org.biojava.nbio.structure

Class ChainImpl

java.lang.Object

org.biojava.nbio.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 used to be an empty space

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 given position, from within Groups with observed density in the chain, i.e.
java.util.List<Group>	getAtomGroups() Return all Groups with observed density in the chain, i.e.
java.util.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.
int	getAtomLength() Return the number of Groups with observed density in the chain, i.e.
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 the name of this chain (Chain id in PDB file ).
Compound	getCompound() Return the Compound for this chain.
Group	getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
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) Deprecated.
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
Structure	getParent() Returns the parent Structure of this chain.
Group	getSeqResGroup(int position) Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
java.util.List<Group>	getSeqResGroups() Return a list of all groups in SEQRES records of the chain, i.e.
java.util.List<Group>	getSeqResGroups(GroupType type) Return a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
int	getSeqResLength() Return the number of groups in the SEQRES records of the chain, i.e.
java.lang.String	getSeqResSequence() Return the PDB SEQRES sequence as a one-letter sequence string.
java.lang.String	getSwissprotId() get the Swissprot id of this chains .
void	setAtomGroups(java.util.List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	setChainID(java.lang.String nam) Set the name of this chain (Chain id in PDB file ).
void	setCompound(Compound mol) Set the Compound
void	setId(java.lang.Long id) Set the ID used by Hibernate.
void	setInternalChainID(java.lang.String internalChainID) Set the internal chain ID that is used in mmCif files
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	toPDB() Convert this Chain to a String in PDB format
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 used to be an empty space

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

setCompound

public void setCompound(Compound mol)

Set the Compound

Specified by:

setCompound in interface Chain

Parameters:

mol - the Compound

See Also:

Chain.getCompound()

getCompound

public Compound getCompound()

Return the Compound for this chain.

Specified by:

getCompound in interface Chain

Returns:

the Compound object

See Also:

Chain.setCompound(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

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:

Chain.getAtomLength(), Chain.getAtomGroups(), Chain.getSeqResGroup(int)

getAtomGroups

public java.util.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:

Chain.setAtomGroups(List)

getAtomGroups

public java.util.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:

Chain.setAtomGroups(List), Chain.getAtomLength(), Chain.getSeqResGroups()

setAtomGroups

public void setAtomGroups(java.util.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:

Chain.getAtomGroups()

getGroupsByPDB

@Deprecated
public Group[] getGroupsByPDB(ResidueNumber start,
                                ResidueNumber end,
                                boolean ignoreMissing)
                       throws StructureException

Deprecated.

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(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

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

getSeqResLength

public int getSeqResLength()

Return 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:

Chain.getSeqResGroup(int), Chain.getSeqResGroups(), Chain.getAtomLength()

setChainID

public void setChainID(java.lang.String nam)

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:

Chain.getChainID()

getChainID

public java.lang.String getChainID()

Get 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:

Chain.setChainID(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.

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()

Return 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 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:

Chain.getSeqResLength(), Chain.getSeqResGroups(), Chain.getAtomGroup(int)

getSeqResGroups

public java.util.List<Group> getSeqResGroups(GroupType type)

Return 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:

Chain.setSeqResGroups(List)

getSeqResGroups

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

Return 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:

Chain.setSeqResGroups(List), Chain.getSeqResLength(), Chain.getAtomGroups()

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 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:

Chain.getAtomGroup(int), Chain.getAtomGroups(), #getSeqResLength())

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

Set the internal chain ID that is used in mmCif files

Specified by:

setInternalChainID in interface Chain

toPDB

public java.lang.String toPDB()

Description copied from interface: Chain

Convert this Chain to a String in PDB format

Specified by:

toPDB in interface Chain

Returns: