org.biojava.nbio.structure

Class ChainImpl

java.lang.Object

org.biojava.nbio.structure.ChainImpl

All Implemented Interfaces:

Serializable, Chain

public class ChainImpl
extends Object
implements Chain, 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 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

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)
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.
List<Group>	getAtomGroups() Return all Groups with observed density in the chain, i.e.
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() Returns the number of Groups with observed density in the chain, i.e.
List<Group>	getAtomLigands() Gets all groups that are not polymer groups and that are not solvent groups.
String	getAtomSequence() Returns the sequence of amino acids as it has been provided in the ATOM records.
Sequence<?>	getBJSequence() Converts the SEQRES groups of a Chain to a Biojava Sequence object.
String	getChainID() Gets the name of this chain (Chain id in PDB file ).
Compound	getCompound() Returns 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.
Long	getId() Get the ID used by Hibernate.
String	getInternalChainID() If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null
Structure	getParent() Deprecated. use getStructure instead.
List<SeqMisMatch>	getSeqMisMatches() Get annotated sequence mismatches for this chain.
Group	getSeqResGroup(int position) Return the Group at given position, from within groups in the SEQRES records of the chain, i.e.
List<Group>	getSeqResGroups() Returns a list of all groups in SEQRES records of the chain, i.e.
List<Group>	getSeqResGroups(GroupType type) Returns a List of all SEQRES groups of a special type, one of: GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE.
int	getSeqResLength() Returns the number of groups in the SEQRES records of the chain, i.e.
String	getSeqResSequence() Returns the PDB SEQRES sequence as a one-letter sequence string.
Structure	getStructure() Returns the parent Structure of this chain.
String	getSwissprotId() get the Swissprot id of this chains .
void	setAtomGroups(List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	setChainID(String nam) Sets the name of this chain (Chain id in PDB file ).
void	setCompound(Compound mol) Sets the Compound
void	setId(Long id) Set the ID used by Hibernate.
void	setInternalChainID(String internalChainID) Sets the internal chain ID that is used in mmCif files
void	setParent(Structure parent) Deprecated.
void	setSeqMisMatches(List<SeqMisMatch> seqMisMatches) Set annotated sequence mismatches for this chain.
void	setSeqResGroups(List<Group> groups) Sets the list of SeqResGroups for this chain.
void	setStructure(Structure parent) Sets the back-reference to its parent Structure.
void	setSwissprotId(String sp_id) set the Swissprot id of this chains .
String	toMMCIF() Convert this Chain to a String in mmCIF format
String	toPDB() Convert this Chain to a String in PDB format
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 used to be 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

@Deprecated
public void setParent(Structure parent)

Deprecated.

Sets 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.getStructure()

setStructure

public void setStructure(Structure parent)

Sets the back-reference to its parent Structure.

Specified by:

setStructure in interface Chain

getStructure

public Structure getStructure()

Returns the parent Structure of this chain.

Specified by:

getStructure in interface Chain

Returns:

the parent Structure object

See Also:

Chain.setStructure(Structure)

getParent

@Deprecated
public Structure getParent()

Deprecated. use getStructure instead.

Returns the parent Structure of this chain.

Specified by:

getParent in interface Chain

Returns:

the parent Structure object

See Also:

Chain.setStructure(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

setCompound

public void setCompound(Compound mol)

Sets the Compound

Specified by:

setCompound in interface Chain

Parameters:

mol - the Compound

See Also:

Chain.getCompound()

getCompound

public Compound getCompound()

Returns the Compound for this chain.

Specified by:

getCompound in interface Chain

Returns:

the Compound object

See Also:

Chain.setCompound(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

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 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 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(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()

Returns 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(String nam)

Sets 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 String getChainID()

Gets 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 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()

Converts 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 String getAtomSequence()

Returns the sequence of amino acids as it has been provided in the ATOM records. Non-standard residues will be present in the string only if the property has been set.

Specified by:

getAtomSequence in interface Chain

Returns:

amino acid sequence as string

See Also:

Chain.getSeqResSequence()

getSeqResSequence

public 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 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 List<Group> getSeqResGroups(GroupType type)

Returns 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 List<Group> getSeqResGroups()

Returns 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(List<Group> groups)

Sets 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()

Returns 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 List<Group> getAtomLigands()

Gets 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 FileParsingParameters#setLoadChemCompInfo(boolean) 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 String getInternalChainID()

Description copied from interface: Chain

If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null

Specified by:

getInternalChainID in interface Chain

Returns:

String or null

setInternalChainID

public void setInternalChainID(String internalChainID)

Description copied from interface: Chain

Sets the internal chain ID that is used in mmCif files

Specified by:

setInternalChainID in interface Chain

toPDB

public String toPDB()

Description copied from interface: Chain

Convert this Chain to a String in PDB format

Specified by:

toPDB in interface Chain

Returns:

toMMCIF

public String toMMCIF()

Description copied from interface: Chain

Convert this Chain to a String in mmCIF format

Specified by:

toMMCIF in interface Chain

Returns:

setSeqMisMatches

public void setSeqMisMatches(List<SeqMisMatch> seqMisMatches)

Description copied from interface: Chain

Set annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category

Specified by:

setSeqMisMatches in interface Chain

getSeqMisMatches

public List<SeqMisMatch> getSeqMisMatches()

Description copied from interface: Chain

Get annotated sequence mismatches for this chain. This is based on the STRUCT_REF_SEQ_DIF mmCif category

Specified by:

getSeqMisMatches in interface Chain