Field Detail

• PDP_NAME_PATTERN

  public static final java.util.regex.Pattern PDP_NAME_PATTERN

Constructor Detail

• PDPDomain

  public PDPDomain(java.lang.String pdpDomainName,
                   java.util.List<ResidueRange> ranges)

Method Detail

• getIdentifier

  public java.lang.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 interface StructureIdentifier

  Returns:

  The String form of this identifier

• getPdbId

  public java.lang.String getPdbId()

• 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 interface StructureIdentifier

  Returns:

  A SubstructureIdentifier equivalent to this

• 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 interface StructureIdentifier

  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)

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• loadStructure

  public Structure loadStructure(AtomCache cache)
                          throws StructureException,
                                 java.io.IOException

  Description copied from interface: StructureIdentifier
  Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to 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.

  Specified by:

  loadStructure in interface StructureIdentifier

  Returns:

  A Structure containing at least the atoms identified by this, or null if Structures are not applicable.

  Throws:

  StructureException - For errors loading and parsing the structure

  java.io.IOException - Errors reading the structure from disk