Package chemaxon.formats

Class MolConverter

java.lang.Object
chemaxon.formats.MolConverter
@PublicApi public class MolConverter extends Object
Converts between molecule file formats. See supported formats and their import and/or export options on the File Formats in Marvin page.

The processing is single-threaded by default. Concurrent mode can be enabled using setThreadCount(int).

Examples:

  • Constructor Details

  • Method Details

    • setIgnoreError

      public void setIgnoreError(boolean ignoreError)
      Sets the 'ignoreError' option. If true then processing is continued with the next molecule on error, otherwise processing is interrupted on error. Default: false.
      Parameters:
      ignoreError - true if processing should be continued on error
      Since:
      Marvin 5.3

    • setThreadCount

      public void setThreadCount(int threadCount) throws IllegalStateException
      Sets the number of threads for concurrent processing. The default value is 1 (single-threaded mode).

      In concurrent mode, multiple threads are started in the background, which adds a considerable overhead to the processing, so only use this mode if the number of molecules is huge. In single-threaded mode, no background thread is used, every action is done on the caller thread.

      Parameters:
      threadCount - the number of threads, set 0 for the number of CPUs, 1 for single-threaded mode
      Throws:
      IllegalStateException - if called after call to convert().
      Since:
      Marvin 5.3

    • convert

      public boolean convert() throws IOException
      Convert the next molecule.
      Returns:
      true if success, false if no more molecules can be read
      Throws:
      IOException - If an I/O error has occurred.
      IllegalCharsetNameException - if the encoding is illegal
      UnsupportedCharsetException - if the encoding is unsupported

    • otell

      public long otell() throws IOException
      Get the current file position.
      Returns:
      the position
      Throws:
      IOException - if the position cannot be determined

    • close

      public void close() throws IOException
      Closes the exporter and the output stream.
      Throws:
      MolExportException - export error.
      IOException - in case of any other I/O error.

    • close

      public void close(int opts) throws IOException
      Closes the exporter. If the output stream is specified by the user, then this method only closes it if the MolExporter.C_CLOSE_STREAM option is used. If the input stream was opened internally, then the opts argument has no effect, the output stream is always closed.
      Parameters:
      opts - closing options for the exporter, applied only if the output stream is specified by the user
      Throws:
      MolExportException - export error.
      IOException - in case of any other I/O error.
      Since:
      Marvin 5.2.2, 04/21/2009
      See Also:

    • createMolConverter

      public static MolConverter createMolConverter(InputStream instream, OutputStream outstream, String[] args, int[] verbosityLevel) throws IOException
      Creates a MolConverter instance with the attributes specified in the parameters. Basically allows two usage scenario:
      • command line usage (from within the main method),
      • programmatica usage (like from within the JChem Cartridge Servlet).
      Parameters:
      instream - the input stream to take the molecule definition from. It must be null when called for command line usage.
      outstream - the output stream to write the result onto. It must be null when called for command line usage.
      args - space separated options of attributes/options for the desired MolConverter instance.
      verbosityLevel - may be used by the caller to retrieve (as the first element of the array) the verbosity level specified in args. Must be either at least one element long or (if the caller is not interested in this value) null.
      Throws:
      IllegalCharsetNameException - if illegal input or output encoding name specified
      UnsupportedCharsetException - if the specified input or output encoding is unsupported
      IOException

    • main

      public static void main(String[] args) throws IOException
      Main method.
      Parameters:
      args - command line arguments
      Throws:
      IOException

    • mainWithoutExit

      public static void mainWithoutExit(String[] args) throws IOException
      Same as main(), but never calls System.exit(). Useful to call from other java programs. Instead of exiting the JVM, a RuntimeException may be thrown with text "molconvert exit: <exit status>"
      Parameters:
      args - arguments passed to main().
      Throws:
      IOException