public class PDPDomain extends java.lang.Object implements StructureIdentifier
Modifier and Type | Field and Description |
---|---|
static java.util.regex.Pattern |
PDP_NAME_PATTERN |
Constructor and Description |
---|
PDPDomain(java.lang.String pdpDomainName,
java.util.List<ResidueRange> ranges) |
Modifier and Type | Method and Description |
---|---|
java.lang.String |
getIdentifier()
Get the String form of this identifier.
|
java.lang.String |
getPdbId() |
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 PDPDomain(java.lang.String pdpDomainName, java.util.List<ResidueRange> ranges)
public java.lang.String getIdentifier()
StructureIdentifier
#toString()
method also return the
identifier, for consistency during serialization.getIdentifier
in interface StructureIdentifier
public java.lang.String getPdbId()
public SubstructureIdentifier toCanonical()
StructureIdentifier
This allows all domains to be converted to a standard format String.
toCanonical
in interface StructureIdentifier
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)
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 disk