chemaxon.formats
Class MFileFormatUtil

java.lang.Object
  chemaxon.formats.MFileFormatUtil

public class MFileFormatUtil
extends java.lang.Object

File format related utility functions.

Since:

Marvin 4.1, 12/15/2005

Version:

5.1.1, 08/28/2008

Author:

Peter Csizmadia, Szilard Dorant, Szilveszter Juhos

Field Summary

static int

MULTISET The multi-molecule file really contains multiple atom sets of one molecule.

Constructor Summary

MFileFormatUtil()

Method Summary

static boolean	canBe1LetterPeptide(java.lang.String s) Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe1LetterPeptide(String) must be used instead
static boolean	canBe3LetterPeptide(java.lang.String s) Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe3LetterPeptide(String) must be used instead
static boolean	canBeAbbrevgroup(java.lang.String line) Deprecated. as of Marvin 5.0, AbbrevGroupRecognizer.testLine(String) must be used instead
static boolean	canBeBase64(java.lang.String line) Deprecated. as of Marvin 5.0, Base64Recognizer.canBeBase64(String) must be used instead
static boolean	canBeChime(java.lang.String s) Deprecated. as of Marvin 5.0, ChimeRecognizer.canBeChime(String) must be used instead
static boolean	canBeJTF(java.lang.String line) Deprecated. as of Marvin 5.0, JTFRecognizer.canBeJTFHeader(String) must be used instead
static boolean	canBePDBRecord(java.lang.String recName) Deprecated. as of Marvin 5.0, PDBRecognizer.testRecord(String) must be used instead
static boolean	canBeSMARTS(java.lang.String s) Deprecated. as of Marvin 5.0, SMILESRecognizer.canBeSMARTS(String) must be used instead
static boolean	canBeSMILES(java.lang.String s) Deprecated. as of Marvin 5.0, SMILESRecognizer.canBeSMILES(String) must be used instead
static java.lang.String[]	convertToSmilingFormat(Molecule m) Tries to convert a molecule to a SMILES related format.
static java.lang.String[]	convertToSmilingFormat(MProp p) Try to convert a property to text with a SMILES related format argument.
static MolExportModule	createExportModule(java.lang.String fmt) Creates an export module for the specified format.
static MRecordReader	createRecordReader(java.io.InputStream is, java.lang.String opts) Creates a record reader for an input stream.
static MFileFormat[]	findFormats(java.lang.String fmt, long flags, long mask) Gets a list of formats.
static java.lang.String[]	getEncodingFromOptions(java.lang.String fmtopts) Gets the encoding that was explicitly given as an import option.
static java.lang.String	getFileExtensionLC(java.io.File f) Gets the file extension in lower case.
static java.lang.String	getFileExtensionLC(java.lang.String fname) Gets the file extension in lower case.
static MFileFormat	getFormat(java.lang.String fmt) Gets the file format descriptor for the specified codename.
static java.lang.String[]	getJTFFields(java.lang.String line) Gets fields delimited with {space} {tab} {;} {:} or {,}.
static java.lang.String	getKnownExtension(java.lang.String fname) Returns the file extension if it is a known extension.
static java.lang.String[]	getMolfileExtensions() Gets the array of known molecule file extensions.
static java.lang.String[]	getMolfileFormats() Gets the array of known molecule file formats.
static java.lang.String	getMostLikelyMolFormat(java.lang.String fname) Gets the most likey molecule file format from the file name extension.
static java.lang.String	getUnguessableFormat(java.lang.String fname) Gets the file format from the file name extension for formats that are not guessable from the file content.
static java.lang.String	guessPeptideFormat(java.lang.String header) Deprecated. as of Marvin 5.0, Base64Recognizer.canBeBase64(String) must be used instead
static boolean	isCubeLine(java.lang.String line, int count) Deprecated. as of Marvin 5.0, CubeRecognizer.isCubeLine(String, int) must be used instead
static boolean	isOutputCleanable(java.lang.String fmt) Tests whether the specified output format is cleanable.
static boolean	isSubFormatOf(java.lang.String f, java.lang.String other) Tests whether a format is a sub-format of another format.
static boolean	isURLOrFileName(java.lang.String s) Tests whether the specified string is an URL (absolute or relative) or file name.
static int	preprocessFormatAndOptions(java.lang.String[] fmtopts) Parses "MULTISET" like universal options.
static java.lang.String	recognizeOneLineFormat(java.lang.String s) Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
static void	registerFormat(MFileFormat mff) Registers a user defined file format.
static java.lang.String[]	splitFileAndOptions(java.lang.String arg) Parses "file{options}" strings used in molecule file import.
static java.lang.String[]	splitFormatAndOptions(java.lang.String opts) Parses "format:options" strings used in molecule file import and export.
static void	testEncoding(java.lang.String enc) Tests whether the given charset name is supported by this JVM

Methods inherited from class java.lang.Object

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

Field Detail

MULTISET

public static final int MULTISET

The multi-molecule file really contains multiple atom sets of one molecule.

See Also:

Constant Field Values

Constructor Detail

MFileFormatUtil

public MFileFormatUtil()

Method Detail

isURLOrFileName

public static boolean isURLOrFileName(java.lang.String s)

Tests whether the specified string is an URL (absolute or relative) or file name.

Parameters:

s - the string

Returns:

true if it is an URL or file name, false otherwise

isSubFormatOf

public static boolean isSubFormatOf(java.lang.String f,
                                    java.lang.String other)

Tests whether a format is a sub-format of another format.

Parameters:

f - the format codename

other - the other format

Returns:

true if it is a format variant of f

Since:

Marvin 4.1, 04/07/2006

canBeBase64

public static boolean canBeBase64(java.lang.String line)

Deprecated. as of Marvin 5.0, Base64Recognizer.canBeBase64(String) must be used instead

canBeChime

public static boolean canBeChime(java.lang.String s)

Deprecated. as of Marvin 5.0, ChimeRecognizer.canBeChime(String) must be used instead

canBeSMARTS

public static boolean canBeSMARTS(java.lang.String s)

Deprecated. as of Marvin 5.0, SMILESRecognizer.canBeSMARTS(String) must be used instead

canBeSMILES

public static boolean canBeSMILES(java.lang.String s)

Deprecated. as of Marvin 5.0, SMILESRecognizer.canBeSMILES(String) must be used instead

canBe1LetterPeptide

public static boolean canBe1LetterPeptide(java.lang.String s)

Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe1LetterPeptide(String) must be used instead

canBe3LetterPeptide

public static boolean canBe3LetterPeptide(java.lang.String s)

Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe3LetterPeptide(String) must be used instead

recognizeOneLineFormat

public static java.lang.String recognizeOneLineFormat(java.lang.String s)

Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.

Parameters:

s - the input string

Returns:

the most probable format or null

Since:

Marvin 4.1, 04/06/2006

canBeAbbrevgroup

public static boolean canBeAbbrevgroup(java.lang.String line)

Deprecated. as of Marvin 5.0, AbbrevGroupRecognizer.testLine(String) must be used instead

canBeJTF

public static boolean canBeJTF(java.lang.String line)

Deprecated. as of Marvin 5.0, JTFRecognizer.canBeJTFHeader(String) must be used instead

canBePDBRecord

public static boolean canBePDBRecord(java.lang.String recName)

Deprecated. as of Marvin 5.0, PDBRecognizer.testRecord(String) must be used instead

isCubeLine

public static boolean isCubeLine(java.lang.String line,
                                 int count)

Deprecated. as of Marvin 5.0, CubeRecognizer.isCubeLine(String, int) must be used instead

getJTFFields

public static java.lang.String[] getJTFFields(java.lang.String line)

Gets fields delimited with {space} {tab} {;} {:} or {,}. Fields are enclosed in "" or '' these can be mixed in a line, but must match for a single field. A valid line for example: "23";'345.45';"asdf asdf";;'CCC1CC1'

Returns:

the contents of the fields.

splitFileAndOptions

public static java.lang.String[] splitFileAndOptions(java.lang.String arg)

Parses "file{options}" strings used in molecule file import.

Parameters:

arg - string containing the filename and the options (if there are)

Returns:

a two-element array containing the filename and the options.

splitFormatAndOptions

public static java.lang.String[] splitFormatAndOptions(java.lang.String opts)

Parses "format:options" strings used in molecule file import and export. Examples:

 splitFormatAndOptions("xyz:f1.4") returns {"xyz", "f1.4"}
 splitFormatAndOptions("f1.4") returns {null, "f1.4"}
 splitFormatAndOptions("xyz:") returns {"xyz", ""}
 splitFormatAndOptions("gzip:xyz:f1.4") returns {"gzip", "xyz:f1.4"}
 

The semicolon can be omitted in case if Marvin's built-in input formats. Example:

 splitFormatAndOptions("xyz") returns { "xyz", ""}
 

Parameters:

opts - string containing the format and the options

Returns:

an array containing the format(s) and the options.

preprocessFormatAndOptions

public static int preprocessFormatAndOptions(java.lang.String[] fmtopts)

Parses "MULTISET" like universal options. Example:

 String[] fmtopts = splitFormatAndOptions("gzip:xyz:MULTISET,f1.4");
 // fmtopts == {"gzip", "xyz:MULTISET,f.14"}
 int result = preprocessFormatAndOptions(fmtopts);
 // fmtopts == {"gzip", "xyz:f.14"}, results == MULTISET
 

Parameters:

fmtopts - two-element array containing the format and the options

Returns:

flags corresponding to the options

See Also:

splitFormatAndOptions(java.lang.String)

getEncodingFromOptions

public static java.lang.String[] getEncodingFromOptions(java.lang.String fmtopts)

Gets the encoding that was explicitly given as an import option. The format is enc{name}, where name is a JAVA supported name of the charset.

Parameters:

fmtopts - the input format and options

Returns:

two element array, the first element is the encoding, the second contains the remaining import options.

Throws:

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

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

testEncoding

public static void testEncoding(java.lang.String enc)
                         throws java.lang.IllegalArgumentException

Tests whether the given charset name is supported by this JVM

Parameters:

enc - the name of the charset

Throws:

java.lang.IllegalArgumentException

getUnguessableFormat

public static java.lang.String getUnguessableFormat(java.lang.String fname)

Gets the file format from the file name extension for formats that are not guessable from the file content. Used to distinguish SMARTS and SMILES.

Parameters:

fname - the filename

Returns:

the file format or null if the file contents can be used to recognize the format

getFileExtensionLC

public static java.lang.String getFileExtensionLC(java.io.File f)

Gets the file extension in lower case.

Parameters:

f - the file

Returns:

the extension in lower case

getFileExtensionLC

public static java.lang.String getFileExtensionLC(java.lang.String fname)

Gets the file extension in lower case.

Parameters:

fname - the filename

Returns:

the extension in lower case

getMostLikelyMolFormat

public static java.lang.String getMostLikelyMolFormat(java.lang.String fname)

Gets the most likey molecule file format from the file name extension.

Parameters:

fname - the filename

Returns:

the file format or null if the format cannot be determined from the file name

getKnownExtension

public static java.lang.String getKnownExtension(java.lang.String fname)

Returns the file extension if it is a known extension. Known extensions are the following: mrv t gz mol mol2 rgf rxn csmol csrgf csrxn sdf cssdf rdf smi smiles sma smarts cml xml xyz txt html htm cgi gif jpg jpeg msbmp png ppm svg svgz

Parameters:

fname - the filename

Returns:

the extension

getMolfileExtensions

public static java.lang.String[] getMolfileExtensions()

Gets the array of known molecule file extensions.

Returns:

the array of known molecule file extensions

getMolfileFormats

public static java.lang.String[] getMolfileFormats()

Gets the array of known molecule file formats.

Returns:

the array of known molecule file formats

isOutputCleanable

public static boolean isOutputCleanable(java.lang.String fmt)
                                 throws java.lang.SecurityException

Tests whether the specified output format is cleanable. For a non-cleanable output format, cleaning is meaningless because coordinates are not stored.

Parameters:

fmt - the format string

Returns:

true if the specified output format is non-cleanable, false otherwise

Throws:

java.lang.SecurityException

Since:

Marvin 4.1, 02/13/2006

guessPeptideFormat

public static java.lang.String guessPeptideFormat(java.lang.String header)

Deprecated. as of Marvin 5.0, Base64Recognizer.canBeBase64(String) must be used instead

registerFormat

public static void registerFormat(MFileFormat mff)

Registers a user defined file format. The MFileFormat.F_USER_DEFINED flag is automatically set.

Parameters:

mff - the file format

Since:

Marvin 5.0, 05/23/2007

getFormat

public static MFileFormat getFormat(java.lang.String fmt)

Gets the file format descriptor for the specified codename.

Parameters:

fmt - the format codename

Returns:

the descriptor or null if not found

Since:

Marvin 5.0, 05/23/2007

findFormats

public static MFileFormat[] findFormats(java.lang.String fmt,
                                        long flags,
                                        long mask)

Gets a list of formats.

Parameters:

fmt - the format name or null if not important

flags - select formats of which the specified flags are set

mask - only bits specified here are taken into account

Returns:

the list

Since:

Marvin 5.0, 05/24/2007

createRecordReader

public static MRecordReader createRecordReader(java.io.InputStream is,
                                               java.lang.String opts)
                                        throws MolFormatException,
                                               java.io.IOException

Creates a record reader for an input stream.

Parameters:

is - the input stream

opts - input options or null

Returns:

the record reader or null if the format was not recognized

Throws:

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

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

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolFormatException

java.io.IOException

Since:

Marvin 5.0, 06/03/2007

See Also:

MFileFormat.createRecordReader(MolInputStream, String)

createExportModule

public static MolExportModule createExportModule(java.lang.String fmt)
                                          throws MolExportException

Creates an export module for the specified format.

Parameters:

fmt - the format name

Throws:

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolExportException

See Also:

MFileFormat.createExportModule()

convertToSmilingFormat

public static java.lang.String[] convertToSmilingFormat(Molecule m)
                                                 throws MolExportException

Tries to convert a molecule to a SMILES related format. SMILES, SMARTS, CxSMILES and CxSMARTS are tried in this order.

Returns:

the result of the first successful conversion, the 0th array element is the converted text, the 1st element is the format

Throws:

MolExportException - if conversion was not successful

Since:

Marvin 5.0, 11/11/2007

convertToSmilingFormat

public static java.lang.String[] convertToSmilingFormat(MProp p)
                                                 throws MolExportException

Try to convert a property to text with a SMILES related format argument. SMILES, SMARTS, CxSMILES and CxSMARTS are tried in this order.

Returns:

the result of the first successful conversion, the 0th array element is the converted text, the 1st element is the format

Throws:

MolExportException - if conversion was not successful

Since:

Marvin 5.0, 11/11/2007