chemaxon.formats
Class MolExporter

java.lang.Object
  chemaxon.formats.MolExporter

public class MolExporter
extends java.lang.Object

Molecule exporter class.

The output file format can be specified as an argument to the constructor of this class. Many different output file formats are supported like "mol", "sdf", "smiles", "png", "jpeg", etc.

Experimental feature (may change in the future!): "chemaxon.struc.Molecule" format for testing Molecule serialization.

Version:

5.1.1, 08/17/2008

Author:

Peter Csizmadia

Field Summary

static int	C_CLOSE_STREAM Close the underlying stream.
static int	C_FLUSH_STREAM Flush the output stream and force any buffered output bytes to be written out.

Constructor Summary

MolExporter(java.io.OutputStream out, java.lang.String fmtWithOpts)
Creates a molecule exporter.

MolExporter(java.io.OutputStream out, java.lang.String fmtWithOpts, boolean text, java.lang.String[] incFields)
Creates a molecule exporter.

MolExporter(java.io.OutputStream out, java.lang.String fmtWithOpts, boolean text, java.lang.String[] incFields, java.lang.String enc)
Creates a molecule exporter.

MolExporter(java.io.OutputStream out, java.lang.String fmtWithOpts, java.lang.String enc)
Creates a molecule exporter.

Method Summary

void	close() Closes the MolExportModule and the underlying stream.
void	close(int opts) Closes the MolExportModule and, optionally, the underlying stream.
protected void	finalize()
void	flush() Flushes the output stream and forces any buffered output bytes to be written out.
java.lang.String	getFormat() Gets the output file format.
boolean	isCleanable() Tests whether cleaning is meaningful for the chosen output format.
void	write(Molecule m) Writes a molecule into the stream.

Methods inherited from class java.lang.Object

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

Field Detail

C_CLOSE_STREAM

public static final int C_CLOSE_STREAM

Close the underlying stream.

Since:

Marvin 5.1.1, 08/17/2008

See Also:

close(int), Constant Field Values

C_FLUSH_STREAM

public static final int C_FLUSH_STREAM

Flush the output stream and force any buffered output bytes to be written out.

Since:

Marvin 5.1.1, 08/17/2008

See Also:

close(int), Constant Field Values

Constructor Detail

MolExporter

public MolExporter(java.io.OutputStream out,
                   java.lang.String fmtWithOpts)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException

Creates a molecule exporter.

Parameters:

out - the output stream

fmtWithOpts - the output file format and the options

Throws:

MolExportException - export error occured

java.io.IOException - output error occurred when writing the header

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

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

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

MolExporter

public MolExporter(java.io.OutputStream out,
                   java.lang.String fmtWithOpts,
                   boolean text,
                   java.lang.String[] incFields)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException

Creates a molecule exporter.

Parameters:

out - the output stream

fmtWithOpts - the output file format and the options

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

incFields - SDF fields to include in table or null

Throws:

MolExportException - export error occured

java.io.IOException - output error occurred when writing the header

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

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

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

MolExporter

public MolExporter(java.io.OutputStream out,
                   java.lang.String fmtWithOpts,
                   java.lang.String enc)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException

Creates a molecule exporter.

Parameters:

out - the output stream

fmtWithOpts - the output file format and the options

enc - charset name or null

Throws:

MolExportException - export error occured

java.io.IOException - output error occurred when writing the header

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

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

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

MolExporter

public MolExporter(java.io.OutputStream out,
                   java.lang.String fmtWithOpts,
                   boolean text,
                   java.lang.String[] incFields,
                   java.lang.String enc)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException

Creates a molecule exporter.

Parameters:

out - the output stream

fmtWithOpts - the output file format and the options

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

incFields - SDF fields to include in table or null

enc - charset name or null

Throws:

MolExportException - export error occured

java.io.IOException - output error occurred when writing the header

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

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

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

Method Detail

getFormat

public java.lang.String getFormat()

Gets the output file format.

Returns:

the format

isCleanable

public boolean isCleanable()

Tests whether cleaning is meaningful for the chosen output format.

Returns:

true if cleaning is meaningful, false otherwise

Since:

Marvin 4.1, 02/12/2006

write

public void write(Molecule m)
           throws MolExportException,
                  java.io.IOException

Writes a molecule into the stream.

Parameters:

m - the molecule

Throws:

MolExportException - export error

java.io.IOException

close

public void close()
           throws MolExportException,
                  java.io.IOException

Closes the MolExportModule and the underlying stream.

Throws:

MolExportException - export error.

java.io.IOException - in case of any other I/O error.

close

public void close(int opts)
           throws MolExportException,
                  java.io.IOException

Closes the MolExportModule and, optionally, the underlying stream.

Parameters:

opts - closing options, C_CLOSE_STREAM or C_FLUSH_STREAM.

Throws:

MolExportException - export error.

java.io.IOException - in case of any other I/O error.

Since:

Marvin 5.1.1, 08/17/2008

flush

public void flush()
           throws java.io.IOException

Flushes the output stream and forces any buffered output bytes to be written out.

Throws:

java.io.IOException - if an I/O error occurs.

Since:

Marvin 5.1.1, 08/15/2008

finalize

protected void finalize()
                 throws MolExportException,
                        java.io.IOException

Overrides:

finalize in class java.lang.Object

Throws:

MolExportException

java.io.IOException