public class ChainImpl extends java.lang.Object implements Chain, java.io.Serializable
GroupType
constants.Modifier and Type | Field and Description |
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static java.lang.String |
DEFAULT_CHAIN_ID
The default chain identifier used to be an empty space
|
Constructor and Description |
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ChainImpl()
Constructs a ChainImpl object.
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Modifier and Type | Method and Description |
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void |
addGroup(Group group)
add a group to the list of ATOM record group of this chain.
|
protected void |
addSeqResGroup(Group g) |
java.lang.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.
|
java.util.List<Group> |
getAtomGroups()
Return all Groups with observed density in the chain, i.e.
|
java.util.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()
Return the number of Groups with observed density in the chain, i.e.
|
java.util.List<Group> |
getAtomLigands()
Gets all groups that are not polymer groups and that are not solvent groups.
|
java.lang.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.
|
java.lang.String |
getChainID()
Gets the name of this chain (Chain id in PDB file ).
|
Compound |
getCompound()
Return the Compound for 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)
Deprecated.
|
java.lang.Long |
getId()
Get the ID used by Hibernate.
|
java.lang.String |
getInternalChainID()
If available, returns the internal chain ID that is used in mmCIF files (asym_id), otherwise null
|
Structure |
getParent()
Returns the parent Structure of this chain.
|
Group |
getSeqResGroup(int position)
Return the Group at given position,
from within groups in the SEQRES records of the chain, i.e.
|
java.util.List<Group> |
getSeqResGroups()
Returns a list of all groups in SEQRES records of the chain, i.e.
|
java.util.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()
Return the number of groups in the SEQRES records of the chain, i.e.
|
java.lang.String |
getSeqResSequence()
Returns the PDB SEQRES sequence as a one-letter sequence string.
|
java.lang.String |
getSwissprotId()
get the Swissprot id of this chains .
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void |
setAtomGroups(java.util.List<Group> groups)
Set all Groups with observed density in the chain, i.e.
|
void |
setChainID(java.lang.String nam)
Sets the name of this chain (Chain id in PDB file ).
|
void |
setCompound(Compound mol)
Set the Compound
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void |
setId(java.lang.Long id)
Set the ID used by Hibernate.
|
void |
setInternalChainID(java.lang.String internalChainID)
Sets the internal chain ID that is used in mmCif files
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void |
setParent(Structure parent)
Sets the back-reference to its parent Structure.
|
void |
setSeqResGroups(java.util.List<Group> groups)
Sets the list of SeqResGroups for this chain.
|
void |
setSwissprotId(java.lang.String sp_id)
set the Swissprot id of this chains .
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java.lang.String |
toMMCIF()
Convert this Chain to a String in mmCIF format
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java.lang.String |
toPDB()
Convert this Chain to a String in PDB format
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java.lang.String |
toString()
String representation.
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public static java.lang.String DEFAULT_CHAIN_ID
public java.lang.Long getId()
getId
in interface Chain
Chain.setId(Long)
public void setId(java.lang.Long id)
setId
in interface Chain
id
- assigned by HibernateChain.getId()
public void setParent(Structure parent)
setParent
in interface Chain
parent
- the parent Structure object for this ChainChain.getParent()
public Structure getParent()
getParent
in interface Chain
Chain.setParent(Structure)
public java.lang.Object clone()
public void setCompound(Compound mol)
setCompound
in interface Chain
mol
- the CompoundChain.getCompound()
public Compound getCompound()
getCompound
in interface Chain
Chain.setCompound(Compound)
public void setSwissprotId(java.lang.String sp_id)
setSwissprotId
in interface Chain
sp_id
- a String specifying the swissprot id valuegetSwissprotId()
public java.lang.String getSwissprotId()
getSwissprotId
in interface Chain
setSwissprotId(java.lang.String)
public void addGroup(Group group)
public Group getAtomGroup(int position)
getAtomGroup
in interface Chain
position
- an intChain.getAtomLength()
,
Chain.getAtomGroups()
,
Chain.getSeqResGroup(int)
public java.util.List<Group> getAtomGroups(GroupType type)
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
.getAtomGroups
in interface Chain
type
- GroupTypeChain.setAtomGroups(List)
public java.util.List<Group> getAtomGroups()
getAtomGroups
in interface Chain
Chain.setAtomGroups(List)
,
Chain.getAtomLength()
,
Chain.getSeqResGroups()
public void setAtomGroups(java.util.List<Group> groups)
setAtomGroups
in interface Chain
groups
- a List object representing the Groups of this Chain.Chain.getAtomGroups()
@Deprecated public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing) throws StructureException
Chain
getGroupsByPDB
in interface Chain
start
- PDB residue number of startend
- PDB residue number of endignoreMissing
- ignore missing groups in this range.StructureException
public Group getGroupByPDB(ResidueNumber resNum) throws StructureException
getGroupByPDB
in interface Chain
resNum
- the PDB residue number of the groupStructureException
public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end) throws StructureException
getGroupsByPDB
in interface Chain
start
- PDB residue number of startend
- PDB residue number of endStructureException
public int getSeqResLength()
getSeqResLength
in interface Chain
Chain.getSeqResGroup(int)
,
Chain.getSeqResGroups()
,
Chain.getAtomLength()
public void setChainID(java.lang.String nam)
setChainID
in interface Chain
nam
- a String specifying the name valueChain.getChainID()
public java.lang.String getChainID()
getChainID
in interface Chain
Chain.setChainID(String)
public java.lang.String toString()
public Sequence<?> getBJSequence()
getBJSequence
in interface Chain
public java.lang.String getAtomSequence()
getAtomSequence
in interface Chain
Chain.getSeqResSequence()
public java.lang.String getSeqResSequence()
getSeqResSequence
in interface Chain
Chain.getAtomSequence()
public Group getSeqResGroup(int position)
getSeqResGroup
in interface Chain
position
- an intChain.getSeqResLength()
,
Chain.getSeqResGroups()
,
Chain.getAtomGroup(int)
public java.util.List<Group> getSeqResGroups(GroupType type)
GroupType.AMINOACID
,
GroupType.HETATM
or GroupType.NUCLEOTIDE
.getSeqResGroups
in interface Chain
type
- a GroupTypeChain.setSeqResGroups(List)
public java.util.List<Group> getSeqResGroups()
getSeqResGroups
in interface Chain
Chain.setSeqResGroups(List)
,
Chain.getSeqResLength()
,
Chain.getAtomGroups()
public void setSeqResGroups(java.util.List<Group> groups)
setSeqResGroups
in interface Chain
groups
- a List of Group objects that from the SEQRES groups of this chain.Chain.getSeqResGroups()
protected void addSeqResGroup(Group g)
public int getAtomLength()
getAtomLength
in interface Chain
Chain.getAtomGroup(int)
,
Chain.getAtomGroups()
,
#getSeqResLength())
public java.util.List<Group> getAtomLigands()
FileParsingParameters.setLoadChemCompInfo(boolean)
has not been set to true.
Otherwise the Ligands could not correctly be identified.getAtomLigands
in interface Chain
public java.lang.String getInternalChainID()
Chain
getInternalChainID
in interface Chain
public void setInternalChainID(java.lang.String internalChainID)
Chain
setInternalChainID
in interface Chain
public java.lang.String toPDB()
Chain