org.biojava.bio.structure

Class ChainImpl

java.lang.Object

org.biojava.bio.structure.ChainImpl

All Implemented Interfaces:

java.io.Serializable, Chain

public class ChainImpl
extends java.lang.Object
implements Chain, java.io.Serializable

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:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_CHAIN_ID The default chain identifier is an empty space.
protected java.util.List<Group>	seqResGroups

Constructor Summary

Constructors

Constructor and Description
ChainImpl() Constructs a ChainImpl object.

Method Summary

Methods

Modifier and Type	Method and Description
void	addGroup(Group group) add a group to the list of ATOM record group of this chain.
protected void	addSeqResGroup(Group g)
java.lang.Object	clone() Returns an identical copy of this Chain .
Group	getAtomGroup(int position) return the group at position .
java.util.List<Group>	getAtomGroups() Return all groups that have been specified in the ATOM section of this chain .
java.util.List<Group>	getAtomGroups(java.lang.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.
java.util.List<Group>	getAtomLigands() Get all groups that are not polymer groups and that are not solvent groups.
java.lang.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.
java.lang.String	getChainID() get and set the name of this chain (Chain id in PDB file ).
Group	getGroup(int position) Deprecated. use getAtomGroup or getSeqResGroup instead
Group	getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
Group	getGroupByPDB(java.lang.String pdbresnum) get a group by its PDB residue numbering.
java.util.List<Group>	getGroups() Deprecated. use getAtomGroups instead
java.util.List<Group>	getGroups(java.lang.String type) Deprecated. use getAtomGroups instead
Group[]	getGroupsByPDB(ResidueNumber start, ResidueNumber end) Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing) Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd) Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.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.
java.lang.Long	getId() Get the ID used by Hibernate.
java.lang.String	getInternalChainID() If available, returns the internal chain ID that is used in mmCif files, otherwise null
int	getLength() Deprecated. use getAtomLength instead
int	getLengthAminos() returns the length of the AminoAcids in the ATOM records of this chain.
java.lang.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.
java.util.List<Group>	getSeqResGroups() Return all groups of this chain.
java.util.List<Group>	getSeqResGroups(java.lang.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.
java.lang.String	getSeqResSequence() Returns the PDB SEQRES sequence as a one-letter sequence string.
java.lang.String	getSequence() Deprecated. use getAtomSequence instead
java.lang.String	getSwissprotId() get the Swissprot id of this chains .
void	setAtomGroups(java.util.List<Group> groups) Set all groups that have been specified in the ATOM section of this chain .
void	setChainID(java.lang.String nam) get and set the name of this chain (Chain id in PDB file ).
void	setHeader(Compound mol) Set the Header from the PDB file.
void	setId(java.lang.Long id) Set the ID used by Hibernate.
void	setInternalChainID(java.lang.String internalChainID) Sets the internal chain ID that is used in mmCif files
void	setName(java.lang.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(java.util.List<Group> groups) Set the list of SeqResGroups for this chain.
void	setSwissprotId(java.lang.String sp_id) set the Swissprot id of this chains .
java.lang.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 java.lang.String DEFAULT_CHAIN_ID

The default chain identifier is an empty space.

seqResGroups

protected java.util.List<Group> seqResGroups

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

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 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

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(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

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 java.util.List<Group> getGroups(java.lang.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 java.util.List<Group> getAtomGroups(java.lang.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 java.util.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 java.util.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(java.util.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(java.lang.String pdbresnumStart,
                     java.lang.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

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

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(java.lang.String pdbresnum)
                    throws StructureException

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

getGroupByPDB

public Group getGroupByPDB(ResidueNumber resNum)
                    throws StructureException

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:

resNum - the PDB residue number of the group

Returns:

the matching group

Throws:

StructureException

getGroupsByPDB

public Group[] getGroupsByPDB(java.lang.String pdbresnumStart,
                     java.lang.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

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

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(java.lang.String nam)

Description copied from interface: Chain

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:

Chain.getName()

getName

public java.lang.String getName()

Description copied from interface: Chain

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:

Chain.setName(java.lang.String)

setChainID

public void setChainID(java.lang.String nam)

get and set 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:

getChainID()

getChainID

public java.lang.String getChainID()

get and set 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:

setName(java.lang.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()

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 java.lang.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 java.lang.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 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 position X.

Specified by:

getSeqResGroup in interface Chain

Parameters:

position - an int

Returns:

a Group object

getSeqResGroups

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

addSeqResGroup

protected void addSeqResGroup(Group g)

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

getAtomLigands

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

Get 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 PDBFileReader.setLoadChemCompInfo(flag) 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, 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