org.biojava.nbio.structure

Interface Chain

All Superinterfaces:

Serializable

All Known Implementing Classes:

ChainImpl

public interface Chain
extends Serializable

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

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() Deprecated. since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric 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() Deprecated. use getId() instead
EntityInfo	getEntityInfo() Returns the EntityInfo for this chain.
EntityType	getEntityType() Returns the EntityType of 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.
String	getId() Get the 'private' asymId (internal chain IDs in mmCif) for this chain.
String	getInternalChainID() Deprecated. use getId() instead
String	getName() Get the 'public' authId (chain ID in PDB file)
Structure	getParent() Deprecated. use getStructure(Structure) instead.
GroupType	getPredominantGroupType() Get the predominant GroupType for a given Chain, following these rules: if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold , then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it
List<SeqMisMatch>	getSeqMisMatches() Gets 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.
boolean	isNucleicAcid() Tell whether given chain is DNA or RNA
boolean	isProtein() Tell whether given chain is a protein chain
boolean	isPureNonPolymer() Returns true if the given chain is composed of non-polymeric (including water) groups only.
boolean	isWaterOnly() Tests if a chain is consisting of water molecules only
void	setAtomGroups(List<Group> groups) Set all Groups with observed density in the chain, i.e.
void	setChainID(String asymId) Deprecated. use setId(String asymId) instead
void	setEntityInfo(EntityInfo entityInfo) Sets the Entity information
void	setId(String asymId) Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
void	setInternalChainID(String internalChainID) Deprecated. use #setId() instead
void	setName(String authId) Set the 'public' authId (chain ID in PDB file)
void	setParent(Structure parent) Deprecated. use setStructure instead
void	setSeqMisMatches(List<SeqMisMatch> seqMisMatches) Sets 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

String getId()

Get the 'private' asymId (internal chain IDs in mmCif) for this chain.

Returns:

the asymId

See Also:

setId(String), getName()

setId

void setId(String asymId)

Set the 'private' asymId (internal chain IDs in mmCif) for this chain.

Parameters:

asymId - the internal chain Id

setName

void setName(String authId)

Set the 'public' authId (chain ID in PDB file)

Parameters:

authId - the 'public' authId (chain ID in PDB file)

See Also:

getId()

getName

String getName()

Get the 'public' authId (chain ID in PDB file)

Returns:

the authId for this chain.

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. If null, defaults to the chain start.

pdbresnumEnd - PDB residue number of end. If null, defaults to the chain 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. If null, defaults to the chain start.

pdbresnumEnd - PDB residue number of end. If null, defaults to the chain 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()

setEntityInfo

void setEntityInfo(EntityInfo entityInfo)

Sets the Entity information

Parameters:

entityInfo - the EntityInfo

See Also:

getEntityInfo()

getEntityInfo

EntityInfo getEntityInfo()

Returns the EntityInfo for this chain.

Returns:

the EntityInfo object

See Also:

setEntityInfo(EntityInfo)

setChainID

@Deprecated
void setChainID(String asymId)

Deprecated. use setId(String asymId) instead

Sets the 'private' asymId of this chain (Chain id in PDB file ).

Parameters:

asymId - a String specifying the name value

See Also:

getChainID()

getChainID

@Deprecated
String getChainID()

Deprecated. use getId() instead

Gets the 'private' asymId of this chain.

Returns:

a String representing the name value

See Also:

setChainID(String)

getInternalChainID

String getInternalChainID()

Deprecated. use getId() instead

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)

Deprecated. use #setId() instead

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

@Deprecated
List<Group> getAtomLigands()

Deprecated. since biojava 5.0 this does not apply anymore. Chains contain either polymeric groups or non-polymeric groups

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)

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

Parameters:

seqMisMatches -

getSeqMisMatches

List<SeqMisMatch> getSeqMisMatches()

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

getEntityType

EntityType getEntityType()

Returns the EntityType of this chain. Equivalent to getEntityInfo().getType()

Returns:

See Also:

EntityType

isWaterOnly

boolean isWaterOnly()

Tests if a chain is consisting of water molecules only

Returns:

true if there are only solvent molecules in this chain.

isPureNonPolymer

boolean isPureNonPolymer()

Returns true if the given chain is composed of non-polymeric (including water) groups only.

Returns:

true if only non-polymeric groups in this chain.

getPredominantGroupType

GroupType getPredominantGroupType()

Get the predominant GroupType for a given Chain, following these rules:

if the ratio of number of residues of a certain GroupType to total non-water residues is above the threshold , then that GroupType is returned if there is no GroupType that is above the threshold then the GroupType with most members is chosen, logging it

See also ChemComp.getPolymerType() and ChemComp.getResidueType() which follow the PDB chemical component dictionary and provide a much more accurate description of groups and their linking.

Returns:

isProtein

boolean isProtein()

Tell whether given chain is a protein chain

Returns:

true if protein, false if nucleotide or ligand

See Also:

getPredominantGroupType()

isNucleicAcid

boolean isNucleicAcid()

Tell whether given chain is DNA or RNA

Returns:

true if nucleic acid, false if protein or ligand

See Also:

getPredominantGroupType()