Chain (biojava 4.2.1 API)

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

All Methods Instance Methods Abstract Methods Deprecated 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

Interface Chain

Method Summary

Method Detail

clone

addGroup

getId

setId

getAtomGroup

getSeqResGroup

getAtomGroups

setAtomGroups

getAtomGroups

getGroupByPDB

getGroupsByPDB

getGroupsByPDB

getAtomLength

getSeqResLength

setCompound

getCompound

setChainID

getChainID

getInternalChainID

setInternalChainID

toString

getBJSequence

getAtomSequence

getSeqResSequence

setSwissprotId

getSwissprotId

getSeqResGroups

getSeqResGroups

setSeqResGroups

setParent

setStructure

getParent

getStructure

getAtomLigands

toPDB

toMMCIF

setSeqMisMatches

getSeqMisMatches