Field Detail

• DEFAULT_CHAIN_ID

  public static java.lang.String DEFAULT_CHAIN_ID

  The default chain identifier used to be an empty space

Constructor Detail

• ChainImpl

  public ChainImpl()

  Constructs a ChainImpl object.

Method Detail

• getId

  public java.lang.Long getId()

  Get the ID used by Hibernate.

  Specified by:

  getId in interface Chain

  Returns:

  the ID used by Hibernate

  See Also:

  Chain.setId(Long)

• setId

  public void setId​(java.lang.Long id)

  Set the ID used by Hibernate.

  Specified by:

  setId in interface Chain

  Parameters:

  id - assigned by Hibernate

  See Also:

  Chain.getId()

• setParent

  @Deprecated
  public void setParent​(Structure parent)

  Deprecated.
  Sets the back-reference to its parent Structure.

  Specified by:

  setParent in interface Chain

  Parameters:

  parent - the parent Structure object for this Chain

  See Also:

  Chain.getStructure()

• setStructure

  public void setStructure​(Structure parent)

  Sets the back-reference to its parent Structure.

  Specified by:

  setStructure in interface Chain

• getStructure

  public Structure getStructure()

  Returns the parent Structure of this chain.

  Specified by:

  getStructure in interface Chain

  Returns:

  the parent Structure object

  See Also:

  Chain.setStructure(Structure)

• getParent

  @Deprecated
  public Structure getParent()

  Deprecated.

  use getStructure instead.
  Returns the parent Structure of this chain.

  Specified by:

  getParent in interface Chain

  Returns:

  the parent Structure object

  See Also:

  Chain.setStructure(Structure)

• clone

  public java.lang.Object clone()

  Returns an identical copy of this Chain .

  Specified by:

  clone in interface Chain

  Overrides:

  clone in class java.lang.Object

  Returns:

  an identical copy of this Chain

• setCompound

  public void setCompound​(Compound mol)

  Sets the Compound

  Specified by:

  setCompound in interface Chain

  Parameters:

  mol - the Compound

  See Also:

  Chain.getCompound()

• getCompound

  public Compound getCompound()

  Returns the Compound for this chain.

  Specified by:

  getCompound in interface Chain

  Returns:

  the Compound object

  See Also:

  Chain.setCompound(Compound)

• setSwissprotId

  public void setSwissprotId​(java.lang.String sp_id)

  set the Swissprot id of this chains .

  Specified by:

  setSwissprotId in interface Chain

  Parameters:

  sp_id - a String specifying the swissprot id value

  See Also:

  getSwissprotId()

• getSwissprotId

  public java.lang.String getSwissprotId()

  get the Swissprot id of this chains .

  Specified by:

  getSwissprotId in interface Chain

  Returns:

  a String representing the swissprot id value

  See Also:

  setSwissprotId(java.lang.String)

• addGroup

  public void addGroup​(Group group)

  add a group to the list of ATOM record group of this chain. To add SEQRES records a more complex alignment between ATOM and SEQRES residues is required, please see SeqRes2AtomAligner for more details on that.

  Specified by:

  addGroup in interface Chain

  Parameters:

  group - a Group object

• getAtomGroup

  public Group getAtomGroup​(int position)

  Return the Group at given position, from within Groups with observed density in the chain, i.e. those with coordinates in ATOM and HETATMS (including waters) records.

  Specified by:

  getAtomGroup in interface Chain

  Parameters:

  position - an int

  Returns:

  a Group object

  See Also:

  Chain.getAtomLength(), Chain.getAtomGroups(), Chain.getSeqResGroup(int)

• getAtomGroups

  public java.util.List<Group> getAtomGroups​(GroupType type)

  Return a List of all (observed) Groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE. Note that if a standard aminoacid appears as a HETATM (because it is part of a ligand) then it is still considered as GroupType.AMINOACID and not as GroupType.HETATM.

  Specified by:

  getAtomGroups in interface Chain

  Parameters:

  type - GroupType

  Returns:

  a List object

  See Also:

  Chain.setAtomGroups(List)

• getAtomGroups

  public java.util.List<Group> getAtomGroups()

  Return all Groups with observed density in the chain, i.e. those with coordinates in ATOM and HETATMS (including waters) records.

  Specified by:

  getAtomGroups in interface Chain

  Returns:

  a List object representing the Groups of this Chain.

  See Also:

  Chain.setAtomGroups(List), Chain.getAtomLength(), Chain.getSeqResGroups()

• setAtomGroups

  public void setAtomGroups​(java.util.List<Group> groups)

  Set all Groups with observed density in the chain, i.e. those with coordinates in ATOM and HETATMs (including waters) records.

  Specified by:

  setAtomGroups in interface Chain

  Parameters:

  groups - a List object representing the Groups of this Chain.

  See Also:

  Chain.getAtomGroups()

• getGroupsByPDB

  @Deprecated
  public Group[] getGroupsByPDB​(ResidueNumber start,
                                ResidueNumber end,
                                boolean ignoreMissing)
                         throws StructureException

  Deprecated.
  Description copied from interface: Chain
  Get all groups that are located between two PDB residue numbers. In contrast to getGroupsByPDB this method call ignores if the exact outer groups are not found. This is useful e.g. when requesting the range of groups as specified by the DBREF records - these frequently are rather inaccurate.

  Specified by:

  getGroupsByPDB in interface Chain

  Parameters:

  start - PDB residue number of start

  end - PDB residue number of end

  ignoreMissing - ignore missing groups in this range.

  Returns:

  Groups in between. or throws a StructureException if either start or end can not be found,

  Throws:

  StructureException

• getGroupByPDB

  public Group getGroupByPDB​(ResidueNumber resNum)
                      throws StructureException

  Get a group by its PDB residue numbering. If the PDB residue number is not known, throws a StructureException.

  Specified by:

  getGroupByPDB in interface Chain

  Parameters:

  resNum - the PDB residue number of the group

  Returns:

  the matching group

  Throws:

  StructureException

• getGroupsByPDB

  public Group[] getGroupsByPDB​(ResidueNumber start,
                                ResidueNumber end)
                         throws StructureException

  Get all groups that are located between two PDB residue numbers.

  Specified by:

  getGroupsByPDB in interface Chain

  Parameters:

  start - PDB residue number of start

  end - PDB residue number of end

  Returns:

  Groups in between. or throws a StructureException if either start or end can not be found,

  Throws:

  StructureException

• getSeqResLength

  public int getSeqResLength()

  Returns the number of groups in the SEQRES records of the chain, i.e. the number of aminoacids/nucleotides in the construct

  Specified by:

  getSeqResLength in interface Chain

  Returns:

  the length

  See Also:

  Chain.getSeqResGroup(int), Chain.getSeqResGroups(), Chain.getAtomLength()

• setChainID

  public void setChainID​(java.lang.String nam)

  Sets the name of this chain (Chain id in PDB file ).

  Specified by:

  setChainID in interface Chain

  Parameters:

  nam - a String specifying the name value

  See Also:

  Chain.getChainID()

• getChainID

  public java.lang.String getChainID()

  Gets the name of this chain (Chain id in PDB file ).

  Specified by:

  getChainID in interface Chain

  Returns:

  a String representing the name value

  See Also:

  Chain.setChainID(String)

• toString

  public java.lang.String toString()

  String representation.

  Specified by:

  toString in interface Chain

  Overrides:

  toString in class java.lang.Object

  Returns:

  String representation of the Chain

• getBJSequence

  public Sequence<?> getBJSequence()

  Converts the SEQRES groups of a Chain to a Biojava Sequence object.

  Specified by:

  getBJSequence in interface Chain

  Returns:

  the SEQRES groups of the Chain as a Sequence object.

• getAtomSequence

  public java.lang.String getAtomSequence()

  Returns the sequence of amino acids as it has been provided in the ATOM records. Non-standard residues will be present in the string only if the property has been set.

  Specified by:

  getAtomSequence in interface Chain

  Returns:

  amino acid sequence as string

  See Also:

  Chain.getSeqResSequence()

• getSeqResSequence

  public java.lang.String getSeqResSequence()

  Returns the PDB SEQRES sequence as a one-letter sequence string. Non-standard residues are represented by an "X".

  Specified by:

  getSeqResSequence in interface Chain

  Returns:

  one-letter PDB SEQRES sequence as string

  See Also:

  Chain.getAtomSequence()

• getSeqResGroup

  public Group getSeqResGroup​(int position)

  Return the Group at given position, from within groups in the SEQRES records of the chain, i.e. the aminoacids/nucleotides in the construct.

  Specified by:

  getSeqResGroup in interface Chain

  Parameters:

  position - an int

  Returns:

  a Group object

  See Also:

  Chain.getSeqResLength(), Chain.getSeqResGroups(), Chain.getAtomGroup(int)

• getSeqResGroups

  public java.util.List<Group> getSeqResGroups​(GroupType type)

  Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.

  Specified by:

  getSeqResGroups in interface Chain

  Parameters:

  type - a GroupType

  Returns:

  an List object

  See Also:

  Chain.setSeqResGroups(List)

• getSeqResGroups

  public java.util.List<Group> getSeqResGroups()

  Returns a list of all groups in SEQRES records of the chain, i.e. the aminoacids/nucleotides in the construct.

  Specified by:

  getSeqResGroups in interface Chain

  Returns:

  a List of all Group objects of this chain

  See Also:

  Chain.setSeqResGroups(List), Chain.getSeqResLength(), Chain.getAtomGroups()

• setSeqResGroups

  public void setSeqResGroups​(java.util.List<Group> groups)

  Sets the list of SeqResGroups for this chain.

  Specified by:

  setSeqResGroups in interface Chain

  Parameters:

  groups - a List of Group objects that from the SEQRES groups of this chain.

  See Also:

  Chain.getSeqResGroups()

• addSeqResGroup

  protected void addSeqResGroup​(Group g)

• getAtomLength

  public int getAtomLength()

  Returns the number of Groups with observed density in the chain, i.e. those with coordinates in ATOM and HETATMs (including waters) records

  Specified by:

  getAtomLength in interface Chain

  Returns:

  the length

  See Also:

  Chain.getAtomGroup(int), Chain.getAtomGroups()

• getAtomLigands

  public java.util.List<Group> getAtomLigands()

  Gets all groups that are not polymer groups and that are not solvent groups. Will automatically fetch Chemical Component files from the PDB web site, even if FileParsingParameters#setLoadChemCompInfo(boolean) has not been set to true. Otherwise the Ligands could not correctly be identified.

  Specified by:

  getAtomLigands in interface Chain

  Returns:

  list of Groups that are ligands

• getInternalChainID

  public java.lang.String getInternalChainID()

  Description copied from interface: Chain
  If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null

  Specified by:

  getInternalChainID in interface Chain

  Returns:

  String or null

• setInternalChainID

  public void setInternalChainID​(java.lang.String internalChainID)

  Description copied from interface: Chain
  Sets the internal chain ID that is used in mmCif files

  Specified by:

  setInternalChainID in interface Chain

• toPDB

  public java.lang.String toPDB()

  Description copied from interface: Chain
  Convert this Chain to a String in PDB format

  Specified by:

  toPDB in interface Chain

  Returns:

• toMMCIF

  public java.lang.String toMMCIF()

  Description copied from interface: Chain
  Convert this Chain to a String in mmCIF format

  Specified by:

  toMMCIF in interface Chain

  Returns:

• setSeqMisMatches

  public void setSeqMisMatches​(java.util.List<SeqMisMatch> seqMisMatches)

  Description copied from interface: Chain
  Set annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category

  Specified by:

  setSeqMisMatches in interface Chain

• getSeqMisMatches

  public java.util.List<SeqMisMatch> getSeqMisMatches()

  Description copied from interface: Chain
  Get annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category

  Specified by:

  getSeqMisMatches in interface Chain