Class CathDomain

Method Details

• getDomainName

  public String getDomainName()

• setDomainName

  public void setDomainName(String domainName)

• getPdbId

  @Deprecated public String getPdbId()

  Deprecated.

  This method is poorly named; use getThePdbId() or getPdbIdAndChain() instead

  Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.

• getThePdbId

  public String getThePdbId()

  Returns the PDB ID.

• getPdbIdAndChain

  public String getPdbIdAndChain()

  Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.

• getDomainId

  public Integer getDomainId()

• getClassId

  public Integer getClassId()

• setClassId

  public void setClassId(Integer classId)

• getArchitectureId

  public Integer getArchitectureId()

• setArchitectureId

  public void setArchitectureId(Integer architectureId)

• getTopologyId

  public Integer getTopologyId()

• setTopologyId

  public void setTopologyId(Integer topologyId)

• getHomologyId

  public Integer getHomologyId()

• setHomologyId

  public void setHomologyId(Integer homologyId)

• getSequenceFamilyId

  public Integer getSequenceFamilyId()

• setSequenceFamilyId

  public void setSequenceFamilyId(Integer sequenceFamilyId)

• getOrthologousSequenceFamilyId

  public Integer getOrthologousSequenceFamilyId()

• setOrthologousSequenceFamilyId

  public void setOrthologousSequenceFamilyId(Integer orthologousSequenceFamilyId)

• getLikeSequenceFamilyId

  public Integer getLikeSequenceFamilyId()

• setLikeSequenceFamilyId

  public void setLikeSequenceFamilyId(Integer likeSequenceFamilyId)

• getIdenticalSequenceFamilyId

  public Integer getIdenticalSequenceFamilyId()

• setIdenticalSequenceFamilyId

  public void setIdenticalSequenceFamilyId(Integer identicalSequenceFamilyId)

• getDomainCounter

  public Integer getDomainCounter()

• setDomainCounter

  public void setDomainCounter(Integer domainCounter)

• getLength

  public Integer getLength()

• setLength

  public void setLength(Integer length)

• getResolution

  public Double getResolution()

• setResolution

  public void setResolution(Double resolution)

• setCATH

  public void setCATH(String cathCode)

• getCATH

  public String getCATH()

• setSOLID

  public void setSOLID(String cathCode)

• getSOILD

  public String getSOILD()

• getClassificationId

  public Integer getClassificationId(CathCategory cathCategory)

• getFormat

  public String getFormat()

• setFormat

  public void setFormat(String format)

• getVersion

  public String getVersion()

• setVersion

  public void setVersion(String version)

• getDate

  public Date getDate()

• setDate

  public void setDate(Date date)

• getName

  public String getName()

• setName

  public void setName(String name)

• getSource

  public String getSource()

• setSource

  public void setSource(String source)

• getSequenceHeader

  public String getSequenceHeader()

• setSequenceHeader

  public void setSequenceHeader(String sequenceHeader)

• getSequence

  public String getSequence()

• setSequence

  public void setSequence(String sequence)

• getSegments

  public List<CathSegment> getSegments()

• setSegments

  public void setSegments(List<CathSegment> segments)

• getComment

  public String getComment()

• setComment

  public void setComment(String comment)

• toString

  public String toString()

  Overrides:

  toString in class Object

• getChains

  public Set<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 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

• 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, 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

  IOException - Errors reading the structure from disk