MFileFormat (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.formats.MFileFormat

```
public class MFileFormat
extends Object
```
File format descriptor class.

Since:

Marvin 5.0, 05/23/2007

Version:

5.3, 09/28/2009

Author:

Peter Csizmadia, Andras Volford

Field Summary

Fields
Modifier and Type	Field and Description
`static MFileFormat`	`ABBREVGROUP` ChemAxon SMILES Abbreviated Groups.
`static MFileFormat`	`ACCORD` ACCORD file format
`static MFileFormat`	`AWT_IMAGE` Image object (java.awt.Image).
`static MFileFormat`	`BASE64` BASE64 encoded file.
`static MFileFormat`	`CDX` ChemDraw CDX file.
`static MFileFormat`	`CDXML` ChemDraw CDXML file.
`static MFileFormat`	`CML` Chemical Markup Language.
`static MFileFormat`	`CSMDL_IN` ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
`static MFileFormat`	`CSMOL_OUT` ChemAxon Compressed Molfiles and Rgfiles.
`static MFileFormat`	`CSRDF` ChemAxon Compressed RDfiles.
`static MFileFormat`	`CSRXN_OUT` ChemAxon Compressed Rxnfiles.
`static MFileFormat`	`CSSDF_OUT` ChemAxon Compressed SDfiles.
`static MFileFormat`	`CXSMARTS` ChemAxon Extended SMARTS.
`static MFileFormat`	`CXSMILES` ChemAxon Extended SMILES.
`static MFileFormat`	`D2S` Any document format recognized by Document to Structure (doc, odt, ...).
`static MFileFormat`	`DNA` DNA sequence.
`static MFileFormat`	`EMF` Windows Enhanced Metafiles.
`static MFileFormat`	`EPS` Encapsulated PostScript vector image format.
`static long`	`F_ARCHIVE` General archive format that stores a file in another format.
`static long`	`F_BINARY` Import/export module handles binary (byte array) data.
`static long`	`F_COORDS` The format can store atom coordinates if this flag is set.
`static long`	`F_EXPORT` Export is possible if this flag is set.
`static long`	`F_GRAPHICS` File format readable by a graphics program (image viewer, ray tracer etc.).
`static long`	`F_IMAGE` 2D image file format, readable by image viewers.
`static long`	`F_IMPORT` Import is possible if this flag is set.
`static long`	`F_MIXED` Storage of records in different formats is possible if this flag is set.
`static long`	`F_MOLECULE` The format can store molecule(s) if this flag is set.
`static long`	`F_MULTIPLE_RECORDS_LEGAL` The format is designed to store multiple records if this flag is set.
`static long`	`F_MULTIPLE_RECORDS_POSSIBLE` The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal.
`static long`	`F_OBJECT` Import/export module creates or reads a java object.
`static long`	`F_REACTION` The format can store reaction(s) if this flag is set.
`static long`	`F_RECOGNIZER` Format recognizer exists if this flag is set.
`static long`	`F_SINGLE_LINE` Format uses one line per structure.
`static long`	`F_USER_DEFINED` User defined format.
`static long`	`F_XML` The format is XML based if this flag is set.
`static MFileFormat`	`FASTA` FASTA file format
`static MFileFormat`	`FASTA_DNA` FASTA file format with DNA sequence
`static MFileFormat`	`FASTA_PEPTIDE` FASTA file format with peptide sequence
`static MFileFormat`	`FASTA_RNA` FASTA file format with RNA sequence
`static MFileFormat`	`GAUSSIAN_CUBE` Gaussian Cube files.
`static MFileFormat`	`GAUSSIAN_INPUT` Gaussian Input Format.
`static MFileFormat`	`GAUSSIAN_INPUTZ` Gaussian Input Format: Z-matrix.
`static MFileFormat`	`GAUSSIAN_OUTPUT` Gaussian output format.
`static MFileFormat`	`GZIP` GZIPped file.
`static MFileFormat`	`INCHI` IUPAC InChI files.
`static MFileFormat`	`INCHIKEY` IUPAC InChIKey.
`static MFileFormat`	`JPEG` JPEG format.
`static MFileFormat`	`MOL` MDL Molfiles and Rgfiles.
`static MFileFormat`	`MOL_V3_OUT` MDL Extended Molfiles and Rgfiles.
`static MFileFormat`	`MOL2` Tripos Mol2 files.
`static MFileFormat`	`MRV` Chemaxon Marvin Document.
`static MFileFormat`	`MSBMP` Windows Bitmap format.
`static MFileFormat`	`NAME` IUPAC Name files.
`static MFileFormat`	`OSRA`
`static MFileFormat`	`PDB` Protein Data Bank format.
`static MFileFormat`	`PDF` Portable Document Format.
`static MFileFormat`	`PEPTIDE_IN` Peptide Sequence.
`static MFileFormat`	`PEPTIDE1_OUT` Peptide Sequence (1-letter).
`static MFileFormat`	`PEPTIDE3_OUT` Peptide Sequence (3-letter).
`static MFileFormat`	`PNG` Portable Network Graphics.
`static MFileFormat`	`POVRAY` POVRay file.
`static MFileFormat`	`RDF` MDL RDfiles.
`static MFileFormat`	`RNA` RNA sequence.
`static MFileFormat`	`RXN` MDL Rxnfiles.
`static MFileFormat`	`RXN_V3_OUT` MDL Extended Rxnfiles.
`static MFileFormat`	`SDF` MDL SDfiles.
`static MFileFormat`	`SKC` SKC file format
`static MFileFormat`	`SMARTS` SMARTS.
`static MFileFormat`	`SMILES` SMILES.
`static MFileFormat`	`SVG` Scalable Vector Graphics.
`static MFileFormat`	`SYBYLMOL` Tripos SYBYL molfiles.
`static MFileFormat`	`TIFF` Tagged Image File Format.
`static MFileFormat`	`XYZ` XYZ files.

Constructor Summary

Constructors
Constructor and Description
`MFileFormat(String desc, String format, String mime, String exts, String rrname, String impname, String expname, String recogn, long f)` Creates a format descriptor.

Method Summary

Methods
Modifier and Type	Method and Description
`MolExportModule`	`createExportModule()` Creates the export module.
`MolExportModule`	`createExportModule(String enc)` Creates the export module.
`MolImportModule`	`createImportModule()` Creates the molecule import module.
`Recognizer`	`createRecognizer()` Creates a recognizer module.
`Recognizer`	`createRecognizer(String fmt)` Deprecated. as of Marvin 2014.07.21.0 use `createRecognizer()` instead
`MRecordReader`	`createRecordReader(MolInputStream mis, String opts)` Creates the record reader.
`MFileFormat`	`getAssociatedNonQueryFormat()` Gets the associated non-query format.
`MFileFormat`	`getAssociatedQueryFormat()` Gets the associated query format.
`String`	`getDescription()` Gets the format description.
`String[]`	`getExtensions()` Gets the extension list.
`long`	`getFlags()` Gets the format descriptor flags.
`String`	`getMIMEType()` Deprecated. as of Marvin 2014.07.21.0 not used
`String`	`getName()` Gets the codename of the format.
`String[]`	`getNames()` Gets all the codenames of the format.
`int`	`getPriority(String subfmt)` Deprecated. as of Marvin 2014.07.21.0 use `getSubFormatPriority(String)` instead
`static int`	`getSubFormatPriority(String subFormatName)` Gets the priority of the specified subformat name.
`boolean`	`isFlagSet(long flag)` Checks whether the format has a given (set of) flag(s) set.
`boolean`	`matches(String fmt, long f, long mask)` Tests whether the format matches the specified pattern.
`String`	`toString()` Overrides Object.toString() to ease debugging.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - MRV
```
public static final MFileFormat MRV
```
    Chemaxon Marvin Document.
  - CML
```
public static final MFileFormat CML
```
    Chemical Markup Language.
  - MOL
```
public static final MFileFormat MOL
```
    MDL Molfiles and Rgfiles.
  - MOL_V3_OUT
```
public static final MFileFormat MOL_V3_OUT
```
    MDL Extended Molfiles and Rgfiles.
  - RXN
```
public static final MFileFormat RXN
```
    MDL Rxnfiles.
  - RXN_V3_OUT
```
public static final MFileFormat RXN_V3_OUT
```
    MDL Extended Rxnfiles.
  - SDF
```
public static final MFileFormat SDF
```
    MDL SDfiles.
  - RDF
```
public static final MFileFormat RDF
```
    MDL RDfiles.
  - CSMDL_IN
```
public static final MFileFormat CSMDL_IN
```
    ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles. Format object for import only.
  - CSMOL_OUT
```
public static final MFileFormat CSMOL_OUT
```
    ChemAxon Compressed Molfiles and Rgfiles.
  - CSRXN_OUT
```
public static final MFileFormat CSRXN_OUT
```
    ChemAxon Compressed Rxnfiles.
  - CSSDF_OUT
```
public static final MFileFormat CSSDF_OUT
```
    ChemAxon Compressed SDfiles.
  - CSRDF
```
public static final MFileFormat CSRDF
```
    ChemAxon Compressed RDfiles.
  - SMILES
```
public static final MFileFormat SMILES
```
    SMILES.
  - SMARTS
```
public static final MFileFormat SMARTS
```
    SMARTS.
  - CXSMILES
```
public static final MFileFormat CXSMILES
```
    ChemAxon Extended SMILES.
  - CXSMARTS
```
public static final MFileFormat CXSMARTS
```
    ChemAxon Extended SMARTS.
  - ABBREVGROUP
```
public static final MFileFormat ABBREVGROUP
```
    ChemAxon SMILES Abbreviated Groups.
  - INCHI
```
public static final MFileFormat INCHI
```
    IUPAC InChI files.
  - INCHIKEY
```
public static final MFileFormat INCHIKEY
```
    IUPAC InChIKey.
  - NAME
```
public static final MFileFormat NAME
```
    IUPAC Name files.
  - PEPTIDE_IN
```
public static final MFileFormat PEPTIDE_IN
```
    Peptide Sequence.
  - PEPTIDE1_OUT
```
public static final MFileFormat PEPTIDE1_OUT
```
    Peptide Sequence (1-letter).
  - PEPTIDE3_OUT
```
public static final MFileFormat PEPTIDE3_OUT
```
    Peptide Sequence (3-letter).
  - RNA
```
public static final MFileFormat RNA
```
    RNA sequence.
  - DNA
```
public static final MFileFormat DNA
```
    DNA sequence.
  - XYZ
```
public static final MFileFormat XYZ
```
    XYZ files.
  - GAUSSIAN_CUBE
```
public static final MFileFormat GAUSSIAN_CUBE
```
    Gaussian Cube files.
  - GAUSSIAN_INPUT
```
public static final MFileFormat GAUSSIAN_INPUT
```
    Gaussian Input Format.
  - GAUSSIAN_INPUTZ
```
public static final MFileFormat GAUSSIAN_INPUTZ
```
    Gaussian Input Format: Z-matrix.
  - GAUSSIAN_OUTPUT
```
public static final MFileFormat GAUSSIAN_OUTPUT
```
    Gaussian output format.
  - SYBYLMOL
```
public static final MFileFormat SYBYLMOL
```
    Tripos SYBYL molfiles.
  - MOL2
```
public static final MFileFormat MOL2
```
    Tripos Mol2 files.
  - PDB
```
public static final MFileFormat PDB
```
    Protein Data Bank format.
  - GZIP
```
public static final MFileFormat GZIP
```
    GZIPped file.
  - BASE64
```
public static final MFileFormat BASE64
```
    BASE64 encoded file.
  - AWT_IMAGE
```
public static final MFileFormat AWT_IMAGE
```
    Image object (java.awt.Image).
  - JPEG
```
public static final MFileFormat JPEG
```
    JPEG format.
  - PNG
```
public static final MFileFormat PNG
```
    Portable Network Graphics.
  - MSBMP
```
public static final MFileFormat MSBMP
```
    Windows Bitmap format.
  - PDF
```
public static final MFileFormat PDF
```
    Portable Document Format.
  - SVG
```
public static final MFileFormat SVG
```
    Scalable Vector Graphics.
  - EPS
```
public static final MFileFormat EPS
```
    Encapsulated PostScript vector image format.
  - TIFF
```
public static final MFileFormat TIFF
```
    Tagged Image File Format.
  - EMF
```
public static final MFileFormat EMF
```
    Windows Enhanced Metafiles.
  - POVRAY
```
public static final MFileFormat POVRAY
```
    POVRay file.
  - OSRA
```
public static final MFileFormat OSRA
```
  - CDX
```
public static final MFileFormat CDX
```
    ChemDraw CDX file.
  - CDXML
```
public static final MFileFormat CDXML
```
    ChemDraw CDXML file.
  - D2S
```
public static final MFileFormat D2S
```
    Any document format recognized by Document to Structure (doc, odt, ...).
  - FASTA
```
public static final MFileFormat FASTA
```
    FASTA file format
  - FASTA_DNA
```
public static final MFileFormat FASTA_DNA
```
    FASTA file format with DNA sequence
  - FASTA_RNA
```
public static final MFileFormat FASTA_RNA
```
    FASTA file format with RNA sequence
  - FASTA_PEPTIDE
```
public static final MFileFormat FASTA_PEPTIDE
```
    FASTA file format with peptide sequence
  - SKC
```
public static final MFileFormat SKC
```
    SKC file format
  - ACCORD
```
public static final MFileFormat ACCORD
```
    ACCORD file format
  - F_EXPORT
```
public static final long F_EXPORT
```
    Export is possible if this flag is set.
    
    See Also:
    Constant Field Values
  - F_IMPORT
```
public static final long F_IMPORT
```
    Import is possible if this flag is set.
    
    See Also:
    Constant Field Values
  - F_RECOGNIZER
```
public static final long F_RECOGNIZER
```
    Format recognizer exists if this flag is set. Automatically set by the constructor if the recognizer argument is not null.
    
    See Also:
    Constant Field Values
  - F_BINARY
```
public static final long F_BINARY
```
    Import/export module handles binary (byte array) data.
    
    See Also:
    Constant Field Values
  - F_OBJECT
```
public static final long F_OBJECT
```
    Import/export module creates or reads a java object.
    
    See Also:
    Constant Field Values
  - F_MOLECULE
```
public static final long F_MOLECULE
```
    The format can store molecule(s) if this flag is set.
    
    See Also:
    Constant Field Values
  - F_REACTION
```
public static final long F_REACTION
```
    The format can store reaction(s) if this flag is set.
    
    See Also:
    Constant Field Values
  - F_ARCHIVE
```
public static final long F_ARCHIVE
```
    General archive format that stores a file in another format.
    
    See Also:
    Constant Field Values
  - F_GRAPHICS
```
public static final long F_GRAPHICS
```
    File format readable by a graphics program (image viewer, ray tracer etc.).
    
    See Also:
    Constant Field Values
  - F_IMAGE
```
public static final long F_IMAGE
```
    2D image file format, readable by image viewers.
    
    See Also:
    Constant Field Values
  - F_COORDS
```
public static final long F_COORDS
```
    The format can store atom coordinates if this flag is set.
    
    See Also:
    Constant Field Values
  - F_MULTIPLE_RECORDS_LEGAL
```
public static final long F_MULTIPLE_RECORDS_LEGAL
```
    The format is designed to store multiple records if this flag is set.
    
    See Also:
    Constant Field Values
  - F_MULTIPLE_RECORDS_POSSIBLE
```
public static final long F_MULTIPLE_RECORDS_POSSIBLE
```
    The import/export modules can handle files with multiple records if this flag is set, but according to the format definition it is not legal. Other programs may not import multiple records just the first one.
    
    See Also:
    Constant Field Values
  - F_MIXED
```
public static final long F_MIXED
```
    Storage of records in different formats is possible if this flag is set.
    
    See Also:
    Constant Field Values
  - F_XML
```
public static final long F_XML
```
    The format is XML based if this flag is set.
    
    See Also:
    Constant Field Values
  - F_USER_DEFINED
```
public static final long F_USER_DEFINED
```
    User defined format.
    
    See Also:
    Constant Field Values
  - F_SINGLE_LINE
```
public static final long F_SINGLE_LINE
```
    Format uses one line per structure.
    
    Since:
    
    Marvin 5.1
    
    See Also:
    Constant Field Values
- Constructor Detail
  - MFileFormat
```
public MFileFormat(String desc,
           String format,
           String mime,
           String exts,
           String rrname,
           String impname,
           String expname,
           String recogn,
           long f)
```
    Creates a format descriptor. The recogn argument specifies the recognizer module name and the priority of the format, separated by a space. If the format has more than one subformats, then their priorities are specified here in the form "format1=priority1 format2=priority2 ...".
    
    Parameters:
    desc - the format description
    format - the format
    mime - the MIME type or null if unknown
    exts - the file extensions separated by spaces
    rrname - name of the record reader module
    impname - name of the import module
    expname - name of the export module
    recogn - the file format recognizer module name and the priority (nonnegative integer)
    f - the flags
- Method Detail
  - getName
```
public String getName()
```
    Gets the codename of the format.
    
    Returns:
    the codename
  - getNames
```
public String[] getNames()
```
    Gets all the codenames of the format.
    
    Returns:
    the codenames
  - getDescription
```
public String getDescription()
```
    Gets the format description.
    
    Returns:
    the description
  - getExtensions
```
public String[] getExtensions()
```
    Gets the extension list.
    
    Returns:
    the extension list
  - getMIMEType
```
@Deprecated
public String getMIMEType()
```
    Deprecated. as of Marvin 2014.07.21.0 not used
    
    Gets the MIME type.
    
    Returns:
    the MIME type or null if unknown
  - getFlags
```
public long getFlags()
```
    Gets the format descriptor flags.
    
    Returns:
    the flags
  - getAssociatedQueryFormat
```
public MFileFormat getAssociatedQueryFormat()
```
    Gets the associated query format.
    
    Returns:
    the associated format or null
  - getAssociatedNonQueryFormat
```
public MFileFormat getAssociatedNonQueryFormat()
```
    Gets the associated non-query format.
    
    Returns:
    the associated format or null
  - getPriority
```
@Deprecated
public int getPriority(String subfmt)
```
    Deprecated. as of Marvin 2014.07.21.0 use getSubFormatPriority(String) instead
    
    Gets the priority determining format recognition order.
    
    Parameters:
    subfmt - the name of the subformat or null
    
    Returns:
    zero or a positive number
    
    Throws:
    
    IllegalArgumentException - if priority for the specified subformat is not defined
    Since:
    
    Marvin 5.1, 07/29/2008
  - getSubFormatPriority
```
public static int getSubFormatPriority(String subFormatName)
```
    Gets the priority of the specified subformat name.
    
    Parameters:
    subFormatName - the name of the subformat
    
    Returns:
    zero or a positive number
    
    Throws:
    
    IllegalArgumentException - if priority for the specified subformat is not defined
    Since:
    
    Marvin 5.1, 07/29/2008
  - matches
```
public boolean matches(String fmt,
              long f,
              long mask)
```
    Tests whether the format matches the specified pattern.
    
    Parameters:
    fmt - the format name or null if not important
    f - these flags must be set
    mask - only bits specified here are taken into account
    
    Returns:
    true if it matches, false otherwise
  - isFlagSet
```
public boolean isFlagSet(long flag)
```
    Checks whether the format has a given (set of) flag(s) set.
    
    Parameters:
    flag - the flag (or set of flags) to be test
    
    Returns:
    true if (all of) the given flag(s) is set, false otherwise
    Since:
    
    Marvin 5.1
  - createRecordReader
```
public MRecordReader createRecordReader(MolInputStream mis,
                               String opts)
                                 throws MolFormatException
```
    Creates the record reader.
    
    Parameters:
    mis - the molecule input stream
    opts - the options or null
    
    Returns:
    the record reader or null if there is no record reader for this format
    
    Throws:
    
    IllegalCharsetNameException - if illegal encoding is used
    
    UnsupportedCharsetException - if unsupported encoding is used
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException
    See Also:
    MFileFormatUtil.createRecordReader(InputStream, String)
  - createImportModule
```
public MolImportModule createImportModule()
                                   throws MolFormatException
```
    Creates the molecule import module.
    
    Returns:
    the molecule import module or null if there is no importer for this format
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException
  - createExportModule
```
public MolExportModule createExportModule()
                                   throws MolExportException
```
    Creates the export module.
    
    Returns:
    the molecul export module or null if there is no exporter for this format
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolExportException
    See Also:
    MFileFormatUtil.createExportModule(String)
  - createExportModule
```
public MolExportModule createExportModule(String enc)
                                   throws MolExportException
```
    Creates the export module.
    
    Parameters:
    enc - the encoding
    
    Returns:
    the molecul export module or null if there is no exporter for this format
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolExportException
    See Also:
    MFileFormatUtil.createExportModule(String)
  - createRecognizer
```
public Recognizer createRecognizer()
                            throws MolFormatException
```
    Creates a recognizer module.
    
    Returns:
    the recognizer module or null if there is no recognizer for this format
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException - if the recognizer module cannot be created
  - createRecognizer
```
@Deprecated
public Recognizer createRecognizer(String fmt)
                            throws MolFormatException
```
    Deprecated. as of Marvin 2014.07.21.0 use createRecognizer() instead
    
    Creates a recognizer module.
    
    Parameters:
    fmt - the (sub)format's codename
    
    Returns:
    the recognizer module or null if there is no recognizer for this format
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException - if the recognizer module cannot be created
  - toString
```
public String toString()
```
    Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', the unsigned hexadecimal representation of the hash code of the object and the format name(s) in square brackets.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation of the object

Class MFileFormat

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MRV

CML

MOL

MOL_V3_OUT

RXN

RXN_V3_OUT

SDF

RDF

CSMDL_IN

CSMOL_OUT

CSRXN_OUT

CSSDF_OUT

CSRDF

SMILES

SMARTS

CXSMILES

CXSMARTS

ABBREVGROUP

INCHI

INCHIKEY

NAME

PEPTIDE_IN

PEPTIDE1_OUT

PEPTIDE3_OUT

RNA

DNA

XYZ

GAUSSIAN_CUBE

GAUSSIAN_INPUT

GAUSSIAN_INPUTZ

GAUSSIAN_OUTPUT

SYBYLMOL

MOL2

PDB

GZIP

BASE64

AWT_IMAGE

JPEG

PNG

MSBMP

PDF

SVG

EPS

TIFF

EMF

POVRAY

OSRA

CDX

CDXML

D2S

FASTA

FASTA_DNA

FASTA_RNA

FASTA_PEPTIDE

SKC

ACCORD

F_EXPORT

F_IMPORT

F_RECOGNIZER

F_BINARY

F_OBJECT

F_MOLECULE

F_REACTION

F_ARCHIVE

F_GRAPHICS

F_IMAGE

F_COORDS

F_MULTIPLE_RECORDS_LEGAL

F_MULTIPLE_RECORDS_POSSIBLE

F_MIXED

F_XML

F_USER_DEFINED

F_SINGLE_LINE

Constructor Detail