org.biojava.nbio.structure.align.client

Class StructureName

java.lang.Object

org.biojava.nbio.structure.align.client.StructureName

All Implemented Interfaces:

Serializable, Comparable<StructureName>, StructureIdentifier

public class StructureName
extends Object
implements Comparable<StructureName>, Serializable, StructureIdentifier

A utility class that makes working with names of structures, domains and ranges easier. Accepts a wide range of identifier formats, including ScopDomain, CathDomain, PDP domains, and SubstructureIdentifier residue ranges. Where possible, data is extracted from the input string. Otherwise, range information may be loaded from one of the factory classes: CathFactory,ScopFactory, etc.

See Also:

the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc., Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StructureName.Source

Field Summary

Fields

Modifier and Type	Field and Description
protected String	chainName
protected String	name
protected String	pdbId

Constructor Summary

Constructors

Constructor and Description
StructureName(String name) Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

Method Summary

Modifier and Type	Method and Description
int	compareTo(StructureName o) Orders identifiers lexicographically by PDB ID and then full Identifier
boolean	equals(Object obj)
StructureIdentifier	getBaseIdentifier() StructureName wraps another StructureIdentifier.
String	getChainId() Gets the chain ID, for structures where it is unique and well-defined.
String	getIdentifier() Get the original form of the identifier
String	getPdbId() Get the PDB ID for this name, if any.
StructureName.Source	getSource()
static ScopDomain	guessScopDomain(String name, ScopDatabase scopDB) Guess a scop domain.
int	hashCode()
boolean	isBioAssembly()
boolean	isCathID()
boolean	isEcodDomain()
boolean	isFile() Indicates that the identifier was determined to correspond to a file.
boolean	isPdbId()
boolean	isPDPDomain()
boolean	isScopName()
boolean	isURL()
Structure	loadStructure(AtomCache cache) Loads a structure encompassing the structure identified.
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.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

name

protected String name

pdbId

protected String pdbId

chainName

protected String chainName

Constructor Detail

StructureName

public StructureName(String name)

Create a new StructureName from the given identifier, which may be a domain name, a substructure identifier, etc.

The source and PDB-Id are extracted at compile time, but fully interpreting the ID, which may require additional parsing or remote calls, is done lazily.

The following sources are supported. Any may be prefixed by the source name followed by a colon (e.g. PDB:4HHB). In this case, that source will be used unequivocally. If no source is specified, StructureName will make a (usually reliable) guess as to which source was intended.

• PDBPDB identifier, optionally followed by chain and/or residue ranges. Internally represented by a SubstructureIdentifier; see that class for the full format specification. Examples: 4hhb, 4hhb.A, 4hhb.A:1-50.
• SCOP SCOP domain (or SCOPe, depending on the ScopFactory.getSCOP() version). Example: d1h6w.2
• PDP Protein Domain Parser domain. PDP domains are not guessed, making the PDP: prefix obligatory. Example: PDP:4HHBAa
• CATH Cath domains. Example: 1qvrC03
• URL Arbitrary URLs. Most common protocols are handled, including http://, ftp://, and file://. Some parsing information can be passed as custom query parameters. Example: http://www.rcsb.org/pdb/files/1B8G.pdb.gz
• FILE A file path. Supports relative paths and expands ~ to the user's home directory. Only existing files will be automatically detected; to refer to a potentially not-yet existing file, prepend the prefix. Internally represented as a URLIdentifier after path expansion. Example: ~/custom_protein.pdb
• ECOD ECOD domain. Example: e1lyw.1
• BIO Biological assembly. These are not guessed, making the BIO: prefix obligatory. Example: BIO:2ehz:1

Parameters:

name - An identifier string

Throws:

IllegalArgumentException - if the name has a recognizable source but is semantically invalid

Method Detail

getPdbId

public String getPdbId()
                throws StructureException

Get the PDB ID for this name, if any. Equivalent to toCanonical().getPdbId()

Returns:

The upper-case PDB Name, or null if not applicable

Throws:

StructureException - Wraps errors which occur when converting to canonical form

getChainId

public String getChainId()

Gets the chain ID, for structures where it is unique and well-defined. May return '.' for multi-chain ranges, '_' for wildcard chains, or null if the information is unavailable.

This method should only be used casually. For precise chainIds, it is better to use toCanonical() and iterate through the residue ranges.

Returns:

getIdentifier

public String getIdentifier()

Get the original form of the identifier

Specified by:

getIdentifier in interface StructureIdentifier

Returns:

The String form of this identifier

toString

public String toString()

Overrides:

toString in class Object

isScopName

public boolean isScopName()

isPDPDomain

public boolean isPDPDomain()

isCathID

public boolean isCathID()

isPdbId

public boolean isPdbId()

isURL

public boolean isURL()

isFile

public boolean isFile()

Indicates that the identifier was determined to correspond to a file. Note that some file identifiers may also be valid URLs; in that case, the URL source is preferred.

Returns:

isEcodDomain

public boolean isEcodDomain()

isBioAssembly

public boolean isBioAssembly()

getSource

public StructureName.Source getSource()

getBaseIdentifier

public StructureIdentifier getBaseIdentifier()
                                      throws StructureException

StructureName wraps another StructureIdentifier. The type of the base identifier depends on the source. Most StructureName methods deligate to the base identifier.

It is possible that future versions of StructureName might change the return type. Except for some specialized uses, it is probably better to create the correct type of identifier directly, rather than creating a StructureName and casting the result of this method.

Returns:

A Str

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.

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 equivalent to this

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

See Also:

StructureTools.getReducedStructure(Structure, String)

loadStructure

public Structure loadStructure(AtomCache cache)
                        throws StructureException,
                               IOException

Description copied from interface: StructureIdentifier

Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure). It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.

Specified by:

loadStructure in interface StructureIdentifier

Returns:

A Structure containing at least the atoms identified by this, or null if Structures are not applicable.

Throws:

StructureException - For errors loading and parsing the structure

IOException - Errors reading the structure from disk

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

compareTo

public int compareTo(StructureName o)

Orders identifiers lexicographically by PDB ID and then full Identifier

Specified by:

compareTo in interface Comparable<StructureName>

guessScopDomain

public static ScopDomain guessScopDomain(String name,
                                         ScopDatabase scopDB)

Guess a scop domain. If an exact match is found, return that.

Otherwise, return the first scop domain found for the specified protein such that

• The chains match, or one of the chains is '_' or '.'.
• The domains match, or one of the domains is '_'.

In some cases there may be several valid matches. In this case a warning will be logged.

Parameters:

name - SCOP domain name, or a guess thereof

scopDB - SCOP domain provider

Returns:

The best match for name among the domains of scopDB, or null if none match.