org.biojava.nbio.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 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 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.
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(Structure) 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() Gets the Swissprot id of this chain.
void	setAtomGroups(List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	setChainID(String name) Sets the name of this chain (Chain id in PDB file ).
void	setCompound(Compound compound) 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. use setStructure instead
void	setSeqMisMatches(List<SeqMisMatch> seqMisMatches) Set annotated sequence mismatches for this chain.
void	setSeqResGroups(List<Group> seqResGroups) 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) Sets the Swissprot id of this chain.
String	toMMCIF() Convert this Chain to a String in mmCIF format
String	toPDB() Convert this Chain to a String in PDB format
String	toString()

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()

getAtomGroup

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.

Parameters:

position - an int

Returns:

a Group object

See Also:

getAtomLength(), getAtomGroups(), getSeqResGroup(int)

getSeqResGroup

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.

Parameters:

position - an int

Returns:

a Group object

See Also:

getSeqResLength(), getSeqResGroups(), getAtomGroup(int)

getAtomGroups

List<Group> getAtomGroups()

Return all Groups with observed density in the chain, i.e. those with coordinates in ATOM and HETATMS (including waters) records.

Returns:

a List object representing the Groups of this Chain.

See Also:

setAtomGroups(List), getAtomLength(), getSeqResGroups()

setAtomGroups

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.

Parameters:

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

See Also:

getAtomGroups()

getAtomGroups

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.

Parameters:

type - GroupType

Returns:

a List object

See Also:

setAtomGroups(List)

getGroupByPDB

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.

Parameters:

resNum - the PDB residue number of the group

Returns:

the matching group

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

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

getAtomLength

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

Returns:

the length

See Also:

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

getSeqResLength

int getSeqResLength()

Returns the number of groups in the SEQRES records of the chain, i.e. the number of aminoacids/nucleotides in the construct

Returns:

the length

See Also:

getSeqResGroup(int), getSeqResGroups(), getAtomLength()

setCompound

void setCompound(Compound compound)

Sets the Compound

Parameters:

compound - the Compound

See Also:

getCompound()

getCompound

Compound getCompound()

Returns the Compound for this chain.

Returns:

the Compound object

See Also:

setCompound(Compound)

setChainID

void setChainID(String name)

Sets the name of this chain (Chain id in PDB file ).

Parameters:

name - a String specifying the name value

See Also:

getChainID()

getChainID

String getChainID()

Gets the name of this chain (Chain id in PDB file ).

Returns:

a String representing the name value

See Also:

setChainID(String)

getInternalChainID

String getInternalChainID()

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

Returns:

String or null

Since:

3.0.5

setInternalChainID

void setInternalChainID(String internalChainID)

Sets the internal chain ID that is used in mmCif files

Parameters:

internalChainID -

Since:

3.0.5

toString

String toString()

Overrides:

toString in class Object

getBJSequence

Sequence<?> getBJSequence()

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

Returns:

the SEQRES groups of the Chain as a Sequence object.

getAtomSequence

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.

Returns:

amino acid sequence as string

See Also:

getSeqResSequence()

getSeqResSequence

String getSeqResSequence()

Returns the PDB SEQRES sequence as a one-letter sequence string. Non-standard residues are represented by an "X".

Returns:

one-letter PDB SEQRES sequence as string

See Also:

getAtomSequence()

setSwissprotId

void setSwissprotId(String sp_id)

Sets the Swissprot id of this chain.

Parameters:

sp_id - a String specifying the swissprot id value

See Also:

getSwissprotId()

getSwissprotId

String getSwissprotId()

Gets the Swissprot id of this chain.

Returns:

a String representing the swissprot id value

See Also:

setSwissprotId(String sp_id)

getSeqResGroups

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.

Parameters:

type - a GroupType

Returns:

an List object

See Also:

setSeqResGroups(List)

getSeqResGroups

List<Group> getSeqResGroups()

Returns a list of all groups in SEQRES records of the chain, i.e. the aminoacids/nucleotides in the construct.

Returns:

a List of all Group objects of this chain

See Also:

setSeqResGroups(List), getSeqResLength(), getAtomGroups()

setSeqResGroups

void setSeqResGroups(List<Group> seqResGroups)

Sets 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

@Deprecated
void setParent(Structure parent)

Deprecated. use setStructure instead

Sets the back-reference to its parent Structure.

Parameters:

parent - the parent Structure object for this Chain

See Also:

getStructure()

setStructure

void setStructure(Structure parent)

Sets the back-reference to its parent Structure.

Parameters:

parent -

getParent

@Deprecated
Structure getParent()

Deprecated. use getStructure(Structure) instead.

Returns the parent Structure of this chain.

Returns:

the parent Structure object

See Also:

setStructure(Structure)

getStructure

Structure getStructure()

Returns the parent Structure of this chain.

Returns:

the parent Structure object

See Also:

setStructure(Structure)

getAtomLigands

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.

Returns:

list of Groups that are ligands

toPDB

String toPDB()

Convert this Chain to a String in PDB format

Returns:

toMMCIF

String toMMCIF()

Convert this Chain to a String in mmCIF format

Returns:

setSeqMisMatches

void setSeqMisMatches(List<SeqMisMatch> seqMisMatches)

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

Parameters:

seqMisMatches -

getSeqMisMatches

List<SeqMisMatch> getSeqMisMatches()

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