chemaxon.formats
Class MolImporter

java.lang.Object
  chemaxon.marvin.io.MDocSource
      chemaxon.formats.MolImporter

public class MolImporter
extends MDocSource

Molecule file importer.

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". For more information on formats, please visit File Formats in Marvin. MolImporter can also import gzip compressed and base64 encoded structures.

Serialized Molecule objects can also be imported using the "chemaxon.struc.Molecule" format.

Version:

5.1.1, 08/28/2008

Author:

Peter Csizmadia, Tamas Vertse, Szilveszter Juhos

Field Summary

static int

F_MOLMOVIE Read multi-molecule XYZ files as movies.

Constructor Summary

MolImporter()
Create an empty MolImporter object.

MolImporter(java.io.File f, java.lang.String opts)
Create a molecule importer for a file.

MolImporter(java.io.InputStream is)
Create a molecule importer for an input stream.

MolImporter(java.io.InputStream is, java.lang.String opts)
Create a molecule importer for an input stream.

MolImporter(java.io.InputStream is, java.lang.String opts, java.lang.String enc)
Create a molecule importer for an input stream.

MolImporter(java.lang.String fname)
Create a molecule importer for a file.

MolImporter(java.lang.String fname, java.lang.Object component, java.lang.String msg)
Create a molecule importer with a progress monitor.

Method Summary

void	close() Close the underlying input stream.
Molecule	createMol() Creates a target molecule object for import.
int	estimateNumRecords() Estimates the total number of records.
java.io.File	getFile() Gets the file object for the input.
java.lang.String	getFileName() Gets the name of the input file
java.lang.String	getFormat() Get the file format.
MPropertyContainer	getGlobalProperties() Gets the global properties in a container that was retrieved from the input stream, earlier.
java.lang.String	getGrabbedMoleculeString() Gets the last grabbed molecule string.
int	getLineCount() Gets the current line number.
int	getOptionFlags() Gets options.
java.lang.String	getOptions() Gets the import options.
boolean	getQueryMode() Gets query mode.
int	getRecordCount() Gets the current record number.
int	getRecordCountMax() Gets the total number of records read.
static MDocument	importDoc(byte[] b) Reads a document from a byte array.
static MDocument	importDoc(byte[] b, java.lang.String opts, java.lang.String enc) Reads a document from a byte array.
static Molecule	importMol(byte[] b) Read a molecule from a byte array.
static boolean	importMol(byte[] b, Molecule mol) Read a molecule from a byte array.
static Molecule	importMol(byte[] b, java.lang.String opts, java.lang.String enc) Read a molecule from a byte array.
static boolean	importMol(byte[] b, java.lang.String opts, java.lang.String enc, Molecule mol) Read a molecule from a byte array.
static Molecule	importMol(java.lang.String s) Read a molecule from a string.
static boolean	importMol(java.lang.String s, Molecule mol) Read a molecule from a string.
static Molecule	importMol(java.lang.String s, java.lang.String opts) Read a molecule from a string.
static Molecule	importMol(java.lang.String s, java.lang.String opts, java.lang.String enc) Read a molecule from a string.
static boolean	importMol(java.lang.String s, java.lang.String opts, java.lang.String enc, Molecule mol) Read a molecule from a string.
boolean	isEndReached() Tests whether the end of input is already reached.
boolean	isGrabbingEnabled() Tests whether molecule file content grabbing is enabled.
boolean	isMultiSet() Are the imported molecules merged into one multi-set molecule?
boolean	isRewindable() Tests whether rewinding (seeking backwards) is possible in the underlying input stream.
MDocument	nextDoc() Reads the next document.
Molecule	read() Read the next molecule.
boolean	read(Molecule mol) Read the next molecule.
MDocument	readDoc(MDocument doc, Molecule buf) Read the next document.
Molecule	readMol(Molecule mol) Read the next molecule.
java.lang.String	readRecordAsText() Reads the next molecule in text format without creating a Molecule object.
void	seekRecord(int k, MProgressMonitor pmon) Seek the specified record.
protected void	seekVisitedRecord(int k) Seeks an already visited position in case of rewindable input.
void	setFileName(java.lang.String fname) Sets the name of the input file and (re)initalize the molecule importer.
void	setGrabbingEnabled(boolean v) Enables or disables molecule file content grabbing.
void	setOptionFlags(int f) Sets options.
void	setOptions(java.lang.String opts) Sets the import options.
void	setQueryMode(boolean q) Sets query mode.
boolean	skipRecord() Skips the next molecule or document instead of reading it into memory.
boolean	skipToNext() Deprecated. As of Marvin 5.0, the record reading/molecule import separation makes this method unusable
long	tell() Returns the current file offset.

Methods inherited from class chemaxon.marvin.io.MDocSource

getDocLabel, getMoleculeIterator, seekForward, seekRecordAtFraction, skipRecords

Methods inherited from class java.lang.Object

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

Field Detail

F_MOLMOVIE

public static final int F_MOLMOVIE

Read multi-molecule XYZ files as movies.

Since:

Marvin 4.1, 04/18/2006

See Also:

Constant Field Values

Constructor Detail

MolImporter

public MolImporter()

Create an empty MolImporter object. Use the "setFileName" method to specify the input file.

See Also:

setFileName(java.lang.String)

MolImporter

public MolImporter(java.io.InputStream is)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format.

Parameters:

is - the input stream to read

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

MolImporter

public MolImporter(java.io.InputStream is,
                   java.lang.String opts)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the options start with the substring "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.

Parameters:

is - the input stream to read

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

MolImporter

public MolImporter(java.io.InputStream is,
                   java.lang.String opts,
                   java.lang.String enc)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the options start with the substring "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. Other parts of the option string are passed to the import module. The character encoding can be specified also.

Parameters:

is - the input stream to read

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - charset name or null

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

Since:

Marvin 3.5.5, 01/02/2006

MolImporter

public MolImporter(java.io.File f,
                   java.lang.String opts)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer for a file. Begins reading the input stream and determines the file format. If the option string starts with "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. * Other parts of the option string are passed to the import module.

Parameters:

f - the file to read

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

MolImporter

public MolImporter(java.lang.String fname)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer for a file. Begins reading the input stream and determines the file format. The filename string can contain options in the "file{options}" form. If the option string starts with "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.

Parameters:

fname - name of the file to read

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

MolImporter

public MolImporter(java.lang.String fname,
                   java.lang.Object component,
                   java.lang.String msg)
            throws java.io.IOException,
                   MolFormatException

Create a molecule importer with a progress monitor. Begins reading the input stream and determines the file format. The filename string can contain options in the "file{options}" form. If the option string starts with "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.

Parameters:

fname - name of the file to read

component - the parent component

msg - displayed message, where %p is replaced by the file path

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

Method Detail

getFileName

public java.lang.String getFileName()

Gets the name of the input file

Returns:

the name of the input file

setFileName

public void setFileName(java.lang.String fname)
                 throws java.io.IOException,
                        MolFormatException

Sets the name of the input file and (re)initalize the molecule importer. Starts reading the input stream and determines the file format. The filename string can contain options in the "file{options}" format. If options are specified in the above format, the import options will be overwritten by the new values. If the options string starts with "MULTISET" or "MULTISET,", then all the molecules in the stream are merged into one molecule containing multiple atom sets. The input character encoding can also be set in "enc{encoding}" form. Other parts of the option string are passed to the import module.

Parameters:

fname - name of the file to read

Throws:

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

MolFormatException - If the molecule file is in a format that cannot be read

See Also:

getOptions(), setOptions(java.lang.String)

getFile

public java.io.File getFile()

Gets the file object for the input.

Returns:

the File or null (if the input is not a File)

getOptions

public java.lang.String getOptions()

Gets the import options.

Returns:

the options

setOptions

public void setOptions(java.lang.String opts)

Sets the import options.

Parameters:

opts - options passed to the import module or null

isGrabbingEnabled

public boolean isGrabbingEnabled()

Tests whether molecule file content grabbing is enabled.

Returns:

true if enabled, false if disabled

Since:

4.0, 01/05/2005

setGrabbingEnabled

public void setGrabbingEnabled(boolean v)

Enables or disables molecule file content grabbing.

Parameters:

v - true enables, false disables it

Since:

4.0, 01/05/2005

getGrabbedMoleculeString

public java.lang.String getGrabbedMoleculeString()

Gets the last grabbed molecule string.

Returns:

the molecule as a string

Since:

4.0, 01/05/2005

getOptionFlags

public int getOptionFlags()

Gets options.

Returns:

the options

Since:

Marvin 4.1, 04/18/2006

See Also:

F_MOLMOVIE

setOptionFlags

public void setOptionFlags(int f)

Sets options.

Parameters:

f - the options

Since:

Marvin 4.1, 04/18/2006

See Also:

F_MOLMOVIE

isMultiSet

public boolean isMultiSet()

Are the imported molecules merged into one multi-set molecule?

Returns:

true if the input is a multi-set molecule

getQueryMode

public boolean getQueryMode()

Gets query mode. SMILES strings are imported as SMARTS if query mode is set.

Returns:

query mode

Since:

Marvin 3.3, 11/14/2003

setQueryMode

public void setQueryMode(boolean q)

Sets query mode. SMILES strings are imported as SMARTS if query mode is set.

Parameters:

q - query mode

Since:

Marvin 3.3, 11/14/2003

read

public Molecule read()
              throws java.io.IOException

Read the next molecule.

Returns:

the next molecule, or null at end of file

Throws:

java.io.IOException - If I/O error occured

createMol

public Molecule createMol()
                   throws java.io.IOException

Creates a target molecule object for import.

Returns:

new target molecule object

Throws:

java.io.IOException

Since:

Marvin 3.4, 05/08/2004

nextDoc

public MDocument nextDoc()
                  throws java.io.IOException

Reads the next document.

Specified by:

nextDoc in class MDocSource

Returns:

the next document or null at end of file

Throws:

java.io.IOException - If I/O error occured

Since:

Marvin 4.1, 04/14/2006

readDoc

public MDocument readDoc(MDocument doc,
                         Molecule buf)
                  throws MolFormatException,
                         java.io.IOException

Read the next document. The target document is cleared before reading.

Parameters:

doc - target document object or null

buf - target molecule object or null

Returns:

the next document or null at end of file

Throws:

java.io.IOException - If I/O error occured

MolFormatException

See Also:

F_MOLMOVIE

readMol

public Molecule readMol(Molecule mol)
                 throws MolFormatException,
                        java.io.IOException

Read the next molecule. All the nodes, edges, and properties are removed from mol before reading.

Parameters:

mol - target molecule object

Returns:

the molecule if success, null at end of file

Throws:

java.io.IOException - If I/O error occured

MolFormatException

read

public boolean read(Molecule mol)
             throws java.io.IOException

Read the next molecule. All the nodes, edges, and properties are removed from mol before reading.

Parameters:

mol - target molecule object

Returns:

true after success, false at end of file

Throws:

java.io.IOException - If I/O error occured

skipRecord

public boolean skipRecord()
                   throws MolFormatException,
                          java.io.IOException

Skips the next molecule or document instead of reading it into memory.

Specified by:

skipRecord in class MDocSource

Returns:

true if the end of molecule is found, false if there is no chance to continue

Throws:

java.io.IOException - if read error occured

MolFormatException

Since:

Marvin 4.1, 04/20/2006

skipToNext

public boolean skipToNext()

Deprecated. As of Marvin 5.0, the record reading/molecule import separation makes this method unusable

readRecordAsText

public java.lang.String readRecordAsText()
                                  throws MRecordParseException,
                                         MolExportException,
                                         java.io.IOException

Reads the next molecule in text format without creating a Molecule object.

Returns:

the grabbed record in its original format or null at end of file

Throws:

MRecordParseException - If the record could not be parsed

MolExportException - if binary data cannot be exported to MRV format text

java.io.IOException - if read error occured

Since:

Marvin 5.0, 11/13/2006

isRewindable

public boolean isRewindable()

Tests whether rewinding (seeking backwards) is possible in the underlying input stream.

Specified by:

isRewindable in class MDocSource

Returns:

true if rewinding is possible, false otherwise

Since:

Marvin 4.1, 04/20/2006

See Also:

seekRecord(int, MProgressMonitor)

seekRecord

public void seekRecord(int k,
                       MProgressMonitor pmon)
                throws java.io.EOFException,
                       java.io.IOException

Seek the specified record. Backward seeking (rewinding) in the stream is only possible if the underlying input stream is seekable. Forward seeking is always possible. Seeking terminates before reaching the specified position if the user cancels the progress dialog.

Specified by:

seekRecord in class MDocSource

Parameters:

k - position

pmon - progress monitor or null

Throws:

java.io.EOFException - if end of file reached while trying to seek

java.io.IOException - if read error occured

Since:

Marvin 4.1, 04/19/2006

See Also:

isRewindable()

seekVisitedRecord

protected void seekVisitedRecord(int k)
                          throws java.io.IOException

Seeks an already visited position in case of rewindable input.

Specified by:

seekVisitedRecord in class MDocSource

Parameters:

k - the record index

Throws:

java.io.IOException - if read error occured

Since:

Marvin 4.1, 06/28/2006

isEndReached

public boolean isEndReached()

Tests whether the end of input is already reached.

Specified by:

isEndReached in class MDocSource

Returns:

true if the end was reached, false otherwise

Since:

Marvin 4.1, 06/18/2006

estimateNumRecords

public int estimateNumRecords()

Estimates the total number of records. If the end of file is already reached, then it returns the exact value. Otherwise, in case of a file with known length, it extrapolates from the last read record index and the value of the file pointer at the last read position. If the input is a stream with unknown total length, then it returns two times the current highest record number.

Specified by:

estimateNumRecords in class MDocSource

Returns:

estimated number of records or -1 at the beginning of file

Since:

Marvin 4.1, 04/18/2006

tell

public long tell()
          throws java.io.IOException

Returns the current file offset.

Returns:

the file pointer

Throws:

java.io.IOException - if the position cannot be determined

getLineCount

public int getLineCount()

Gets the current line number.

Returns:

the line number

getRecordCount

public int getRecordCount()

Gets the current record number.

Specified by:

getRecordCount in class MDocSource

Returns:

the record number

Since:

Marvin 4.1, 04/18/2006

getRecordCountMax

public int getRecordCountMax()

Gets the total number of records read.

Specified by:

getRecordCountMax in class MDocSource

Returns:

the number of records

Since:

Marvin 4.1, 04/18/2006

close

public void close()
           throws java.io.IOException

Close the underlying input stream. Needed only if the input file name is set in the constructor.

Throws:

java.io.IOException - If an I/O error has occurred.

getFormat

public java.lang.String getFormat()

Get the file format.

Returns:

the format

importMol

public static Molecule importMol(byte[] b)
                          throws MolFormatException

Read a molecule from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the molecule file contents

Returns:

the molecule

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

importMol

public static Molecule importMol(byte[] b,
                                 java.lang.String opts,
                                 java.lang.String enc)
                          throws MolFormatException

Read a molecule from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the molecule file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - encoding or null

Returns:

the molecule

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

Since:

Marvin 5.0, 12/27/2007

importMol

public static boolean importMol(byte[] b,
                                Molecule mol)
                         throws MolFormatException

Read a molecule from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the molecule file contents

mol - target molecule object

Returns:

true in case of successful reading, false if no more molecules

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

importMol

public static boolean importMol(byte[] b,
                                java.lang.String opts,
                                java.lang.String enc,
                                Molecule mol)
                         throws MolFormatException

Read a molecule from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the molecule file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - encoding or null

mol - target molecule object

Returns:

true in case of successful reading, false if no more molecules

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

Since:

Marvin 5.0, 12/27/2007

importDoc

public static MDocument importDoc(byte[] b)
                           throws MolFormatException

Reads a document from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the file contents

Returns:

the document or null if no document found in input

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

Since:

Marvin 4.1.8, 04/20/2007

importDoc

public static MDocument importDoc(byte[] b,
                                  java.lang.String opts,
                                  java.lang.String enc)
                           throws MolFormatException

Reads a document from a byte array. If the array contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

b - the file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - encoding or null

Returns:

the document or null if no document found in input

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

Since:

Marvin 5.0, 12/27/2007

importMol

public static Molecule importMol(java.lang.String s)
                          throws MolFormatException

Read a molecule from a string. If the string contains multiple molecules (it is an SDfile for example), read only the first one. If the format is known, it is faster to use importMol(String,String) to avoid wasting time with format recognition.

Parameters:

s - the molecule file contents

Returns:

the molecule

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

importMol

public static Molecule importMol(java.lang.String s,
                                 java.lang.String opts)
                          throws MolFormatException

Read a molecule from a string. If the string contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

s - the molecule file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

Returns:

the molecule

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

importMol

public static Molecule importMol(java.lang.String s,
                                 java.lang.String opts,
                                 java.lang.String enc)
                          throws MolFormatException

Read a molecule from a string. If the string contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

s - the molecule file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - encoding or null

Returns:

the molecule

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

Since:

Marvin 5.0, 12/27/2007

importMol

public static boolean importMol(java.lang.String s,
                                Molecule mol)
                         throws MolFormatException

Read a molecule from a string. If the string contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

s - the file contents

mol - target molecule object

Returns:

true in case of successful reading, false if no more molecules

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

importMol

public static boolean importMol(java.lang.String s,
                                java.lang.String opts,
                                java.lang.String enc,
                                Molecule mol)
                         throws MolFormatException

Read a molecule from a string. If the string contains multiple molecules (it is an SDfile for example), read only the first one.

Parameters:

s - the file contents

opts - the file format and/or options separated by a colon; use null for automatic format recognition and default options

enc - encoding or null

mol - target molecule object

Returns:

true in case of successful reading, false if no more molecules

Throws:

MolFormatException - If the molecule file is in a format that cannot be read

getGlobalProperties

public MPropertyContainer getGlobalProperties()

Gets the global properties in a container that was retrieved from the input stream, earlier. Only MRV import supports global properties. Reads them by the initalization of the record importer.

Returns:

global properties in a container or null.

Since:

Marvin 5.0 06/05/2007