Package org.biojava.nbio.structure
Class URLIdentifier
java.lang.Object
org.biojava.nbio.structure.URLIdentifier
- All Implemented Interfaces:
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
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final StringURL parameter specifying a single chain to include; overridden by residuesstatic final StringURL parameter specifying the file format (PDB or CIF)static final StringURL parameter specifying the PDB IDstatic final StringURL parameter specifying residue ranges to include, e.g. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionGet the String form of this identifier.getURL()static StringguessPDBID(String name) Recognizes PDB IDs that occur at the beginning of name followed by some delimiter.loadStructure(AtomCache cache) Load the structure from the URLTakes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.Convert to a canonical SubstructureIdentifier.
-
Field Details
-
FORMAT_PARAM
URL parameter specifying the file format (PDB or CIF)- See Also:
-
PDBID_PARAM
URL parameter specifying the PDB ID- See Also:
-
CHAINID_PARAM
URL parameter specifying a single chain to include; overridden by residues- See Also:
-
RESIDUES_PARAM
URL parameter specifying residue ranges to include, e.g. residues=A:1-70- See Also:
-
-
Constructor Details
-
URLIdentifier
-
URLIdentifier
- Throws:
MalformedURLException
-
-
Method Details
-
getURL
-
getIdentifier
Description copied from interface:StructureIdentifierGet the String form of this identifier. It is recommended that the#toString()method also return the identifier, for consistency during serialization.- Specified by:
getIdentifierin interfaceStructureIdentifier- Returns:
- The String form of this identifier
-
toCanonical
Description copied from interface:StructureIdentifierConvert to a canonical SubstructureIdentifier.This allows all domains to be converted to a standard format String.
- Specified by:
toCanonicalin interfaceStructureIdentifier- Returns:
- A SubstructureIdentifier without ranges (e.g. including all residues)
-
reduce
Description copied from interface:StructureIdentifierTakes 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:
reducein 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:
-
loadStructure
Load the structure from the URL- Specified by:
loadStructurein interfaceStructureIdentifier- Returns:
- null
- Throws:
StructureException- For errors loading and parsing the structureIOException- Errors reading the structure from disk
-
guessPDBID
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
-