org.biojava.bio.structure

Interface Chain

All Known Implementing Classes:

ChainImpl

public interface Chain

Defines the interface for a Chain. A Chain corresponds to a Chain in a PDB file. A chain consists out of a list of Group objects. A Group can either be an AminoAcid, Hetatom or Nucleotide.

The BioJava API provides access to both the ATOM and SEQRES records in a PDB file. During parsing of a PDB file it aligns the ATOM and SEQRES groups and joins them. The SEQRES sequence can be accessed via getSeqResGroups() and the ATOM groups via getAtomGroups(). Groups that have been observed (i.e. they are in the ATOM records) can be detected by Group.has3D()

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

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.
Object	clone() returns an identical copy of this Chain.
Group	getAtomGroup(int position) return the Group at position X.
List<Group>	getAtomGroups() Return all groups that have been specified in the ATOM section of this chain .
List<Group>	getAtomGroups(String type) Return a List of all groups of a special type (e.g. amino, hetatm, nucleotide).
int	getAtomLength() Return the number of Groups in the ATOM records of the chain.
List<Group>	getAtomLigands() Get all groups that are not polymer groups and that are not solvent groups.
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.
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. if the PDB residue number is not know, throws a StructureException.
Group	getGroupByPDB(String pdbresnum) Deprecated. replaced by getGroupByPDB(ResidueNumber)
List<Group>	getGroups() Deprecated. use getAtomGroups or getSeqResGroups instead
List<Group>	getGroups(String type) Deprecated. use getAtomGroups or getSeqResGroups instead
Group[]	getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd) Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd, boolean ignoreMissing) Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd) Deprecated. replaced by getGroupsByPDB(ResidueNumber, ResidueNumber)
Group[]	getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing) Deprecated. replaced by #getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)
Compound	getHeader() Returns the Header ( a Compound object) for this chain.
Long	getId() Get the ID used by Hibernate.
int	getLength() Deprecated. please use getAtomLength or getLengthSeqRes instead
int	getLengthAminos() Deprecated. use getAtomGroups("amino").size() instead.
String	getName() Deprecated. replaced by getChainID()
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. amino, hetatm, nucleotide).
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 chain.
void	setAtomGroups(List<Group> groups) Set all groups that have been specified in the ATOM section of this chain .
void	setChainID(String name) get and set the name of this chain (Chain id in PDB file ).
void	setHeader(Compound molId) Set the Header from the PDB file.
void	setId(Long id) Set the ID used by Hibernate.
void	setName(String name) Deprecated. replaced by setChainID(String)
void	setParent(Structure parent) Set the back-reference to its parent Structure.
void	setSeqResGroups(List<Group> seqResGroups) Set the list of SeqResGroups for this chain.
void	setSwissprotId(String sp_id) Set the Swissprot id of this chain.
String	toString() string representation.

Method Detail

clone

Object clone()

returns an identical copy of this Chain.

Returns:

an identical copy of this Chain

addGroup

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.

Parameters:

group - a Group object

getId

Long getId()

Get the ID used by Hibernate.

Returns:

the ID used by Hibernate

See Also:

setId(Long)

setId

void setId(Long id)

Set the ID used by Hibernate.

Parameters:

id - assigned by Hibernate

See Also:

getId()

getGroup

Group getGroup(int position)

Deprecated. use getAtomGroup or getSeqResGroup instead

return the amino acid at position X.

Parameters:

position - an int

Returns:

a Group object

See Also:

getAtomGroup(int), getSeqResGroup(int)

getAtomGroup

Group getAtomGroup(int position)

return the Group at position X.

Parameters:

position - an int

Returns:

a Group object

getSeqResGroup

Group getSeqResGroup(int position)

return the Group at position X.

Parameters:

position - an int

Returns:

a Group object

getGroups

List<Group> getGroups(String type)

Deprecated. use getAtomGroups or getSeqResGroups instead

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

Parameters:

type - a String

Returns:

a List object

getGroups

List<Group> getGroups()

Deprecated. use getAtomGroups or getSeqResGroups instead

return all groups of this chain.

Returns:

a List of all Group objects of this chain

getAtomGroups

List<Group> getAtomGroups()

Return all groups that have been specified in the ATOM section of this chain .

Returns:

a List object representing the Groups of this Chain.

See Also:

setAtomGroups(List)

setAtomGroups

void setAtomGroups(List<Group> groups)

Set all groups that have been specified in the ATOM section of this chain .

Parameters:

groups - a List object representing the Groups of this Chain.

See Also:

getAtomGroups()

getAtomGroups

List<Group> getAtomGroups(String type)

Return a List of all groups of a special type (e.g. amino, hetatm, nucleotide).

Parameters:

type - a String

Returns:

a List object

See Also:

setAtomGroups(List)

getGroupByPDB

@Deprecated
Group getGroupByPDB(String pdbresnum)
                    throws StructureException

Deprecated. replaced by getGroupByPDB(ResidueNumber)

get a group by its PDB residue numbering. if the PDB residue number is not know, throws a StructureException.

Parameters:

pdbresnum - the PDB residue number of the group

Returns:

the matching group

Throws:

StructureException

getGroupByPDB

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.

Parameters:

resNum - the PDB residue number of the group

Returns:

the matching group

Throws:

StructureException

getGroupsByPDB

@Deprecated
Group[] getGroupsByPDB(String pdbresnumStart,
                                String pdbresnumEnd)
                       throws StructureException

Deprecated. replaced by getGroupsByPDB(ResidueNumber, ResidueNumber)

Get all groups that are located between two PDB residue numbers.

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

Group[] getGroupsByPDB(ResidueNumber pdbresnumStart,
                     ResidueNumber pdbresnumEnd)
                       throws StructureException

Get all groups that are located between two PDB residue numbers.

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

@Deprecated
Group[] getGroupsByPDB(String pdbresnumStart,
                                String pdbresnumEnd,
                                boolean ignoreMissing)
                       throws StructureException

Deprecated. replaced by #getGroupsByPDB(ResidueNumber, ResidueNumber, boolean)

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.

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

Group[] getGroupsByPDB(ResidueNumber pdbresnumStart,
                     ResidueNumber 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.

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

getLength

int getLength()

Deprecated. please use getAtomLength or getLengthSeqRes instead

get total length of chain, including HETATMs..

Returns:

an int representing the length of the whole chain including HETATMs

See Also:

getAtomLength(), getSeqResLength()

getAtomLength

int getAtomLength()

Return the number of Groups in the ATOM records of the chain.

Returns:

the length

getSeqResLength

int getSeqResLength()

Returns the number of groups in the SEQRES records of the chain.

Returns:

the length

getLengthAminos

int getLengthAminos()

Deprecated. use getAtomGroups("amino").size() instead.

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!

Returns:

an int representing the length of the AminoAcids in the ATOM records of the chain.

setHeader

void setHeader(Compound molId)

Set the Header from the PDB file.

Parameters:

molId - the Compound that contains the header information for this chain

See Also:

getHeader()

getHeader

Compound getHeader()

Returns the Header ( a Compound object) for this chain.

Returns:

the Compound object that contains the Header information

See Also:

setHeader(Compound)

setName

void setName(String name)

Deprecated. replaced by setChainID(String)

get and set the name of this chain (Chain id in PDB file ).

Parameters:

name - a String specifying the name value

See Also:

getName()

getName

String getName()

Deprecated. replaced by getChainID()

get and set the name of this chain (Chain id in PDB file ).

Returns:

a String representing the name value

See Also:

setName(java.lang.String)

setChainID

void setChainID(String name)

get and set the name of this chain (Chain id in PDB file ).

Parameters:

name - a String specifying the name value

See Also:

getChainID()

getChainID

String getChainID()

get and set the name of this chain (Chain id in PDB file ).

Returns:

a String representing the name value

See Also:

setChainID(String)

toString

String toString()

string representation.

Overrides:

toString in class Object

getBJSequence

Sequence<?> getBJSequence()

Convert the SEQRES groups of a Chain to a Biojava Sequence object.

Returns:

the SEQRES groups of the Chain as a Sequence object.

Throws:

IllegalSymbolException

getSequence

String getSequence()

Deprecated. use getAtomSequence instead

return the amino acid sequence of this chain ( all aminos even if they do not have 3D data ...).

Returns:

the sequence as a string

See Also:

getAtomSequence()

getAtomSequence

String getAtomSequence()

Return the sequence of amino acids as it has been provided in the ATOM records.

Returns:

amino acid sequence as string

See Also:

getSeqResSequence()

getSeqResSequence

String getSeqResSequence()

Get the sequence for all amino acids as it is specified in the SEQRES residues.

Returns:

the amino acid sequence of the SEQRES sequence as a string

See Also:

getAtomSequence()

setSwissprotId

void setSwissprotId(String sp_id)

Set the Swissprot id of this chain.

Parameters:

sp_id - a String specifying the swissprot id value

See Also:

getSwissprotId()

getSwissprotId

String getSwissprotId()

Get the Swissprot id of this chain.

Returns:

a String representing the swissprot id value

See Also:

setSwissprotId(String sp_id)

getSeqResGroups

List<Group> getSeqResGroups(String type)

Return a List of all groups of a special type (e.g. amino, hetatm, nucleotide).

Parameters:

type - a String

Returns:

an List object

See Also:

setSeqResGroups(List)

getSeqResGroups

List<Group> getSeqResGroups()

Return all groups of this chain.

Returns:

a List of all Group objects of this chain

See Also:

setSeqResGroups(List)

setSeqResGroups

void setSeqResGroups(List<Group> seqResGroups)

Set the list of SeqResGroups for this chain.

Parameters:

seqResGroups - a List of Group objects that from the SEQRES groups of this chain.

See Also:

getSeqResGroups()

setParent

void setParent(Structure parent)

Set the back-reference to its parent Structure.

Parameters:

parent - the parent Structure object for this Chain

See Also:

getParent()

getParent

Structure getParent()

Returns the parent Structure of this chain.

Returns:

the parent Structure object

See Also:

setParent(Structure)

getAtomLigands

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.

Returns:

list of Groups that are ligands