chemaxon.formats
Class MolConverter

java.lang.Object
  chemaxon.formats.MolConverter

public class MolConverter
extends java.lang.Object

Converts between molecule file formats. See supported formats and their import and/or export options on the File Formats in Marvin page.

Version:

5.1.3, 10/20/2008

Author:

Peter Csizmadia, Szilveszter Juhos

Constructor Summary

MolConverter(java.io.InputStream in, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)
Create a MolConverter object.

MolConverter(java.io.InputStream in, java.lang.String ofname, java.lang.String fmtopts, boolean useSysEOL)
Use this constructor if you do not need output buffering but want to determine output file positions.

MolConverter(java.util.Vector inFiles, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)
Create a MolConverter object.

MolConverter(java.util.Vector inFiles, java.lang.String ofname, java.lang.String fmtopts, boolean useSysEOL)
Use this constructor if you do not need output buffering but want to determine output file positions.

MolConverter(java.util.Vector inFiles, java.util.Vector inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)
Create a MolConverter object.

MolConverter(java.util.Vector inFiles, java.util.Vector inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL, java.lang.String[] incFields)
Create a MolConverter object.

MolConverter(java.util.Vector inFiles, java.util.Vector inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL, java.lang.String[] incFields, java.lang.String enc)
Create a MolConverter object.

MolConverter(java.util.Vector inFiles, java.util.Vector inOptions, java.lang.String ofname, java.lang.String fmtopts, boolean useSysEOL)
Use this constructor if you do not need output buffering but want to determine output file positions.

Method Summary

void	close() Close the underlying RandomAccessFile.
boolean	convert() Convert the next molecule.
static MolConverter	createMolConverter(java.io.InputStream instream, java.io.OutputStream outstream, java.lang.String[] args, java.io.OutputStream[] theOut, int[] theVerbose) Creates a MolConverter instance with the attributes specified in the parameters.
static boolean	isSupportedEncoding(java.lang.String enc) Test, whether the given charset name is supported by this JVM
static void	main(java.lang.String[] args) Main method.
static void	mainWithoutExit(java.lang.String[] args) Same as main(), but never calls System.exit().
long	otell() Get the current file position.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MolConverter

public MolConverter(java.io.InputStream in,
                    java.io.OutputStream out,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Create a MolConverter object.

Parameters:

in - the input molecule stream to convert

out - the output stream

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.util.Vector inOptions,
                    java.io.OutputStream out,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Create a MolConverter object.

Parameters:

inFiles - input file list

inOptions - import options

out - output stream

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.util.Vector inOptions,
                    java.io.OutputStream out,
                    java.lang.String fmtopts,
                    boolean useSysEOL,
                    java.lang.String[] incFields)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Create a MolConverter object.

Parameters:

inFiles - input file list

inOptions - import options

out - output stream

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

incFields - included fields of an SDfile to be shown in a table

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.util.Vector inOptions,
                    java.io.OutputStream out,
                    java.lang.String fmtopts,
                    boolean useSysEOL,
                    java.lang.String[] incFields,
                    java.lang.String enc)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Create a MolConverter object.

Parameters:

inFiles - input file list

inOptions - import options

out - output stream

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

incFields - included fields of an SDfile to be shown in a table

enc - the input and/or output encodings in INCHARSET..OUTCHARSET format

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.nio.charset.IllegalCharsetNameException - if illegal input or output encoding name specified

java.nio.charset.UnsupportedCharsetException - if the specified input or output encoding is unsupported

java.lang.IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.io.OutputStream out,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Create a MolConverter object.

Parameters:

inFiles - input file list

out - output stream

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(java.io.InputStream in,
                    java.lang.String ofname,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Use this constructor if you do not need output buffering but want to determine output file positions.

Parameters:

in - the input molecule stream to convert

ofname - the output file name

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

See Also:

otell(), close()

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.lang.String ofname,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Use this constructor if you do not need output buffering but want to determine output file positions.

Parameters:

inFiles - input file list

ofname - output file name

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

See Also:

otell(), close()

MolConverter

public MolConverter(java.util.Vector inFiles,
                    java.util.Vector inOptions,
                    java.lang.String ofname,
                    java.lang.String fmtopts,
                    boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.IllegalArgumentException

Use this constructor if you do not need output buffering but want to determine output file positions.

Parameters:

inFiles - input file list

inOptions - import options

ofname - output file name

fmtopts - output file format with or without options

useSysEOL - write OS dependent line.separators instead of '\n'

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

MolExportException - If the molecule cannot be exported in the specified format

java.io.IOException - If I/O error occured when determining the file format.

java.lang.IllegalArgumentException - Invalid format string (fmt).

See Also:

otell(), close()

Method Detail

convert

public boolean convert()
                throws MolExportException,
                       java.io.IOException

Convert the next molecule.

Returns:

true if success, false if no more molecules can be read

Throws:

java.io.IOException - If an I/O error has occurred.

java.nio.charset.IllegalCharsetNameException - if the encoding is illegal

java.nio.charset.UnsupportedCharsetException - if the encoding is unsupported

MolExportException

otell

public long otell()
           throws java.io.IOException

Get the current file position.

Returns:

the position

Throws:

java.io.IOException - if the position cannot be determined

close

public void close()
           throws java.io.IOException

Close the underlying RandomAccessFile. Needed only if the output file name is set in the constructor.

Throws:

java.io.IOException - If an I/O error has occurred.

isSupportedEncoding

public static boolean isSupportedEncoding(java.lang.String enc)

Test, whether the given charset name is supported by this JVM

Parameters:

enc - the name of the charset

Returns:

true if the charset is supported by this JVM, false if not

createMolConverter

public static MolConverter createMolConverter(java.io.InputStream instream,
                                              java.io.OutputStream outstream,
                                              java.lang.String[] args,
                                              java.io.OutputStream[] theOut,
                                              int[] theVerbose)
                                       throws java.io.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.

Throws:

java.nio.charset.IllegalCharsetNameException - if illegal input or output encoding name specified

java.nio.charset.UnsupportedCharsetException - if the specified input or output encoding is unsupported

java.io.IOException

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException

Main method.

Parameters:

args - command line arguments

Throws:

java.io.IOException

mainWithoutExit

public static void mainWithoutExit(java.lang.String[] args)
                            throws java.io.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:

java.io.IOException