StructureIdentifier
public class BioAssemblyIdentifier extends java.lang.Object implements StructureIdentifier
Modifier and Type | Field | Description |
---|---|---|
static java.util.regex.Pattern |
BIO_NAME_PATTERN |
Constructor | Description |
---|---|
BioAssemblyIdentifier(java.lang.String name) |
|
BioAssemblyIdentifier(java.lang.String pdbCode,
int biolNr) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
getIdentifier() |
Get the String form of this identifier.
|
Structure |
loadStructure(AtomCache cache) |
Loads a structure encompassing the structure identified.
|
Structure |
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.
|
java.lang.String |
toString() |
public BioAssemblyIdentifier(java.lang.String name)
public BioAssemblyIdentifier(java.lang.String pdbCode, int biolNr)
public java.lang.String getIdentifier()
StructureIdentifier
#toString()
method also return the
identifier, for consistency during serialization.getIdentifier
in interface StructureIdentifier
public java.lang.String toString()
toString
in class java.lang.Object
public Structure loadStructure(AtomCache cache) throws StructureException, java.io.IOException
StructureIdentifier
StructureIdentifier.reduce(Structure)
.
It is recommended that the most complete structure available be returned
(e.g. the full PDB) to allow processing of unselected portions where
appropriate.loadStructure
in interface StructureIdentifier
StructureException
- For errors loading and parsing the structurejava.io.IOException
- Errors reading the structure from diskpublic SubstructureIdentifier toCanonical() throws StructureException
StructureIdentifier
This allows all domains to be converted to a standard format String.
toCanonical
in interface StructureIdentifier
StructureException
- Wraps exceptions that may be thrown by individual
implementations. For example, a SCOP identifier may require that the
domain definitions be available for download.public Structure reduce(Structure input) throws StructureException
StructureIdentifier
The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.
reduce
in interface StructureIdentifier
input
- A full structure, e.g. as loaded from the PDB. The structure
ID should match that returned by getPdbId(), if applicable.StructureException
StructureTools.getReducedStructure(Structure, String)