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