Package org.biojava.nbio.structure

Class ChainImpl

java.lang.Object
org.biojava.nbio.structure.ChainImpl
All Implemented Interfaces:
Serializable, Chain
public class ChainImpl extends Object implements Chain
A Chain in a PDB file. It contains several groups which can be of one of the types defined in the GroupType constants.
Since:
1.4
Author:
Andreas Prlic, Jules Jacobsen
See Also:

  • Constructor Details

    • ChainImpl

      public ChainImpl()
      Constructs a ChainImpl object.

  • Method Details

    • getId

      public String getId()
      Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
      Specified by:
      getId in interface Chain
      Returns:
      the asymId
      See Also:

    • setId

      public void setId(String asymId)
      Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
      Specified by:
      setId in interface Chain
      Parameters:
      asymId - the internal chain Id

    • getName

      public String getName()
      Get the 'public' authId (chain ID in PDB file)
      Specified by:
      getName in interface Chain
      Returns:
      the authId for this chain.
      See Also:

    • setName

      public void setName(String authId)
      Set the 'public' authId (chain ID in PDB file)
      Specified by:
      setName in interface Chain
      Parameters:
      authId - the 'public' authId (chain ID in PDB file)
      See Also:

    • 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:

    • 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:

    • 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:

    • clone

      public Object clone()
      Returns an identical copy of this Chain .
      Specified by:
      clone in interface Chain
      Overrides:
      clone in class Object
      Returns:
      an identical copy of this Chain

    • setEntityInfo

      public void setEntityInfo(EntityInfo mol)
      Sets the Entity information
      Specified by:
      setEntityInfo in interface Chain
      Parameters:
      mol - the EntityInfo
      See Also:

    • getEntityInfo

      public EntityInfo getEntityInfo()
      Returns the EntityInfo for this chain.
      Specified by:
      getEntityInfo in interface Chain
      Returns:
      the EntityInfo object
      See Also:

    • setSwissprotId

      public void setSwissprotId(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

      public 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:

    • 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:

    • getAtomGroups

      public 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:

    • getAtomGroups

      public 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:

    • setAtomGroups

      public void setAtomGroups(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:

    • getGroupsByPDB

      public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing) throws StructureException
      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. If null, defaults to the chain start.
      end - PDB residue number of end. If null, defaults to the chain 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. If null, defaults to the chain start.
      end - PDB residue number of end. If null, defaults to the chain 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:

    • setChainID

      public void setChainID(String asymId)
      Sets the 'private' asymId of this chain (Chain id in PDB file ).
      Specified by:
      setChainID in interface Chain
      Parameters:
      asymId - a String specifying the name value
      See Also:

    • getChainID

      public String getChainID()
      Gets the 'private' asymId of this chain.
      Specified by:
      getChainID in interface Chain
      Returns:
      a String representing the name value
      See Also:

    • toString

      public String toString()
      String representation.
      Specified by:
      toString in interface Chain
      Overrides:
      toString in class 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 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:

    • getSeqResSequence

      public 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:

    • getSeqResOneLetterSeq

      public String getSeqResOneLetterSeq()
      Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups. Method related to https://github.com/biojava/biojava/issues/457
      Returns:
      a string of the sequence guaranteed to be the same length as seqResGroups.

    • 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:

    • getSeqResGroups

      public 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:

    • getSeqResGroups

      public 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:

    • setSeqResGroups

      public void setSeqResGroups(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:

    • 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:

    • getAtomLigands

      public 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 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(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 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 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(List<SeqMisMatch> seqMisMatches)
      Description copied from interface: Chain
      Sets 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 List<SeqMisMatch> getSeqMisMatches()
      Description copied from interface: Chain
      Gets annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category
      Specified by:
      getSeqMisMatches in interface Chain

    • getEntityType

      public EntityType getEntityType()
      Description copied from interface: Chain
      Returns the EntityType of this chain. Equivalent to getEntityInfo().getType()
      Specified by:
      getEntityType in interface Chain
      Returns:
      See Also:

    • isWaterOnly

      public boolean isWaterOnly()
      Description copied from interface: Chain
      Tests if a chain is consisting of water molecules only
      Specified by:
      isWaterOnly in interface Chain
      Returns:
      true if there are only solvent molecules in this chain.

    • isPureNonPolymer

      public boolean isPureNonPolymer()
      Description copied from interface: Chain
      Returns true if the given chain is composed of non-polymeric (including water) groups only.
      Specified by:
      isPureNonPolymer in interface Chain
      Returns:
      true if only non-polymeric groups in this chain.

    • getPredominantGroupType

      public GroupType getPredominantGroupType()
      Description copied from interface: Chain
      Get the predominant GroupType for a given Chain, following these rules:
    • if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold {@value #org.biojava.nbio.structure.StructureTools.RATIO_RESIDUES_TO_TOTAL}, then that GroupType is returned
    • if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it

      • See also ChemComp.getPolymerType() and ChemComp.getResidueType() which follow the PDB chemical component dictionary and provide a much more accurate description of groups and their linking.

      Specified by:
      getPredominantGroupType in interface Chain
      Returns:

    • isProtein

      public boolean isProtein()
      Description copied from interface: Chain
      Tell whether given chain is a protein chain
      Specified by:
      isProtein in interface Chain
      Returns:
      true if protein, false if nucleotide or ligand
      See Also:

    • isNucleicAcid

      public boolean isNucleicAcid()
      Description copied from interface: Chain
      Tell whether given chain is DNA or RNA
      Specified by:
      isNucleicAcid in interface Chain
      Returns:
      true if nucleic acid, false if protein or ligand
      See Also: