MolConverter (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.formats
Class MolConverter

java.lang.Object
  chemaxon.formats.MolConverter

public class MolConverter
extends java.lang.Object
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. 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
`static class`	`MolConverter.Builder` MolConverter builder.
`static class`	`MolConverter.Options` Deprecated. as of Marvin 5.2.3, use `MolConverter.Builder` instead.

Constructor Summary
`MolConverter(java.io.InputStream in, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)` Creates 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.List<java.lang.Object> inFiles, java.util.List<java.lang.String> inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)` Deprecated. as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
`MolConverter(java.util.List<java.lang.Object> inFiles, java.util.List<java.lang.String> inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL, java.lang.String[] incFields)` Deprecated. as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
`MolConverter(java.util.List<java.lang.Object> inFiles, java.util.List<java.lang.String> inOptions, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL, java.lang.String[] incFields, java.lang.String enc)` Deprecated. as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
`MolConverter(java.util.List<java.lang.Object> inFiles, java.util.List<java.lang.String> inOptions, java.lang.String ofname, java.lang.String fmtopts, boolean useSysEOL)` Deprecated. as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
`MolConverter(java.util.List<java.lang.Object> inFiles, java.io.OutputStream out, java.lang.String fmtopts, boolean useSysEOL)` Deprecated. as of Marvin 5.2.3, replaced by `MolConverter(Builder)`
`MolConverter(java.util.List<java.lang.Object> inFiles, java.lang.String ofname, java.lang.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
`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(java.io.InputStream instream, java.io.OutputStream outstream, java.lang.String[] args, int[] verbosityLevel)` Creates a MolConverter instance with the attributes specified in the parameters.
`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.
`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,
                    java.io.IOException,
                    java.lang.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; java.io.IOException - If I/O error occured when determining the file format.; java.lang.IllegalArgumentException - Invalid format string (fmt).
Since:: Marvin 5.2.3, 05/28/2009

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

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; 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

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.io.OutputStream out,
                               java.lang.String fmtopts,
                               boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.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.; java.io.IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.lang.String ofname,
                               java.lang.String fmtopts,
                               boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.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.; java.io.IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.util.List<java.lang.String> inOptions,
                               java.lang.String ofname,
                               java.lang.String fmtopts,
                               boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.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.; java.io.IOException - not thrown from this method since it is unsupported now.; java.lang.IllegalArgumentException

MolConverter

@Deprecated
public MolConverter(MolConverter.Options opts)
             throws MolFormatException,
                    MolExportException,
                    java.io.IOException,
                    java.lang.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.; java.io.IOException - not thrown from this method since it is unsupported now.; java.lang.IllegalArgumentException

MolConverter

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.util.List<java.lang.String> inOptions,
                               java.io.OutputStream out,
                               java.lang.String fmtopts,
                               boolean useSysEOL)
             throws MolFormatException,
                    MolExportException,
                    java.io.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.; java.io.IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.util.List<java.lang.String> inOptions,
                               java.io.OutputStream out,
                               java.lang.String fmtopts,
                               boolean useSysEOL,
                               java.lang.String[] incFields)
             throws MolFormatException,
                    MolExportException,
                    java.io.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.; java.io.IOException - not thrown from this method since it is unsupported now.

MolConverter

@Deprecated
public MolConverter(java.util.List<java.lang.Object> inFiles,
                               java.util.List<java.lang.String> 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

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.; java.io.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 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 convert().
Since:: Marvin 5.3

convert

public boolean convert()
                throws 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

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

Closes the exporter and the output stream.

Throws:: MolExportException - export error.; java.io.IOException - in case of any other I/O error.

close

public void close(int opts)
           throws java.io.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.; java.io.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(java.io.InputStream instream,
                                              java.io.OutputStream outstream,
                                              java.lang.String[] args,
                                              int[] verbosityLevel)
                                       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.; 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:: 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

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.formats Class MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

MolConverter

setIgnoreError

setThreadCount

convert

otell

close

close

createMolConverter

main

mainWithoutExit

chemaxon.formats
Class MolConverter