Package 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

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

Constructor Summary

Constructors

Constructor	Description
ChainImpl()	Constructs a ChainImpl object.

Method Summary

Modifier and Type	Method	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.
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.
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 start, ResidueNumber end)	Get all groups that are located between two PDB residue numbers.
Group[]	getGroupsByPDB(ResidueNumber start, ResidueNumber end, 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	getName()	Get the 'public' authId (chain ID in PDB file)
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 0.95, 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	getSeqResOneLetterSeq()	Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups.
String	getSeqResSequence()	Returns the PDB SEQRES sequence as a one-letter sequence string.
Structure	getStructure()	Returns the parent Structure 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	setEntityInfo(EntityInfo mol)	Sets the Entity information
void	setId(String asymId)	Set the 'private' asymId (internal chain IDs in mmCif) for this chain.
void	setName(String authId)	Set the 'public' authId (chain ID in PDB file)
void	setSeqMisMatches(List<SeqMisMatch> seqMisMatches)	Sets 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.
String	toMMCIF()	Convert this Chain to a String in mmCIF format
String	toPDB()	Convert this Chain to a String in PDB format
String	toString()

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

ChainImpl

public ChainImpl()

Constructs a ChainImpl object.

Method Details

getId

public String getId()

Description copied from interface: Chain

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

Specified by:

getId in interface Chain

Returns:

the asymId

See Also:

• Chain.setId(String)
• Chain.getName()

setId

public void setId(String asymId)

Description copied from interface: Chain

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

Specified by:

setId in interface Chain

Parameters:

asymId - the internal chain Id

getName

public String getName()

Description copied from interface: Chain

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

Specified by:

getName in interface Chain

Returns:

the authId for this chain.

See Also:

• Chain.getId()

setName

public void setName(String authId)

Description copied from interface: Chain

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

Specified by:

setName in interface Chain

Parameters:

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

See Also:

• Chain.getId()

setStructure

public void setStructure(Structure parent)

Description copied from interface: Chain

Sets the back-reference to its parent Structure.

Specified by:

setStructure in interface Chain

Parameters:

parent -

getStructure

public Structure getStructure()

Description copied from interface: Chain

Returns the parent Structure of this chain.

Specified by:

getStructure in interface Chain

Returns:

the parent Structure object

See Also:

• Chain.setStructure(Structure)

clone

public Object clone()

Description copied from interface: Chain

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

setEntityInfo

public void setEntityInfo(EntityInfo mol)

Description copied from interface: Chain

Sets the Entity information

Specified by:

setEntityInfo in interface Chain

Parameters:

mol - the EntityInfo

See Also:

• Chain.getEntityInfo()

getEntityInfo

public EntityInfo getEntityInfo()

Description copied from interface: Chain

Returns the EntityInfo for this chain.

Specified by:

getEntityInfo in interface Chain

Returns:

the EntityInfo object

See Also:

• Chain.setEntityInfo(EntityInfo)

addGroup

public void addGroup(Group group)

Description copied from interface: Chain

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)

Description copied from interface: Chain

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)

Description copied from interface: Chain

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()

Description copied from interface: Chain

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)

Description copied from interface: Chain

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

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

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. If null, defaults to the chain start.

end - 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

getGroupByPDB

public Group getGroupByPDB(ResidueNumber resNum)
                    throws StructureException

Description copied from interface: Chain

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

Description copied from interface: Chain

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

Specified by:

getGroupsByPDB in interface Chain

Parameters:

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

end - 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

getSeqResLength

public int getSeqResLength()

Description copied from interface: Chain

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()

toString

public String toString()

Specified by:

toString in interface Chain

Overrides:

toString in class Object

getBJSequence

public Sequence<?> getBJSequence()

Description copied from interface: Chain

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()

Description copied from interface: Chain

Returns 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 String getSeqResSequence()

Description copied from interface: Chain

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()

getSeqResOneLetterSeq

public String getSeqResOneLetterSeq()

Get the one letter sequence so that Sequence is guaranteed to be the same length as seqResGroups. Method related to https://github.com/biojava/biojava/issues/457

Returns:

a string of the sequence guaranteed to be the same length as seqResGroups.

getSeqResGroup

public Group getSeqResGroup(int position)

Description copied from interface: Chain

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)

Description copied from interface: Chain

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()

Description copied from interface: Chain

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)

Description copied from interface: Chain

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()

getAtomLength

public int getAtomLength()

Description copied from interface: Chain

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()
• Chain.getSeqResLength()

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

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

Specified by:

setSeqMisMatches in interface Chain

Parameters:

seqMisMatches -

getSeqMisMatches

public List<SeqMisMatch> getSeqMisMatches()

Description copied from interface: Chain

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

Specified by:

getSeqMisMatches in interface Chain

Returns:

a list of sequence mismatches (or null if none found)

getEntityType

public EntityType getEntityType()

Description copied from interface: Chain

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

Specified by:

getEntityType in interface Chain

Returns:

See Also:

• EntityType

isWaterOnly

public boolean isWaterOnly()

Description copied from interface: Chain

Tests if a chain is consisting of water molecules only

Specified by:

isWaterOnly in interface Chain

Returns:

true if there are only solvent molecules in this chain.

isPureNonPolymer

public boolean isPureNonPolymer()

Description copied from interface: Chain

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

Specified by:

isPureNonPolymer in interface Chain

Returns:

true if only non-polymeric groups in this chain.

getPredominantGroupType

public GroupType getPredominantGroupType()

Description copied from interface: Chain

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 0.95, 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.

Specified by:

getPredominantGroupType in interface Chain

Returns:

the predominant group type

isProtein

public boolean isProtein()

Description copied from interface: Chain

Tell whether given chain is a protein chain

Specified by:

isProtein in interface Chain

Returns:

true if protein, false if nucleotide or ligand

See Also:

• Chain.getPredominantGroupType()

isNucleicAcid

public boolean isNucleicAcid()

Description copied from interface: Chain

Tell whether given chain is DNA or RNA

Specified by:

isNucleicAcid in interface Chain

Returns:

true if nucleic acid, false if protein or ligand

See Also:

• Chain.getPredominantGroupType()