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chemaxon.formats
Class MolExporter

java.lang.Object
  extended by 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.

By default, in case of machines with multiple processors processing is concurrent, otherwise single-threaded. By default, the number of worker threads is the number of processors - the number of concurrent threads can be set in setThreadCount(int). Experimental feature (may change in the future!): "chemaxon.struc.Molecule" format for testing Molecule serialization. In this case processing is single-threaded.

Version:
5.3, 07/07/2009
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.
static MolFilter FILTER_DIM0
          Molecule filter for cleaning 0D molecules only.
static int MULTIPLE
          Use this flag to produce multiple output files.
static int TEXT
          Use this flag to write text files with OS dependent line separators.
 
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.
MolExporter(java.lang.String fname, java.lang.String fmtWithOpts)
          Creates a molecule exporter.
MolExporter(java.lang.String fname, java.lang.String fmtWithOpts, int outflags, java.lang.String[] incFields, 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.
static java.lang.String convertToString(MDocument document, java.lang.String fmt, int flags)
          Converts the document to text format.
static byte[] exportToBinFormat(MDocument document, java.lang.String fmt)
          Creates a binary representation of the document.
static byte[] exportToBinFormat(Molecule molecule, java.lang.String fmt)
          Creates a binary representation of the molecule.
static java.lang.String exportToFormat(MDocument document, java.lang.String fmt)
          Creates a string representation of the document.
static java.lang.String exportToFormat(Molecule molecule, java.lang.String fmt)
          Creates a string representation of the molecule.
static java.lang.Object exportToObject(MDocument document, java.lang.String fmt)
          Creates a String, byte[] array or Image representation of the document.
static java.lang.Object exportToObject(Molecule[] mols, java.lang.String fmt, MolExportModule cv)
          Creates a String, byte[] array or Image representation of the given molecules.
static java.lang.Object exportToObject(Molecule molecule, java.lang.String fmt)
          Creates a String, byte[] array or Image representation of the molecule.
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 setClean(int cleanDim, java.lang.String cleanOpts)
          Sets molecule cleaning in exporter.
 void setClean(int cleanDim, java.lang.String cleanOpts, MolFilter cleanFilter)
          Sets molecule cleaning in exporter.
 void setErrorProcessor(ErrorProcessor errorProcessor)
          Sets the error handler interface for concurrent mode.
 void setThreadCount(int threadCount)
          Sets the number of threads for concurrent processing.
 boolean 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

TEXT

public static final int TEXT
Use this flag to write text files with OS dependent line separators. If not specified, then LF ('\n') is used as in Unix.

Since:
Marvin 5.2.2, 04/20/2009
See Also:
MolExporter(String, String, int, String[], String), MolConverter.Builder.setOutputFlags(int), Constant Field Values

MULTIPLE

public static final int MULTIPLE
Use this flag to produce multiple output files.

Since:
Marvin 5.2.2, 04/20/2009
See Also:
MolExporter(String, String, int, String[], String), MolConverter.Builder.setOutputFlags(int), Constant Field Values

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

FILTER_DIM0

public static final MolFilter FILTER_DIM0
Molecule filter for cleaning 0D molecules only.

See Also:
setClean(int, java.lang.String, chemaxon.util.MolFilter)
Constructor Detail

MolExporter

public MolExporter(java.lang.String fname,
                   java.lang.String fmtWithOpts,
                   int outflags,
                   java.lang.String[] incFields,
                   java.lang.String enc)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException
Creates a molecule exporter.

Parameters:
fname - the output filename
fmtWithOpts - the output file format and the options
outflags - output flags, it can be a combination of TEXT and MULTIPLE
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
Since:
Marvin 5.2.2, 04/20/2009

MolExporter

public MolExporter(java.lang.String fname,
                   java.lang.String fmtWithOpts)
            throws MolExportException,
                   java.io.IOException,
                   java.lang.IllegalArgumentException
Creates a molecule exporter.

Parameters:
fname - the output filename with extension
fmtWithOpts - the output file format and the options
Throws:
MolExportException - export error occurred
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
Since:
Marvin 5.4.1, 01/10/2010

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

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
Method Detail

setThreadCount

public void setThreadCount(int threadCount)
                    throws java.lang.IllegalStateException
Sets the number of threads for concurrent processing. Default: the number of CPUs, single-threaded processing if there is 1 CPU.

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

setClean

public void setClean(int cleanDim,
                     java.lang.String cleanOpts)
              throws java.lang.IllegalStateException
Sets molecule cleaning in exporter. Sets cleaning dimension and options. If processing is in concurrent mode, then cleaning is also performed concurrently.

Parameters:
cleanDim - the cleaning dimension
cleanOpts - the cleaning options
Throws:
java.lang.IllegalStateException - if called after call to write(chemaxon.struc.Molecule)
Since:
Marvin 5.3
See Also:
setThreadCount(int)

setClean

public void setClean(int cleanDim,
                     java.lang.String cleanOpts,
                     MolFilter cleanFilter)
              throws java.lang.IllegalStateException
Sets molecule cleaning in exporter. Sets cleaning dimension and options. If processing is in concurrent mode, then cleaning is also performed concurrently.

Parameters:
cleanDim - the cleaning dimension
cleanOpts - the cleaning options
cleanFilter - the molecule filter to tell which molecule is to be cleaned, set FILTER_DIM0 to clean only 0D molecules null for no filtering (cleaning all)
Throws:
java.lang.IllegalStateException - if called after call to write(chemaxon.struc.Molecule)
Since:
Marvin 5.3
See Also:
setThreadCount(int)

setErrorProcessor

public void setErrorProcessor(ErrorProcessor errorProcessor)
                       throws java.lang.IllegalStateException
Sets the error handler interface for concurrent mode. By default, export is stopped on first error and this error is thrown in close() in concurrent mode. To change this, set specific ErrorProcessor implementation which can handle each error individually during the writing process and can decide whether to continue the export or not. If the export is stopped on an error then this error is always thrown in close(). In single-threaded mode export errors are thrown in write(chemaxon.struc.Molecule), separately for each molecule.

Throws:
java.lang.IllegalStateException - if called after call to write(chemaxon.struc.Molecule)
Since:
Marvin 5.3
See Also:
setThreadCount(int)

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 boolean write(Molecule m)
              throws MolExportException,
                     java.io.IOException
Writes a molecule into the stream.

Parameters:
m - the molecule
Returns:
true on success, false if Molecule is not written due to a previous error in concurrent mode - in this case, call close() which will throw the error and close the exporter
Throws:
MolExportException - export error
java.io.IOException

close

public void close()
           throws MolExportException,
                  java.io.IOException
Closes the MolExportModule and the underlying stream. IMPORTANT: call this or close(int) at the end, after the last call to write(chemaxon.struc.Molecule), because this method flushes the output stream and closes concurrent processing properly.

Throws:
MolExportException - on 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. IMPORTANT: call this or close() at the end, after the last call to write(chemaxon.struc.Molecule), because this method flushes the output stream and closes concurrent processing properly.

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 MolExportException,
                  java.io.IOException
Flushes the output stream and forces any buffered output bytes to be written out.

Throws:
MolExportException - on export error.
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

exportToObject

public static java.lang.Object exportToObject(MDocument document,
                                              java.lang.String fmt)
                                       throws java.io.IOException
Creates a String, byte[] array or Image representation of the document. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples: 
 import java.awt.Image;
 ...
 String s1 = (String)MolExporter.exportToObject(document, "mol");
 String s2 = (String)MolExporter.exportToObject(document, "smiles:a-H"); // aromatize, remove H
 Image img = (Image)MolExporter.exportToObject(document, "image:w300,h300,#ffff00");
 byte[] d3 = (byte[])MolExporter.exportToObject(document, "ppm:w300,h300,#ffff00");
 byte[] d4 = (byte[])MolExporter.exportToObject(document, "png:w300,h300,b32,#00ffff00");
 byte[] d5 = (byte[])MolExporter.exportToObject(document, "jpeg:w300,h300,Q95,#ffff00,spacefill");

Parameters:
document - the document to export
fmt - the format descriptor string
Returns:
a String, a byte[] array or an Image
Throws:
java.io.IOException - Export error.
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005
See Also:
exportToFormat(chemaxon.struc.MDocument, java.lang.String), exportToBinFormat(chemaxon.struc.MDocument, java.lang.String)

convertToString

public static java.lang.String convertToString(MDocument document,
                                               java.lang.String fmt,
                                               int flags)
                                        throws java.io.IOException
Converts the document to text format.

Parameters:
document - the document to convert
fmt - the molecule file format or null
flags - conversion options
Returns:
the string
Throws:
java.io.IOException - Export error
Since:
Marvin 5.0, 11/05/2007

exportToFormat

public static final java.lang.String exportToFormat(MDocument document,
                                                    java.lang.String fmt)
                                             throws java.io.IOException
Creates a string representation of the document. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples: 
 s1 = MolExporter.exportToFormat(document, "mol");
 s2 = MolExporter.exportToFormat(document, "smiles:a-H"); // aromatize and remove Hydrogens

Parameters:
document - the document to export
fmt - the format descriptor string
Returns:
string representation of the document in the specified format
Throws:
java.io.IOException - Export error
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005
See Also:
exportToBinFormat(chemaxon.struc.MDocument, java.lang.String), exportToObject(chemaxon.struc.MDocument, java.lang.String)

exportToBinFormat

public static final byte[] exportToBinFormat(MDocument document,
                                             java.lang.String fmt)
                                      throws java.io.IOException
Creates a binary representation of the document. Works with all the text formats that are supported by the exportToFormat method, and also with the binary image formats (jpeg, msbmp, png, ppm). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples: 
 byte[] d1 = MolExporter.exportToBinFormat(document, "mrv");
 byte[] d2 = MolExporter.exportToBinFormat(document, "smiles:a-H"); // aromatize and remove H
 byte[] d3 = MolExporter.exportToBinFormat(document, "ppm:w300,h300,#ffff00");
 byte[] d4 = MolExporter.exportToBinFormat(document, "png:w300,h300,b32,#00ffff00");
 byte[] d5 = MolExporter.exportToBinFormat(document, "jpeg:w300,h300,Q95,#ffff00,spacefill");

Parameters:
document - the document to export
fmt - the format descriptor string
Returns:
a binary representation of the document in the specified format
Throws:
java.io.IOException - Export error.
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005
See Also:
exportToFormat(chemaxon.struc.MDocument, java.lang.String), exportToObject(chemaxon.struc.MDocument, java.lang.String)

exportToFormat

public static final java.lang.String exportToFormat(Molecule molecule,
                                                    java.lang.String fmt)
                                             throws java.io.IOException
Creates a string representation of the molecule. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples: 
 s1 = MolExporter.exportToFormat(molecule, "mol");
 s2 = MolExporter.exportToFormat(molecule, "smiles:a-H"); // aromatize and remove Hydrogens

Parameters:
molecule - the molecule to export
fmt - the format descriptor string
Returns:
string representation of the molecule in the specified format
Throws:
java.io.IOException - Export error.
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005

exportToBinFormat

public static final byte[] exportToBinFormat(Molecule molecule,
                                             java.lang.String fmt)
                                      throws java.io.IOException
Creates a binary representation of the molecule. Works with all the text formats that are supported by the exportToFormat method, and also with the binary image formats (jpeg, msbmp, png, ppm). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples: 
 byte[] d1 = MolExporter.exportToBinFormat(molecule, "mol");
 byte[] d2 = MolExporter.exportToBinFormat(molecule, "smiles:a-H"); // aromatize and remove H
 byte[] d3 = MolExporter.exportToBinFormat(molecule, "ppm:w300,h300,#ffff00");
 byte[] d4 = MolExporter.exportToBinFormat(molecule, "png:w300,h300,b32,#00ffff00");
 byte[] d5 = MolExporter.exportToBinFormat(molecule, "jpeg:w300,h300,Q95,#ffff00,spacefill");

Parameters:
molecule - the molecule to export
fmt - the format descriptor string
Returns:
a binary representation of the molecule in the specified format
Throws:
java.io.IOException - Export error.
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005

exportToObject

public static java.lang.Object exportToObject(Molecule molecule,
                                              java.lang.String fmt)
                                       throws java.io.IOException
Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples: 
 import java.awt.Image;
 ...
 String s1 = (String)MolExporter.exportToObject(molecule, "mol");
 String s2 = (String)MolExporter.exportToObject(molecule, "smiles:a-H"); // aromatize, remove H
 Image img = (Image)MolExporter.exportToObject(molecule, "image:w300,h300,#ffff00");
 byte[] d3 = (byte[])MolExporter.exportToObject(molecule, "ppm:w300,h300,#ffff00");
 byte[] d4 = (byte[])MolExporter.exportToObject(molecule, "png:w300,h300,b32,#00ffff00");
 byte[] d5 = (byte[])MolExporter.exportToObject(molecule, "jpeg:w300,h300,Q95,#ffff00,spacefill");

Parameters:
molecule - the molecule to export
fmt - the format descriptor string
Returns:
a String, a byte[] array or an Image
Throws:
java.io.IOException - Export error.
java.lang.IllegalArgumentException - Invalid format string.
java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
Since:
Marvin 4.0, 07/01/2005

exportToObject

public static java.lang.Object exportToObject(Molecule[] mols,
                                              java.lang.String fmt,
                                              MolExportModule cv)
                                       throws java.io.IOException
Creates a String, byte[] array or Image representation of the given molecules.

Parameters:
mols - the molecules to export
fmt - the format descriptor string
cv - the export module
Returns:
a String, a byte[] array or an Image
Throws:
java.io.IOException - export error
See Also:
exportToObject(Molecule, String)
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