chemaxon.marvin.io.formats

Class MoleculeImporter

java.lang.Object

chemaxon.marvin.io.formats.MoleculeImporter

All Implemented Interfaces:

chemaxon.marvin.io.formats.MoleculeImporterIface

@PublicAPI
public class MoleculeImporter
extends java.lang.Object
implements chemaxon.marvin.io.formats.MoleculeImporterIface

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

Author:

Peter Vadasz

Field Summary

Fields

Modifier and Type	Field and Description
protected chemaxon.marvin.io.formats.MoleculeImporterIface	importer The wrapped importer.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	close()
java.util.Iterator<Molecule>	getIterator() Returns an iterator that iterates through all molecules in the file/stream.
Molecule	read()

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 Detail

importer

protected final chemaxon.marvin.io.formats.MoleculeImporterIface importer

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

Constructor Detail

MoleculeImporter

public MoleculeImporter(java.lang.String fileName)
                 throws java.io.IOException

Constructs a new importer for the file.

Parameters:

fileName - the name of the file to import.

Throws:

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

MoleculeImporter

public MoleculeImporter(java.lang.String fileName,
                        java.lang.String opts)
                 throws java.io.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:

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

MoleculeImporter

public MoleculeImporter(java.io.File f)
                 throws java.io.IOException

Constructs a new importer for the file.

Parameters:

f - the file to import.

Throws:

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

MoleculeImporter

public MoleculeImporter(java.io.File f,
                        java.lang.String opts)
                 throws java.io.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:

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

MoleculeImporter

public MoleculeImporter(java.io.InputStream inputStream)
                 throws java.io.IOException

Constructs a new importer for the input stream.

Parameters:

inputStream - the stream to import from.

Throws:

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

MoleculeImporter

public MoleculeImporter(java.io.InputStream inputStream,
                        java.lang.String opts)
                 throws java.io.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:

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

MoleculeImporter

public MoleculeImporter(java.io.InputStream inputStream,
                        java.lang.String opts,
                        java.lang.String enc)
                 throws java.io.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:

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

Method Detail

read

public Molecule read()
              throws java.io.IOException

Specified by:

read in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Throws:

java.io.IOException

getIterator

public java.util.Iterator<Molecule> getIterator()

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

Returns:

the iterator.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface chemaxon.marvin.io.formats.MoleculeImporterIface

Throws:

java.io.IOException