Package org.biojava.nbio.structure.io.cif

Class CifStructureConverter

java.lang.Object

org.biojava.nbio.structure.io.cif.CifStructureConverter

public class CifStructureConverter
extends Object

Convert BioJava structures to CifFiles and vice versa.

Since:

6.0.0

Author:

Sebastian Bittrich

Constructor Summary

Constructors

Constructor	Description
CifStructureConverter()

Method Summary

Modifier and Type	Method	Description
static Structure	fromCifFile(org.rcsb.cif.model.CifFile cifFile)	Convert CifFile to Structure without any FileParsingParameters.
static Structure	fromCifFile(org.rcsb.cif.model.CifFile cifFile, FileParsingParameters parameters)	Convert CifFile to Structure.
static Structure	fromInputStream(InputStream inputStream)	Convert InputStream to Structure without any FileParsingParameters.
static Structure	fromInputStream(InputStream inputStream, FileParsingParameters parameters)	Convert InputStream to Structure.
static Structure	fromPath(Path path)	Read data from a file and convert to Structure without any FileParsingParameters.
static Structure	fromPath(Path path, FileParsingParameters parameters)	Read data from a file and convert to Structure.
static Structure	fromURL(URL url)	Get data from a URL and convert to Structure without any FileParsingParameters.
static Structure	fromURL(URL url, FileParsingParameters parameters)	Get data from a URL and convert to Structure.
static byte[]	toBinary(Structure structure)	Convert a structure to BCIF format.
static void	toBinaryFile(Structure structure, Path path)	Write a structure to a BCIF file.
static org.rcsb.cif.model.CifFile	toCifFile(Chain chain)	Convert Chain to CifFile
static org.rcsb.cif.model.CifFile	toCifFile(Structure structure)	Convert Structure to CifFile.
static String	toText(Chain chain)	Convert a chain to mmCIF format.
static String	toText(Structure structure)	Convert a structure to mmCIF format.
static void	toTextFile(Structure structure, Path path)	Write a structure to a CIF file.

Methods inherited from class java.lang.Object

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

Constructor Details

CifStructureConverter

public CifStructureConverter()

Method Details

fromPath

public static Structure fromPath(Path path)
                          throws IOException

Read data from a file and convert to Structure without any FileParsingParameters.

Parameters:

path - the source of information - can be gzipped or binary or text data

Returns:

the target

Throws:

IOException

fromPath

public static Structure fromPath(Path path,
 FileParsingParameters parameters)
                          throws IOException

Read data from a file and convert to Structure.

Parameters:

path - the source of information - can be gzipped or binary or text data

parameters - parameters for parsing

Returns:

the target

Throws:

IOException

fromURL

public static Structure fromURL(URL url)
                         throws IOException

Get data from a URL and convert to Structure without any FileParsingParameters.

Parameters:

url - the source of information - can be gzipped or binary or text data

Returns:

the target

Throws:

IOException - thrown when reading fails

fromURL

public static Structure fromURL(URL url,
 FileParsingParameters parameters)
                         throws IOException

Get data from a URL and convert to Structure.

Parameters:

url - the source of information - can be gzipped or binary or text data

parameters - parameters for parsing

Returns:

the target

Throws:

IOException - thrown when reading fails

fromInputStream

public static Structure fromInputStream(InputStream inputStream)
                                 throws IOException

Convert InputStream to Structure without any FileParsingParameters.

Parameters:

inputStream - the InputStream of information - can be gzipped or binary or text data

Returns:

the target

Throws:

IOException - thrown when reading fails

See Also:

• fromInputStream(InputStream, FileParsingParameters)

fromInputStream

public static Structure fromInputStream(InputStream inputStream,
 FileParsingParameters parameters)
                                 throws IOException

Convert InputStream to Structure.

Parameters:

inputStream - the InputStream of information - can be gzipped or binary or text data

parameters - parameters for parsing

Returns:

the target

Throws:

IOException - thrown when reading fails

fromCifFile

public static Structure fromCifFile(org.rcsb.cif.model.CifFile cifFile)

Convert CifFile to Structure without any FileParsingParameters.

Parameters:

cifFile - the source

Returns:

the target

See Also:

• fromCifFile(CifFile, FileParsingParameters)

fromCifFile

public static Structure fromCifFile(org.rcsb.cif.model.CifFile cifFile,
 FileParsingParameters parameters)

Convert CifFile to Structure.

Parameters:

cifFile - the source

parameters - parameters for parsing

Returns:

the target

toTextFile

public static void toTextFile(Structure structure,
 Path path)
                       throws IOException

Write a structure to a CIF file.

Parameters:

structure - the source

path - where to write to

Throws:

IOException - thrown when writing fails

toBinaryFile

public static void toBinaryFile(Structure structure,
 Path path)
                         throws IOException

Write a structure to a BCIF file.

Parameters:

structure - the source

path - where to write to

Throws:

IOException - thrown when writing fails

toBinary

public static byte[] toBinary(Structure structure)

Convert a structure to BCIF format.

Parameters:

structure - the source

Returns:

the binary representation of the structure

toText

public static String toText(Structure structure)

Convert a structure to mmCIF format.

Parameters:

structure - the source

Returns:

the mmCIF String representation of the structure

toText

public static String toText(Chain chain)

Convert a chain to mmCIF format.

Parameters:

chain - the source

Returns:

the mmCIF String representation of the chain

toCifFile

public static org.rcsb.cif.model.CifFile toCifFile(Structure structure)

Convert Structure to CifFile.

Parameters:

structure - the source

Returns:

the target

toCifFile

public static org.rcsb.cif.model.CifFile toCifFile(Chain chain)

Convert Chain to CifFile

Parameters:

chain - the source

Returns:

the target