Constructor Detail

• ScopDomain

  public ScopDomain()

Method Detail

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• getScopId

  public java.lang.String getScopId()

• setScopId

  public void setScopId​(java.lang.String scopId)

• getPdbId

  public java.lang.String getPdbId()

• setPdbId

  public void setPdbId​(java.lang.String pdbId)

• getRanges

  public java.util.List<java.lang.String> getRanges()

• setRanges

  public void setRanges​(java.util.List<java.lang.String> ranges)

• getClassificationId

  public java.lang.String getClassificationId()

• setClassificationId

  public void setClassificationId​(java.lang.String classificationId)

• getSunid

  public java.lang.Integer getSunid()

• setSunid

  public void setSunid​(java.lang.Integer sunid)

• getClassId

  public int getClassId()

• setClassId

  public void setClassId​(int classId)

• getFoldId

  public int getFoldId()

• setFoldId

  public void setFoldId​(int foldId)

• getSuperfamilyId

  public int getSuperfamilyId()

• setSuperfamilyId

  public void setSuperfamilyId​(int superfamilyId)

• getFamilyId

  public int getFamilyId()

• setFamilyId

  public void setFamilyId​(int familyId)

• getDomainId

  public int getDomainId()

• setDomainId

  public void setDomainId​(int domainId)

• getSpeciesId

  public int getSpeciesId()

• setSpeciesId

  public void setSpeciesId​(int speciesId)

• getPx

  public int getPx()

• setPx

  public void setPx​(int px)

• clone

  protected java.lang.Object clone()
                            throws java.lang.CloneNotSupportedException

  Overrides:

  clone in class java.lang.Object

  Throws:

  java.lang.CloneNotSupportedException

• getChains

  public java.util.Set<java.lang.String> getChains()

  Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.

• 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

• getResidueRanges

  public java.util.List<ResidueRange> getResidueRanges()

• 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)

• 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