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 type "amino", "hetatm", "nucleotide".

Since:

1.4

Author:

Andreas Prlic

Field Summary

static String

DEFAULT_CHAIN_ID

Constructor Summary

ChainImpl()
Constructs a ChainImpl object.

Method Summary

void	addGroup(Group group) add a group to this chain.
Object	clone() returns an identical copy of this Chain .
Annotation	getAnnotation() get/set the Annotation of a Chain.
Group	getGroup(int position) return the amino acid at position .
Group	getGroupByPDB(String pdbresnum) get a group by its PDB residue numbering.
List	getGroups() return all groups of this chain .
List	getGroups(String type) return an array of all groups of a special type (e.g.
Group[]	getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd) get all groups that are located between two PDB residue numbers
int	getLength() get total length of chain, including HETATMs..
int	getLengthAminos() returns the length of the AminoAcids in chain, without HETATMs.
String	getName() get and set the name of this chain (Chain id in PDB file ).
String	getSequence() get amino acid sequence.
String	getSwissprotId() get the Swissprot id of this chains .
void	setAnnotation(Annotation anno) get/set the Annotation of a Chain.
void	setName(String nam) get and set the name of this chain (Chain id in PDB file ).
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

Constructor Detail

ChainImpl

public ChainImpl()

Constructs a ChainImpl object.

Method Detail

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)

Description copied from interface: Chain

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.

getAnnotation

public Annotation getAnnotation()

Description copied from interface: Chain

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

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)

Description copied from interface: Chain

add a group to this chain.

Specified by:

addGroup in interface Chain

Parameters:

group - a Group object

getGroup

public Group getGroup(int position)

return the amino acid at position .

Specified by:

getGroup in interface Chain

Parameters:

position - an int

Returns:

a Group object

getGroups

public List getGroups(String type)

return an array of all groups of a special type (e.g. amino, hetatm, nucleotide).

Specified by:

getGroups in interface Chain

Parameters:

type - a String

Returns:

an List object containing the groups of type...

getGroups

public List getGroups()

return all groups of this chain .

Specified by:

getGroups in interface Chain

Returns:

an ArrayList object representing the Groups of this Chain.

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

Description copied from interface: Chain

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()

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

getLengthAminos

public int getLengthAminos()

Description copied from interface: Chain

returns the length of the AminoAcids in chain, without HETATMs. note: not all amino acids need to have 3D coords, in fact in could be that none has! so length always corresponds to Sequence ( = uniprot,swissprot) length.

Specified by:

getLengthAminos in interface Chain

Returns:

an int representing the length of the AminoAcids in chain, without HETATMs.

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

getSequence

public String getSequence()

get amino acid sequence.

Specified by:

getSequence in interface Chain

Returns:

a String representing the sequence.