Package org.biojava.nbio.structure

Class URLIdentifier

java.lang.Object

org.biojava.nbio.structure.URLIdentifier

All Implemented Interfaces:

Serializable, StructureIdentifier

public class URLIdentifier
extends Object
implements StructureIdentifier

Represents a structure loaded from a URL (including a file URL)

A few custom query parameters are supported:

• format=[pdb|cif] Specify the file format (will otherwise be guessed from the extension)
• pdbId=[String] Specify the PDB ID (also guessed from the filename)
• chainID=[String] A single chain from the structure
• residues=[String] Residue ranges, in a form understood by SubstructureIdentifier

Author:

Spencer Bliven

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CHAINID_PARAM	URL parameter specifying a single chain to include; overridden by residues
static final String	FORMAT_PARAM	URL parameter specifying the file format (PDB or CIF)
static final String	PDBID_PARAM	URL parameter specifying the PDB ID
static final String	RESIDUES_PARAM	URL parameter specifying residue ranges to include, e.g.

Constructor Summary

Constructors

Constructor	Description
URLIdentifier(String url)
URLIdentifier(URL url)

Method Summary

Modifier and Type	Method	Description
String	getIdentifier()	Get the String form of this identifier.
URL	getURL()
static String	guessPDBID(String name)	Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.
Structure	loadStructure(AtomCache cache)	Load the structure from the URL
Structure	reduce(Structure input)	Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
SubstructureIdentifier	toCanonical()	Convert to a canonical SubstructureIdentifier.

Methods inherited from class java.lang.Object

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

Field Details

FORMAT_PARAM

public static final String FORMAT_PARAM

URL parameter specifying the file format (PDB or CIF)

See Also:

• Constant Field Values

PDBID_PARAM

public static final String PDBID_PARAM

URL parameter specifying the PDB ID

See Also:

• Constant Field Values

CHAINID_PARAM

public static final String CHAINID_PARAM

URL parameter specifying a single chain to include; overridden by residues

See Also:

• Constant Field Values

RESIDUES_PARAM

public static final String RESIDUES_PARAM

URL parameter specifying residue ranges to include, e.g. residues=A:1-70

See Also:

• SubstructureIdentifier
• Constant Field Values

Constructor Details

URLIdentifier

public URLIdentifier(URL url)

URLIdentifier

public URLIdentifier(String url)
              throws MalformedURLException

Throws:

MalformedURLException

Method Details

getURL

public URL getURL()

getIdentifier

public String getIdentifier()

Description copied from interface: StructureIdentifier

Get the String form of this identifier. It is recommended that the toString() method also return the identifier, for consistency during serialization.

Specified by:

getIdentifier in interface StructureIdentifier

Returns:

The String form of this identifier

toCanonical

public SubstructureIdentifier toCanonical()
                                   throws StructureException

Description copied from interface: StructureIdentifier

Convert to a canonical SubstructureIdentifier.

This allows all domains to be converted to a standard format String.

Specified by:

toCanonical in interface StructureIdentifier

Returns:

A SubstructureIdentifier without ranges (e.g. including all residues)

Throws:

StructureException - Wraps exceptions that may be thrown by individual implementations. For example, a SCOP identifier may require that the domain definitions be available for download.

reduce

public Structure reduce(Structure input)
                 throws StructureException

Description copied from interface: StructureIdentifier

Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

Specified by:

reduce in interface StructureIdentifier

Parameters:

input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.

Returns:

Throws:

StructureException

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws StructureException,
IOException

Load the structure from the URL

Specified by:

loadStructure in interface StructureIdentifier

Parameters:

cache - A potential sources of structures

Returns:

null

Throws:

StructureException - For errors loading and parsing the structure

IOException - Errors reading the structure from disk

guessPDBID

public static String guessPDBID(String name)

Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.

Parameters:

name - Input filename

Returns:

A 4-character id-like string, or null if none is found