Package org.openscience.cdk.io

Class MDLV3000Writer

  • All Implemented Interfaces:
    Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter
    public final class MDLV3000Writer
extends DefaultChemObjectWriter
    Ctab V3000 format output. This writer provides output to the more modern (but less widely supported) V3000 format. Unlikely the V2000 format that is limited to 999 atoms or bonds V3000 can write arbitrarily large molecules. Beyond this the format removes some (but not all) ambiguities and simplifies output values with tagging (e.g 'CHG=-1' instead of '5').

    Supported Features:
    • Atom Block, non-query features
    • Bond Block, supported are query bond types 4 aromatic, 5 single or double, 6 single or aromatic, 7 double or aromatic, and 8 any as well as the query property that indicates whether a bond is located in a ring or in a chain
    • Sgroup Block, partial support for all chemical Sgroups, complete support for: Abbreviations, MultipleGroup, SRUs, (Un)ordered Mixtures
    The 3D block and enhanced stereochemistry is not currently supported.

    • Constructor Detail

      • MDLV3000Writer

        public MDLV3000Writer​(Writer writer)
        Create a new V3000 writer, output to the provided JDK writer.
        Parameters:
        writer - output location

      • MDLV3000Writer

        public MDLV3000Writer​(OutputStream out)
               throws CDKException
        Create a new V3000 writer, output to the provided JDK output stream.
        Parameters:
        out - output location
        Throws:
        CDKException

      • MDLV3000Writer

        public MDLV3000Writer()
        Default empty constructor.

    • Method Detail

      • write

        public void write​(IChemObject object)
           throws CDKException
        Writes a molecule to the V3000 format. Writes the content of "object" to output.
        Parameters:
        object - the object of which the content is outputted
        Throws:
        CDKException - state exception (e.g undef bonds), unsupported format feature, object not supported etc

      • setWriter

        public void setWriter​(Writer writer)
               throws CDKException
        Sets the Writer from which this ChemObjectWriter should write the contents.
        Throws:
        CDKException

      • setWriter

        public void setWriter​(OutputStream writer)
               throws CDKException
        Sets the OutputStream from which this ChemObjectWriter should write the contents.
        Throws:
        CDKException

      • accepts

        public boolean accepts​(Class<? extends IChemObject> c)
        Returns whether the given IChemObject can be read or written.
        Parameters:
        c - IChemObject of which is tested if it can be handled.
        Returns:
        true, if the IChemObject can be handled.

      • close

        public void close()
           throws IOException
        Closes this IChemObjectIO's resources.
        Throws:
        IOException - when the wrapper IO class cannot be closed.

      • customizeJob

        public void customizeJob()