Package org.biojava.nbio.structure.io.sifts

Class SiftsChainToUniprotMapping

java.lang.Object

org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping

public class SiftsChainToUniprotMapping
extends Object

A mapping between UniProt entries and PDB chains. For example

 SiftsChainToUniprot sifts = SiftsChainToUniprot.load();
 SiftsChainEntry entry1 = sifts.getByUniProtId("P04585");
 System.out.println(entry1.getPdbId() + "." + entry1.getChainName()); // 1hiv.A
 System.out.println(entry1.getPdbStart() + "-" + entry1.getPdbStop()); // 1-99
 SiftsChainEntry entry2 = sifts.getByChainId("1hiv", "A");
 System.out.println(entry1.equals(entry2)); // true
 

See SIFTS project documentation: https://www.ebi.ac.uk/pdbe/docs/sifts/

Since:

3.0.7

Author:

dmyersturnbull

See Also:

• SiftsChainEntry

Field Summary

Fields

Modifier and Type	Field	Description
protected static File	DEFAULT_FILE

Method Summary

Modifier and Type	Method	Description
protected static SiftsChainToUniprotMapping	build()	Builds the mapping by reading SIFTS the tsv file set in DEFAULT_FILE variable.
Set<Map.Entry<String,SiftsChainEntry>>	chainEntrySet()
boolean	containsChainId(String pdbId, String chainId)
boolean	containsUniProtId(String uniProtId)
SiftsChainEntry	getByChainId(String pdbId, String chainId)
SiftsChainEntry	getByUniProtId(String uniProtId)
Set<String>	keySet()
static SiftsChainToUniprotMapping	load()	Loads the SIFTS mapping.
static SiftsChainToUniprotMapping	load(boolean useOnlyLocal)	Loads the SIFTS mapping.
int	size()	Returns the number of mapped entries.
Set<Map.Entry<String,SiftsChainEntry>>	uniProtEntrySet()
Collection<SiftsChainEntry>	values()

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_FILE

protected static File DEFAULT_FILE

Method Details

load

public static SiftsChainToUniprotMapping load()
                                       throws IOException

Loads the SIFTS mapping. Attempts to load the mapping file in the PDB cache directory. If the file does not exist or could not be parsed, downloads and stores a GZ-compressed file.

Returns:

Throws:

IOException - If the local file could not be read and could not be downloaded

load

public static SiftsChainToUniprotMapping load(boolean useOnlyLocal)
                                       throws IOException

Loads the SIFTS mapping. Attempts to load the mapping file in the PDB cache directory. If the file does not exist or could not be parsed, downloads and stores a GZ-compressed file.

Parameters:

useOnlyLocal - If true, will throw an IOException if the file needs to be downloaded

Returns:

Throws:

IOException - If the local file could not be read and could not be downloaded (including if onlyLocal is true)

build

protected static SiftsChainToUniprotMapping build()
                                           throws IOException

Builds the mapping by reading SIFTS the tsv file set in DEFAULT_FILE variable.

Returns:

Throws:

IOException

chainEntrySet

public Set<Map.Entry<String,SiftsChainEntry>> chainEntrySet()

containsChainId

public boolean containsChainId(String pdbId,
 String chainId)

containsUniProtId

public boolean containsUniProtId(String uniProtId)

getByChainId

public SiftsChainEntry getByChainId(String pdbId,
 String chainId)

getByUniProtId

public SiftsChainEntry getByUniProtId(String uniProtId)

keySet

public Set<String> keySet()

size

public int size()

Returns the number of mapped entries.

uniProtEntrySet

public Set<Map.Entry<String,SiftsChainEntry>> uniProtEntrySet()

values

public Collection<SiftsChainEntry> values()