jniinchi-support" module to be loaded (or the full JNI InChI lib to be on the class path).

      • getStatus

        public io.github.dan2097.jnainchi.InchiStatus getStatus()
        Access the status of the InChI output.
        Returns:
        the status

      • getInchi

        public String getInchi()
        Gets generated InChI string.

      • getAuxInfo

        public String getAuxInfo()
        Gets auxillary information.

      • getMessage

        public String getMessage()
        Gets generated (error/warning) messages.

      • getLog

        public String getLog()
        Gets generated log.