Class SiftsChainToUniprotMapping
- java.lang.Object
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- org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMapping
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public class SiftsChainToUniprotMapping extends Object
A mapping between UniProt entries and PDB chains. For exampleSiftsChainToUniprot 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
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Field Summary
Fields Modifier and Type Field Description protected static File
DEFAULT_FILE
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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 inDEFAULT_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()
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Field Detail
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DEFAULT_FILE
protected static File DEFAULT_FILE
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Method Detail
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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
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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)
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build
protected static SiftsChainToUniprotMapping build() throws IOException
Builds the mapping by reading SIFTS the tsv file set inDEFAULT_FILE
variable.- Returns:
- Throws:
IOException
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chainEntrySet
public Set<Map.Entry<String,SiftsChainEntry>> chainEntrySet()
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containsChainId
public boolean containsChainId(String pdbId, String chainId)
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containsUniProtId
public boolean containsUniProtId(String uniProtId)
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getByChainId
public SiftsChainEntry getByChainId(String pdbId, String chainId)
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getByUniProtId
public SiftsChainEntry getByUniProtId(String uniProtId)
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size
public int size()
Returns the number of mapped entries.
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uniProtEntrySet
public Set<Map.Entry<String,SiftsChainEntry>> uniProtEntrySet()
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values
public Collection<SiftsChainEntry> values()
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