Package chemaxon.marvin.io.formats

Class MoleculeImporter

java.lang.Object

chemaxon.marvin.io.formats.MoleculeImporter

All Implemented Interfaces:

MoleculeImporterIface, AutoCloseable

@PublicApi
public class MoleculeImporter
extends Object
implements MoleculeImporterIface, AutoCloseable

Molecule importer. Wrapper for MolImporter. Can only read the stream forward (not seekable stream). In some cases (mrv, cml) it can be faster than MolImporter.

The input file format is guessed automatically or specified as an import option to the constructor. Many different formats are supported like "mol", "rgf", "sdf", "rdf", "csmol", "csrgf", "cssdf", "csrdf", "mol2", "cml", "mrv", "smiles", "cxsmiles", "pdb", "xyz", "cube", "name". For more information on formats, please visit File Formats in Marvin.

Since:

Marvin 5.7

Field Summary

Fields

Modifier and Type	Field	Description
protected final MoleculeImporterIface	importer	The wrapped importer.

Constructor Summary

Constructors

Constructor	Description
MoleculeImporter(File f)	Constructs a new importer for the file.
MoleculeImporter(File f, String opts)	Constructs a new importer for the file.
MoleculeImporter(InputStream inputStream)	Constructs a new importer for the input stream.
MoleculeImporter(InputStream inputStream, String opts)	Constructs a new importer for the stream.
MoleculeImporter(InputStream inputStream, String opts, String enc)	Constructs a new importer for the stream.
MoleculeImporter(String fileName)	Constructs a new importer for the file.
MoleculeImporter(String fileName, String opts)	Constructs a new importer for the file.

Method Summary

Modifier and Type	Method	Description
void	close()	Close the underlying input stream.
Iterator<Molecule>	getIterator()	Returns an iterator that iterates through all molecules in the file/stream.
Molecule	read()	Read the next molecule from the stream/file.

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.marvin.io.formats.MoleculeImporterIface

getMDocumentStream, getMolStream

Field Details

importer

protected final MoleculeImporterIface importer

The wrapped importer. Created in the constructor, the interface methods delegates the functionality to this importer.

Constructor Details

MoleculeImporter

public MoleculeImporter(String fileName)
                 throws IOException

Constructs a new importer for the file.

Parameters:

fileName - the name of the file to import.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(String fileName,
 String opts)
                 throws IOException

Constructs a new importer for the file.

Parameters:

fileName - the name of the file to import.

opts - the file format and options separated by a colon. Autorecognition is called if null or format is not specified.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(File f)
                 throws IOException

Constructs a new importer for the file.

Parameters:

f - the file to import.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(File f,
 String opts)
                 throws IOException

Constructs a new importer for the file.

Parameters:

f - the file to import.

opts - the file format and options separated by a colon. Autorecognition is called if null or format is not specified.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(InputStream inputStream)
                 throws IOException

Constructs a new importer for the input stream.

Parameters:

inputStream - the stream to import from.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(InputStream inputStream,
 String opts)
                 throws IOException

Constructs a new importer for the stream.

Parameters:

inputStream - the stream to import from.

opts - the file format and options separated by a colon. Autorecognition is called if null or format is not specified.

Throws:

IOException - if an I/O error occurs.

MoleculeImporter

public MoleculeImporter(InputStream inputStream,
 String opts,
 String enc)
                 throws IOException

Constructs a new importer for the stream.

Parameters:

inputStream - the stream to import from.

opts - the file format and options separated by a colon. Autorecognition is called if null or format is not specified.

enc - the encoding of the stream. Autorecognition may be called if null.

Throws:

IOException - if an I/O error occurs.

Method Details

read

public Molecule read()
              throws IOException

Description copied from interface: MoleculeImporterIface

Read the next molecule from the stream/file.

Specified by:

read in interface MoleculeImporterIface

Returns:

the next molecule, or null if no more molecules can be imported.

Throws:

IOException - If an error occurred during reading.

getIterator

public Iterator<Molecule> getIterator()

Returns an iterator that iterates through all molecules in the file/stream.

Returns:

the iterator.

close

public void close()
           throws IOException

Description copied from interface: MoleculeImporterIface

Close the underlying input stream. IMPORTANT: call this after reading molecules to close concurrent processing properly.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface MoleculeImporterIface

Throws:

IOException - If an error has occurred.