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## org.biojava.bio.structure
Class ChainImpl

    java.lang.Object
      org.biojava.bio.structure.ChainImpl

All Implemented Interfaces:
  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

Field Summary
`static String` | `DEFAULT_CHAIN_ID` The default chain identifier is an empty space.

Constructor Summary
`ChainImpl()` Constructs a ChainImpl object.

Method Summary
`void` | `addGroup(Group group)` add a group to the list of ATOM record group of this chain.
`Object` | `clone()` Returns an identical copy of this Chain .
`Annotation` | `getAnnotation()` get/set the Annotation of a Chain.
`Group` | `getAtomGroup(int position)` return the group at position .
`List<Group>` | `getAtomGroups()` Return all groups that have been specified in the ATOM section of this chain .
`List<Group>` | `getAtomGroups(String type)` Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
`int` | `getAtomLength()` Return the number of Groups in the ATOM records of the chain.
`String` | `getAtomSequence()` Return the sequence of amino acids as it has been provided in the ATOM records.
`Sequence` | `getBJSequence()` Convert the SEQRES groups of a Chain to a Biojava Sequence object.
`Group` | `getGroup(int position)` Deprecated. use getAtomGroup or getSeqResGroup instead
`Group` | `getGroupByPDB(String pdbresnum)` get a group by its PDB residue numbering.
`List<Group>` | `getGroups()` Deprecated. use getAtomGroups instead
`List<Group>` | `getGroups(String type)` Deprecated. use getAtomGroups instead
`Group[]` | `getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` Get all groups that are located between two PDB residue numbers.
`Group[]` | `getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing)` Get all groups that are located between two PDB residue numbers.
`Compound` | `getHeader()` Returns the Header ( a Compound object) for this chain.
`Long` | `getId()` Get the ID used by Hibernate.
`int` | `getLength()` Deprecated. use getAtomLength instead
`int` | `getLengthAminos()` returns the length of the AminoAcids in the ATOM records of this chain.
`String` | `getName()` get and set the name of this chain (Chain id in PDB file ).
`Structure` | `getParent()` Returns the parent Structure of this chain.
`Group` | `getSeqResGroup(int position)` return the Group at position X.
`List<Group>` | `getSeqResGroups()` Return all groups of this chain.
`List<Group>` | `getSeqResGroups(String type)` Return a List of all groups of a special type (e.g.
`int` | `getSeqResLength()` Returns the number of groups in the SEQRES records of the chain.
`String` | `getSeqResSequence()` Get the sequence for all amino acids as it is specified in the SEQRES residues.
`String` | `getSequence()` Deprecated. use getAtomSequence instead
`String` | `getSwissprotId()` get the Swissprot id of this chains .
`void` | `setAnnotation(Annotation anno)` get/set the Annotation of a Chain.
`void` | `setAtomGroups(List<Group> groups)` Set all groups that have been specified in the ATOM section of this chain .
`void` | `setHeader(Compound mol)` Set the Header from the PDB file.
`void` | `setId(Long id)` Set the ID used by Hibernate.
`void` | `setName(String nam)` get and set the name of this chain (Chain id in PDB file ).
`void` | `setParent(Structure parent)` Set the back-reference to its parent Structure.
`void` | `setSeqResGroups(List<Group> groups)` Set the list of SeqResGroups for this chain.
`void` | `setSwissprotId(String sp_id)` set the Swissprot id of this chains .
`String` | `toString()` String representation.

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

### DEFAULT_CHAIN_ID

    public static String DEFAULT_CHAIN_ID

  The default chain identifier is an empty space.

Constructor Detail

### ChainImpl

    public ChainImpl()

  Constructs a ChainImpl object.

Method Detail

### getId

    public 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(Long id)

  Set the ID used by Hibernate.

  Specified by:
    `setId` in interface `Chain`
  Parameters:
    `id` - assigned by Hibernate
  See Also:
    `Chain.getId()`

### setParent

    public void setParent(Structure parent)

  Set 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.getParent()`

### getParent

    public Structure getParent()

  Returns the parent Structure of this chain.

  Specified by:
    `getParent` in interface `Chain`
  Returns:
    the parent Structure object
  See Also:
    `Chain.setParent(Structure)`

### 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

### setAnnotation

    public void setAnnotation(Annotation anno)

  get/set the Annotation of a Chain. allows to annotate a protein chain, e.g. molecule description "AZURIN" for pdb 1a4a.A

  Specified by:
    `setAnnotation` in interface `Chain`
  Parameters:
    `anno` - the Annotation to be provided.
  See Also:
    `Chain.getAnnotation()`

### getAnnotation

    public Annotation getAnnotation()

  get/set the Annotation of a Chain. allows to annotate a protein chain, e.g. molecule description "AZURIN" for pdb 1a4a.A

  Specified by:
    `getAnnotation` in interface `Chain`
  Returns:
    the Annotation of this chain
  See Also:
    `Chain.setAnnotation(Annotation)`

### setHeader

    public void setHeader(Compound mol)

  Set the Header from the PDB file.

  Specified by:
    `setHeader` in interface `Chain`
  Parameters:
    `mol` - the Compound that contains the header information for this chain
  See Also:
    `Chain.getHeader()`

### getHeader

    public Compound getHeader()

  Returns the Header ( a Compound object) for this chain.

  Specified by:
    `getHeader` in interface `Chain`
  Returns:
    the Compound object that contains the Header information
  See Also:
    `Chain.setHeader(Compound)`

### 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()`

### 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:
    `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

### getGroup

    public Group getGroup(int position)

  Deprecated. use getAtomGroup or getSeqResGroup instead

  return the group at position .

  Specified by:
    `getGroup` in interface `Chain`
  Parameters:
    `position` - an int
  Returns:
    a Group object
  See Also:
    `Chain.getAtomGroup(int)`, `Chain.getSeqResGroup(int)`

### getAtomGroup

    public Group getAtomGroup(int position)

  return the group at position .

  Specified by:
    `getAtomGroup` in interface `Chain`
  Parameters:
    `position` - an int
  Returns:
    a Group object

### getGroups

    public List<Group> getGroups(String type)

  Deprecated. use getAtomGroups instead

  Return a list of all groups of one of the types defined in hte `GroupType` constants.

  Specified by:
    `getGroups` in interface `Chain`
  Parameters:
    `type` - a String
  Returns:
    an List object containing the groups of type...

### getAtomGroups

    public List<Group> getAtomGroups(String type)

  Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.

  Specified by:
    `getAtomGroups` in interface `Chain`
  Parameters:
    `type` - the type of the groups to return. Can be one of the 3 types defined in the `GroupType` constants
  Returns:
    a list of group objects
  See Also:
    `Chain.setAtomGroups(List)`

### getGroups

    public List<Group> getGroups()

  Deprecated. use getAtomGroups instead

  return all groups of this chain .

  Specified by:
    `getGroups` in interface `Chain`
  Returns:
    a List object representing the Groups of this Chain.

### getAtomGroups

    public List<Group> getAtomGroups()

  Return all groups that have been specified in the ATOM section of this chain .

  Specified by:
    `getAtomGroups` in interface `Chain`
  Returns:
    a List object representing the Groups of this Chain.
  See Also:
    `Chain.setAtomGroups(List)`

### setAtomGroups

    public void setAtomGroups(List<Group> groups)

  Set all groups that have been specified in the ATOM section of this chain .

  Specified by:
    `setAtomGroups` in interface `Chain`
  Parameters:
    `groups` - a List object representing the Groups of this Chain.
  See Also:
    `Chain.getAtomGroups()`

### getGroupsByPDB

    public Group[] getGroupsByPDB(String pdbresnumStart,
                                  String pdbresnumEnd,
                                  boolean ignoreMissing)
                           throws StructureException

  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:
    `pdbresnumStart` - PDB residue number of start
    `pdbresnumEnd` - 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(String pdbresnum)
                        throws StructureException

  Description copied from interface: `Chain`
  get a group by its PDB residue numbering. if the PDB residue number is not know, throws a StructureException.

  Specified by:
    `getGroupByPDB` in interface `Chain`
  Parameters:
    `pdbresnum` - the PDB residue number of the group
  Returns:
    the matching group
  Throws:
    `StructureException`

### getGroupsByPDB

    public Group[] getGroupsByPDB(String pdbresnumStart,
                                  String pdbresnumEnd)
                           throws StructureException

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

  Specified by:
    `getGroupsByPDB` in interface `Chain`
  Parameters:
    `pdbresnumStart` - PDB residue number of start
    `pdbresnumEnd` - PDB residue number of end
  Returns:
    Groups in between. or throws a StructureException if either start or end can not be found,
  Throws:
    `StructureException`

### getLength

    public int getLength()

  Deprecated. use getAtomLength instead

  Description copied from interface: `Chain`
  get total length of chain, including HETATMs..

  Specified by:
    `getLength` in interface `Chain`
  Returns:
    an int representing the length of the whole chain including HETATMs
  See Also:
    `Chain.getAtomLength()`, `Chain.getSeqResLength()`

### getLengthAminos

    public int getLengthAminos()

  returns the length of the AminoAcids in the ATOM records of this chain. note: not all amino acids need to have 3D coords, in fact in could be that none has!

  Specified by:
    `getLengthAminos` in interface `Chain`
  Returns:
    an int representing the length of the AminoAcids in the ATOM records of the chain.

### getSeqResLength

    public int getSeqResLength()

  Description copied from interface: `Chain`
  Returns the number of groups in the SEQRES records of the chain.

  Specified by:
    `getSeqResLength` in interface `Chain`
  Returns:
    the length

### setName

    public void setName(String nam)

  get and set the name of this chain (Chain id in PDB file ).

  Specified by:
    `setName` in interface `Chain`
  Parameters:
    `nam` - a String specifying the name value
  See Also:
    `getName()`

### getName

    public String getName()

  get and set the name of this chain (Chain id in PDB file ).

  Specified by:
    `getName` in interface `Chain`
  Returns:
    a String representing the name value
  See Also:
    `setName(java.lang.String)`

### 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()
                           throws IllegalSymbolException

  Convert 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.
  Throws:
    `IllegalSymbolException`

### getSequence

    public String getSequence()

  Deprecated. use getAtomSequence instead

  get amino acid sequence of the chain. for backwards compatibility this returns the Atom sequence of the chain.

  Specified by:
    `getSequence` in interface `Chain`
  Returns:
    a String representing the sequence.
  See Also:
    `getAtomSequence()`, `getSeqResSequence()`

### getAtomSequence

    public String getAtomSequence()

  Return the sequence of amino acids as it has been provided in the ATOM records.

  Specified by:
    `getAtomSequence` in interface `Chain`
  Returns:
    amino acid sequence as string
  See Also:
    `Chain.getSeqResSequence()`

### getSeqResSequence

    public String getSeqResSequence()

  Get the sequence for all amino acids as it is specified in the SEQRES residues.

  Specified by:
    `getSeqResSequence` in interface `Chain`
  Returns:
    the amino acid sequence of the SEQRES sequence as a string
  See Also:
    `Chain.getAtomSequence()`

### getSeqResGroup

    public Group getSeqResGroup(int position)

  return the Group at position X.

  Specified by:
    `getSeqResGroup` in interface `Chain`
  Parameters:
    `position` - an int
  Returns:
    a Group object

### getSeqResGroups

    public List<Group> getSeqResGroups(String type)

  Return a List of all groups of a special type (e.g. amino, hetatm, nucleotide).

  Specified by:
    `getSeqResGroups` in interface `Chain`
  Parameters:
    `type` - a String
  Returns:
    an List object
  See Also:
    `Chain.setSeqResGroups(List)`

### getSeqResGroups

    public List<Group> getSeqResGroups()

  Return all groups of this chain.

  Specified by:
    `getSeqResGroups` in interface `Chain`
  Returns:
    a List of all Group objects of this chain
  See Also:
    `Chain.setSeqResGroups(List)`

### setSeqResGroups

    public void setSeqResGroups(List<Group> groups)

  Set 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()`

### getAtomLength

    public int getAtomLength()

  Return the number of Groups in the ATOM records of the chain.

  Specified by:
    `getAtomLength` in interface `Chain`
  Returns:
    the length

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