Package org.openscience.cdk.io

Class PDBReader

    • Constructor Detail

      • PDBReader

        public PDBReader​(InputStream oIn)
        Constructs a new PDBReader that can read Molecules from a given InputStream.
        Parameters:
        oIn - The InputStream to read from

      • PDBReader

        public PDBReader​(Reader oIn)
        Constructs a new PDBReader that can read Molecules from a given Reader.
        Parameters:
        oIn - The Reader to read from

      • PDBReader

        public PDBReader()

    • Method Detail

      • accepts

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

      • read

        public <T extends IChemObject> T read​(T oObj)
                               throws CDKException
        Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.
        Parameters:
        oObj - The object that subclasses IChemObject
        Returns:
        The IChemObject read
        Throws:
        CDKException

      • close

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

      • customizeJob

        public void customizeJob()