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

All Methods Static Methods Instance Methods Concrete Methods
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 Detail
- DEFAULT_FILE
```
protected static File DEFAULT_FILE
```

Method Detail

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()

Class SiftsChainToUniprotMapping

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_FILE