Class InChIToStructure

  • public class InChIToStructure
    extends Object

    This class generates a CDK IAtomContainer from an InChI string. It places calls to a JNI wrapper for the InChI C++ library.

    The generated IAtomContainer will have all 2D and 3D coordinates set to 0.0, but may have atom parities set. Double bond and allene stereochemistry are not currently recorded.
    Example usage // Generate factory - throws CDKException if native code does not load
    InChIGeneratorFactory factory = new InChIGeneratorFactory();
    // Get InChIToStructure
    InChIToStructure intostruct = factory.getInChIToStructure(
    inchi, DefaultChemObjectBuilder.getInstance()

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

    IAtomContainer container = intostruct.getAtomContainer();

    Sam Adams
    Source code:
    Belongs to CDK module:
    • Field Detail

      • output

        protected io.github.dan2097.jnainchi.InchiInputFromInchiOutput output
      • options

        protected io.github.dan2097.jnainchi.InchiOptions options
    • Method Detail

      • generateAtomContainerFromInchi

        protected void generateAtomContainerFromInchi​(IChemObjectBuilder builder)
                                               throws CDKException
        Gets structure from InChI, and converts InChI library data structure into an IAtomContainer.
      • getAtomContainer

        public IAtomContainer getAtomContainer()
        Returns generated molecule.
        An AtomContainer object
      • getReturnStatus

        public INCHI_RET getReturnStatus()
        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.
        the status
      • getMessage

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

        public String getLog()
        Gets generated log.
      • getWarningFlags

        public long[][] getWarningFlags()

        Returns warning flags, see INCHIDIFF in inchicmp.h.

        x=0 => Reconnected if present in InChI otherwise Disconnected/Normal
        x=1 => Disconnected layer if Reconnected layer is present
        y=1 => Main layer or Mobile-H
        y=0 => Fixed-H layer