Package org.biojava.nbio.structure
Class URLIdentifier
- java.lang.Object
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- org.biojava.nbio.structure.URLIdentifier
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- 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
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Field Summary
Fields Modifier and Type Field Description static String
CHAINID_PARAM
URL parameter specifying a single chain to include; overridden by residuesstatic String
FORMAT_PARAM
URL parameter specifying the file format (PDB or CIF)static String
PDBID_PARAM
URL parameter specifying the PDB IDstatic String
RESIDUES_PARAM
URL parameter specifying residue ranges to include, e.g.
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Constructor Summary
Constructors Constructor Description URLIdentifier(String url)
URLIdentifier(URL url)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 URLStructure
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.
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Field Detail
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FORMAT_PARAM
public static final String FORMAT_PARAM
URL parameter specifying the file format (PDB or CIF)- See Also:
- Constant Field Values
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PDBID_PARAM
public static final String PDBID_PARAM
URL parameter specifying the PDB ID- See Also:
- Constant Field Values
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CHAINID_PARAM
public static final String CHAINID_PARAM
URL parameter specifying a single chain to include; overridden by residues- See Also:
- Constant Field Values
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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
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Constructor Detail
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URLIdentifier
public URLIdentifier(URL url)
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URLIdentifier
public URLIdentifier(String url) throws MalformedURLException
- Throws:
MalformedURLException
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Method Detail
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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 interfaceStructureIdentifier
- Returns:
- The String form of this identifier
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toCanonical
public SubstructureIdentifier toCanonical()
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 interfaceStructureIdentifier
- Returns:
- A SubstructureIdentifier without ranges (e.g. including all residues)
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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 interfaceStructureIdentifier
- 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)
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loadStructure
public Structure loadStructure(AtomCache cache) throws StructureException, IOException
Load the structure from the URL- Specified by:
loadStructure
in interfaceStructureIdentifier
- Returns:
- null
- Throws:
StructureException
- For errors loading and parsing the structureIOException
- Errors reading the structure from disk
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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
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