chemaxon.formats

Class MolConverter

java.lang.Object

chemaxon.formats.MolConverter

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. By default, in case of machines with multiple processors processing is concurrent, otherwise single-threaded.

Examples:

• Simple SDfile to SMILES conversion:

       MolConverter.Builder mcbld = new MolConverter.Builder();
       mcbld.addInput("input.sdf", "");
       mcbld.setOutput("out.smiles", "smiles");
       mcbld.setOutputFlags(MolExporter.TEXT);
       MolConverter mc = mcbld.build();
       while(mc.convert());
       mc.close();
       

• To split a multi-molecule input file into multiple Molfiles named out1.mol, out2.mol etc., use the following settings:

       mcbld.setOutput("out.mol", "mol");
       mcbld.setOutputFlags(MolExporter.TEXT|MolExporter.MULTIPLE);
       

Version:

5.3, 07/07/2009

Author:

Peter Csizmadia, Szilveszter Juhos

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MolConverter.Builder MolConverter builder.
static class	MolConverter.Options Deprecated. as of Marvin 5.2.3, use MolConverter.Builder instead.

Constructor Summary

Constructors

Constructor and Description
MolConverter(InputStream in, OutputStream out, String fmtopts, boolean useSysEOL) Creates a MolConverter object.
MolConverter(InputStream in, String ofname, String fmtopts, boolean useSysEOL) Use this constructor if you do not need output buffering but want to determine output file positions.
MolConverter(List<Object> inFiles, List<String> inOptions, OutputStream out, String fmtopts, boolean useSysEOL) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object> inFiles, List<String> inOptions, OutputStream out, String fmtopts, boolean useSysEOL, String[] incFields) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object> inFiles, List<String> inOptions, OutputStream out, String fmtopts, boolean useSysEOL, String[] incFields, String enc) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object> inFiles, List<String> inOptions, String ofname, String fmtopts, boolean useSysEOL) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object> inFiles, OutputStream out, String fmtopts, boolean useSysEOL) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(List<Object> inFiles, String ofname, String fmtopts, boolean useSysEOL) Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)
MolConverter(MolConverter.Builder mcbld) Creates a MolConverter object.
MolConverter(MolConverter.Options opts) Deprecated. as of Marvin 5.2.3, use MolConverter.Builder.build() instead.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes the exporter and the output stream.
void	close(int opts) Closes the exporter.
boolean	convert() Convert the next molecule.
static MolConverter	createMolConverter(InputStream instream, OutputStream outstream, String[] args, int[] verbosityLevel) Creates a MolConverter instance with the attributes specified in the parameters.
static void	main(String[] args) Main method.
static void	mainWithoutExit(String[] args) Same as main(), but never calls System.exit().
long	otell() Get the current file position.
void	setIgnoreError(boolean ignoreError) Sets the 'ignoreError' option.
void	setThreadCount(int threadCount) Sets the number of threads for concurrent processing.

Methods inherited from class java.lang.Object

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

Constructor Detail

MolConverter

public MolConverter(MolConverter.Builder mcbld)
             throws MolFormatException,
                    MolExportException,
                    IOException,
                    IllegalArgumentException

Creates a MolConverter object.

Parameters:

mcbld - the builder

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

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

IllegalArgumentException - Invalid format string (fmt).

Since:

Marvin 5.2.3, 05/28/2009

MolConverter

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

Creates 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

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

IllegalArgumentException - Invalid format string (fmt).

MolConverter

public MolConverter(InputStream in,
            String ofname,
            String fmtopts,
            boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    IOException,
                    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

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

IllegalArgumentException - Invalid format string (fmt).

See Also:

otell(), close()

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       OutputStream out,
                       String fmtopts,
                       boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    IOException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

out - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       String ofname,
                       String fmtopts,
                       boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    IOException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

ofname - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       List<String> inOptions,
                       String ofname,
                       String fmtopts,
                       boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    IOException,
                    IllegalArgumentException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

inOptions - not used in this method since it is unsupported now.

ofname - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

IllegalArgumentException

MolConverter

@Deprecated
public MolConverter(MolConverter.Options opts)
             throws MolFormatException,
                    MolExportException,
                    IOException,
                    IllegalArgumentException

Deprecated. as of Marvin 5.2.3, use MolConverter.Builder.build() instead.

Parameters:

opts - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

IllegalArgumentException

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       List<String> inOptions,
                       OutputStream out,
                       String fmtopts,
                       boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    IOException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

inOptions - not used in this method since it is unsupported now.

out - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       List<String> inOptions,
                       OutputStream out,
                       String fmtopts,
                       boolean useSysEOL,
                       String[] incFields)
             throws MolFormatException,
                    MolExportException,
                    IOException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

inOptions - not used in this method since it is unsupported now.

out - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

incFields - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(List<Object> inFiles,
                       List<String> inOptions,
                       OutputStream out,
                       String fmtopts,
                       boolean useSysEOL,
                       String[] incFields,
                       String enc)
             throws MolFormatException,
                    MolExportException,
                    IOException

Deprecated. as of Marvin 5.2.3, replaced by MolConverter(Builder)

Parameters:

inFiles - not used in this method since it is unsupported now.

inOptions - not used in this method since it is unsupported now.

out - not used in this method since it is unsupported now.

fmtopts - not used in this method since it is unsupported now.

useSysEOL - not used in this method since it is unsupported now.

incFields - not used in this method since it is unsupported now.

enc - not used in this method since it is unsupported now.

Throws:

MolFormatException - not thrown from this method since it is unsupported now.

MolExportException - not thrown from this method since it is unsupported now.

IOException - not thrown from this method since it is unsupported now.

Method Detail

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. 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:

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:

MolExporter.C_CLOSE_STREAM, MolExporter.C_FLUSH_STREAM

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