Package org.biojava.nbio.structure.io

Class MMCIFFileReader

java.lang.Object

org.biojava.nbio.structure.io.LocalPDBDirectory

org.biojava.nbio.structure.io.MMCIFFileReader

All Implemented Interfaces:

StructureIOFile, StructureProvider

public class MMCIFFileReader
extends LocalPDBDirectory

How to parse an mmCif file:

public static void main(String[] args) throws Exception {
        String filename =  "/path/to/something.cif.gz" ;

        StructureIOFile reader = new MMCIFFileReader();

        Structure struc = reader.getStructure(filename);
        System.out.println(struc);
}

Since:

1.7

Author:

Andreas Prlic

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior

Field Summary

Fields

Modifier and Type	Field	Description
static String[]	MMCIF_OBSOLETE_DIR
static String[]	MMCIF_SPLIT_DIR

Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, MIN_PDB_FILE_SIZE, PDB_FILE_SERVER_PROPERTY

Constructor Summary

Constructors

Constructor	Description
MMCIFFileReader()	Constructs a new MMCIFFileReader, initializing the extensions member variable.
MMCIFFileReader(String path)	Constructs a new PDBFileReader, initializing the extensions member variable.

Method Summary

Modifier and Type	Method	Description
protected String	getFilename(String pdbId)	Converts a PDB ID into a filename with the proper extension
SimpleMMcifConsumer	getMMcifConsumer()
protected String[]	getObsoleteDirPath()	Location of obsolete files within the directory, as an array of paths.
protected String[]	getSplitDirPath()	Location of split files within the directory, as an array of paths.
Structure	getStructure(InputStream inStream)	Handles the actual parsing of the file into a Structure object.
static void	main(String[] args)

Methods inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

addExtension, checkFileExists, clearExtensions, deleteStructure, downloadStructure, getDir, getExtensions, getFetchBehavior, getFileParsingParameters, getInputStream, getLocalFile, getObsoleteBehavior, getPath, getServerName, getStructure, getStructure, getStructure, getStructureById, initPaths, prefetchStructure, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath

Methods inherited from class java.lang.Object

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

Field Detail

MMCIF_SPLIT_DIR

public static final String[] MMCIF_SPLIT_DIR

MMCIF_OBSOLETE_DIR

public static final String[] MMCIF_OBSOLETE_DIR

Constructor Detail

MMCIFFileReader

public MMCIFFileReader()

Constructs a new MMCIFFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false

MMCIFFileReader

public MMCIFFileReader(String path)

Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.

Method Detail

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception

getStructure

public Structure getStructure(InputStream inStream)
                       throws IOException

Description copied from class: LocalPDBDirectory

Handles the actual parsing of the file into a Structure object.

Specified by:

getStructure in class LocalPDBDirectory

Returns:

Throws:

IOException

getMMcifConsumer

public SimpleMMcifConsumer getMMcifConsumer()

getFilename

protected String getFilename(String pdbId)

Description copied from class: LocalPDBDirectory

Converts a PDB ID into a filename with the proper extension

Specified by:

getFilename in class LocalPDBDirectory

Returns:

The filename, e.g. "4hhb.pdb.gz"

getSplitDirPath

protected String[] getSplitDirPath()

Description copied from class: LocalPDBDirectory

Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.

Specified by:

getSplitDirPath in class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server

getObsoleteDirPath

protected String[] getObsoleteDirPath()

Description copied from class: LocalPDBDirectory

Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.

Specified by:

getObsoleteDirPath in class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server