chemaxon.formats

Class MolImporter

java.lang.Object

chemaxon.marvin.io.MDocSource

chemaxon.formats.MolImporter

All Implemented Interfaces:

chemaxon.marvin.io.formats.MoleculeImporterIface, Closeable, AutoCloseable, Iterable<Molecule>

public class MolImporter
extends MDocSource
implements chemaxon.marvin.io.formats.MoleculeImporterIface

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

By default, in case of machines with multiple processors processing is concurrent, otherwise single-threaded. By default, the number of worker threads is the number of processors - the number of concurrent threads can be set in setThreadCount(int). Serialized Molecule objects can also be imported using the "chemaxon.struc.Molecule" format. In this case processing is single-threaded.

Version:

6.3,

Author:

Peter Csizmadia, Tamas Vertse, Szilveszter Juhos

Constructor Summary

Constructors

Constructor and Description
MolImporter(File f) Create a molecule importer for a file.
MolImporter(File f, String opts) Create a molecule importer for a file.
MolImporter(InputStream is) Create a molecule importer for an input stream.
MolImporter(InputStream is, String opts) Create a molecule importer for an input stream.
MolImporter(InputStream is, String opts, String enc) Create a molecule importer for an input stream.
MolImporter(InputStream is, String opts, String enc, String fileName) Create a molecule importer for an input stream.
MolImporter(String fname) Create a molecule importer for a file.
MolImporter(String fname, Object component, String msg) Create a molecule importer with a progress monitor.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Close the underlying input stream.
Molecule	createMol() Creates a target molecule object for import.
int	estimateNumRecords() Estimates the total number of records.
File	getFile() Gets the file object for the input.
String	getFileName() Gets the name of the input file
String	getFormat() Get the file format.
MPropertyContainer	getGlobalProperties() Gets the global properties in a container that was retrieved from the input stream, earlier.
String	getGrabbedMoleculeString() Gets the last grabbed molecule string with LF style line endings by default.
int	getLineCount() Gets the current line number.
MolImportModule	getMolImportModule()
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, String opts, 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, String opts, String enc) Read a molecule from a byte array.
static boolean	importMol(byte[] b, String opts, String enc, Molecule mol) Read a molecule from a byte array.
static Molecule	importMol(String s) Read a molecule from a string.
static Molecule	importMol(String s, chemaxon.formats.ImportOptions options) Read a molecule from a string with the given options.
static boolean	importMol(String s, Molecule mol) Read a molecule from a string.
static Molecule	importMol(String s, String opts) Read a molecule from a string.
static Molecule	importMol(String s, String opts, String enc) Deprecated. (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call importMol(String,String); if you have a byte array, call importMol(byte[], String, String).
static boolean	importMol(String s, String opts, String enc, Molecule mol) Deprecated. (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call importMol(String, String); if you have a byte array, call importMol(byte[], String, String, Molecule).
boolean	isEndReached() Tests whether the end of input is already reached.
boolean	isGrabbingEnabled() Deprecated. as of Marvin 6.2. It has no effect on the code.
boolean	isMolMovie() Are the imported molecules merged into one multi-set molecule?
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.
static MDocument	parseMRV(String sval) Parses a document from a string in Marvin Document (MRV) format.
Molecule	read() Read the next molecule.
boolean	read(Molecule mol) Deprecated. as of Marvin 14.7.7. use read() instead
MDocument	readDoc(MDocument doc, Molecule buf) Deprecated. as of Marvin 14.7.7. usenextDoc() instead
Molecule	readMol(Molecule mol) Deprecated. as of Marvin 14.7.7. use read() instead
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	setGrabbingEnabled(boolean v) Deprecated. as of Marvin 6.2. It has no effect on the code.
void	setQueryMode(boolean q) Sets query mode.
void	setThreadCount(int threadCount) Sets the number of threads for concurrent processing.
boolean	skipRecord() Skips the next molecule or document instead of reading it into memory.
long	tell() Returns the current file offset.

Methods inherited from class chemaxon.marvin.io.MDocSource

getDocLabel, getMoleculeIterator, iterator, seekForward, seekRecordAtFraction, skipRecords

Methods inherited from class java.lang.Object

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

Constructor Detail

MolImporter

public MolImporter(InputStream is)
            throws 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:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

MolImporter

public MolImporter(InputStream is,
           String opts)
            throws IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.

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:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

MolImporter

public MolImporter(InputStream is,
           String opts,
           String enc)
            throws IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.

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:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

Since:

Marvin 3.5.5, 01/02/2006

MolImporter

public MolImporter(InputStream is,
           String opts,
           String enc,
           String fileName)
            throws IOException,
                   MolFormatException

Create a molecule importer for an input stream. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.

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

fileName - the original filename the stream is reading from

Throws:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

Since:

Marvin 5.8

MolImporter

public MolImporter(File f,
           String opts)
            throws IOException

Create a molecule importer for a file. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. 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:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

MolImporter

public MolImporter(File f)
            throws IOException

Create a molecule importer for a file. Begins reading the input stream and determines the file format. If the option string starts with the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. 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

Throws:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

Since:

Marinv 6.3

See Also:

tell(), close()

MolImporter

public MolImporter(String fname)
            throws 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 the substring "MULTISET", then all the molecules in the stream are merged into one molecule object containing multiple atom sets. If it starts with "MOLMOVIE", then molecules are read taken to be frames of a molecule movie (default in XYZ format). If it starts with "NOMOLMOVIE", then multimolecule XYZ files are not interpreted as molecule movies. Other parts of the option string are passed to the import module. The input character encoding can also be set in "enc{encoding}" form.

Parameters:

fname - name of the file to read

Throws:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

MolImporter

public MolImporter(String fname,
           Object component,
           String msg)
            throws 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:

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

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

IllegalCharsetNameException - if illegal encoding is used

UnsupportedCharsetException - if unsupported encoding is used

See Also:

tell(), close()

Method Detail

getFileName

public String getFileName()

Gets the name of the input file

Returns:

the name of the input file

getFile

public File getFile()

Gets the file object for the input.

Returns:

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

getOptions

public String getOptions()

Gets the import options.

Returns:

the options

getMolImportModule

public MolImportModule getMolImportModule()

isGrabbingEnabled

@Deprecated
public boolean isGrabbingEnabled()

Deprecated. as of Marvin 6.2. It has no effect on the code.

Tests whether molecule file content grabbing is enabled.

Returns:

true if enabled, false if disabled

Since:

4.0, 01/05/2005

setGrabbingEnabled

@Deprecated
public void setGrabbingEnabled(boolean v)

Deprecated. as of Marvin 6.2. It has no effect on the code.

Enables or disables molecule file content grabbing.

Parameters:

v - true enables, false disables it

Since:

4.0, 01/05/2005

getGrabbedMoleculeString

public String getGrabbedMoleculeString()

Gets the last grabbed molecule string with LF style line endings by default. If the "noLF" import option was set for MolImporter, then original line endings are kept. E.g. new MolImporter(stream, "mrv:noLF");

Returns:

the molecule as a string

Since:

4.0, 01/05/2005

isMultiSet

public boolean isMultiSet()

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

Returns:

true if the input is a multi-set molecule

isMolMovie

public boolean isMolMovie()

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

Returns:

true if the input is a multi-set molecule

Since:

Marvin 5.2, 02/12/2009

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 concurrent processing is already started or if object input stream is used instead of record importer

Since:

Marvin 5.3

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 IOException

Read the next molecule.

Specified by:

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

Returns:

the next molecule, or null at end of file

Throws:

IOException - If I/O error occured

createMol

public Molecule createMol()

Creates a target molecule object for import.

Returns:

new target molecule object

Since:

Marvin 3.4, 05/08/2004

nextDoc

public MDocument nextDoc()
                  throws IOException

Reads the next document.

Specified by:

nextDoc in class MDocSource

Returns:

the next document or null at end of file

Throws:

IOException - If I/O error occured

Since:

Marvin 4.1, 04/14/2006

readDoc

@Deprecated
public MDocument readDoc(MDocument doc,
                           Molecule buf)
                  throws MolFormatException,
                         IOException

Deprecated. as of Marvin 14.7.7. usenextDoc() instead

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:

IOException - If I/O error occured

MolFormatException

readMol

@Deprecated
public Molecule readMol(Molecule mol)
                 throws MolFormatException,
                        IOException

Deprecated. as of Marvin 14.7.7. use read() instead

Read the next molecule. All the nodes, edges, and properties are removed from mol before reading. If the 'mol' parameter is not null then processing is single-threaded.

Parameters:

mol - target molecule object

Returns:

the molecule if success, null at end of file

Throws:

IOException - If I/O error occured

MolFormatException

read

@Deprecated
public boolean read(Molecule mol)
             throws IOException

Deprecated. as of Marvin 14.7.7. use read() instead

Read the next molecule. All the nodes, edges, and properties are removed from mol before reading. If the 'mol' parameter is not null then the processing is single-threaded. This method requires the parameter 'mol' molecule to be created with MolImporter.createMol() method.

Parameters:

mol - target molecule object

Returns:

true after success, false at end of file

Throws:

IOException - If I/O error occured

skipRecord

public boolean skipRecord()
                   throws MolFormatException,
                          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:

IOException - if read error occured

MolFormatException

Since:

Marvin 4.1, 04/20/2006

readRecordAsText

public String readRecordAsText()
                        throws MRecordParseException,
                               MolExportException,
                               IOException

Reads the next molecule in text format without creating a Molecule object. Processing is single-threaded.

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

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. In concurrent mode always returns false. Therefore this method should not be called before calling setThreadCount(int).

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), setThreadCount(int)

seekRecord

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

Seek the specified record. This method should not be called before calling setThreadCount(int). Backward seeking (rewinding) in the stream is only possible if the underlying input stream is seekable. Note, that in concurrent mode this is not true, the import is not rewindable. 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:

EOFException - if end of file reached while trying to seek

IOException - if read error occured

Since:

Marvin 4.1, 04/19/2006

See Also:

isRewindable(), setThreadCount(int)

seekVisitedRecord

protected void seekVisitedRecord(int k)
                          throws IOException

Seeks an already visited position in case of rewindable input. This method should not be called before calling setThreadCount(int).

Specified by:

seekVisitedRecord in class MDocSource

Parameters:

k - the record index

Throws:

IOException - if read error occured

Since:

Marvin 4.1, 06/28/2006

See Also:

setThreadCount(int)

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 IOException

Returns the current file offset.

Returns:

the file pointer

Throws:

IOException - if the position cannot be determined

getLineCount

public int getLineCount()

Gets the current line number. This method should not be called before calling setThreadCount(int).

Returns:

the line number

See Also:

setThreadCount(int)

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 IOException

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

Specified by:

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

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class MDocSource

Throws:

IOException - If an I/O error has occurred.

getFormat

public String getFormat()

Get the file format.

Returns:

"mrv", "mol", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz", "cube", "inchi", "gzip:{inner file format}" or "chemaxon.struc.Molecule" if imported from ObjectInputStream (serialized molecule)

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. Processing is single-threaded.

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,
                 String opts,
                 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. Processing is single-threaded.

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. Processing is single-threaded.

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,
                String opts,
                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. Processing is single-threaded.

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. Processing is single-threaded.

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,
                  String opts,
                  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. Processing is single-threaded.

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(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. Processing is single-threaded.

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(String s,
                 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. Processing is single-threaded.

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(String s,
                 chemaxon.formats.ImportOptions options)
                          throws MolFormatException

Read a molecule from a string with the given options. If the string contains multiple molecules (it is an SDfile for example), read only the first one. Processing is single-threaded. If an encoding is specified in the option, its value will not be used since the input is a string which can not be encoded.

Parameters:

s - the molecule file contents

options - options defined by an options object

Returns:

the molecule

Throws:

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

importMol

@Deprecated
public static Molecule importMol(String s,
                            String opts,
                            String enc)
                          throws MolFormatException

Deprecated. (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call importMol(String,String); if you have a byte array, call importMol(byte[], String, String).

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

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(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. Processing is single-threaded.

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

@Deprecated
public static boolean importMol(String s,
                           String opts,
                           String enc,
                           Molecule mol)
                         throws MolFormatException

Deprecated. (Since Marvin 5.5) There is no need to specify an encoding for a String input. Instead, if you have a String to import, call importMol(String, String); if you have a byte array, call importMol(byte[], String, String, Molecule).

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

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

parseMRV

public static MDocument parseMRV(String sval)
                          throws IOException

Parses a document from a string in Marvin Document (MRV) format.

Parameters:

sval - the string

Returns:

the imported document

Throws:

IOException

Since:

Marvin 5.8, 08/25/2011