org.biojava.bio.structure
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 is an empty space.
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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.
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java.lang.Object |
clone()
Returns an identical copy of this Chain .
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Group |
getAtomGroup(int position)
return the group at position .
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java.util.List<Group> |
getAtomGroups()
Return all groups that have been specified in the ATOM section of this chain .
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java.util.List<Group> |
getAtomGroups(java.lang.String type)
Get the Groups of a certain type, that are listed int the ATOM records of the PDB file.
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int |
getAtomLength()
Return the number of Groups in the ATOM records of the chain.
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java.util.List<Group> |
getAtomLigands()
Get all groups that are not polymer groups and that are not solvent groups.
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java.lang.String |
getAtomSequence()
Return the sequence of amino acids as it has been provided in the ATOM records.
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Sequence<?> |
getBJSequence()
Convert the SEQRES groups of a Chain to a Biojava Sequence object.
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java.lang.String |
getChainID()
get and set the name of this chain (Chain id in PDB file ).
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Group |
getGroup(int position)
Deprecated.
use getAtomGroup or getSeqResGroup instead
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Group |
getGroupByPDB(ResidueNumber resNum)
Get a group by its PDB residue numbering.
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Group |
getGroupByPDB(java.lang.String pdbresnum)
get a group by its PDB residue numbering.
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java.util.List<Group> |
getGroups()
Deprecated.
use getAtomGroups instead
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java.util.List<Group> |
getGroups(java.lang.String type)
Deprecated.
use getAtomGroups instead
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Group[] |
getGroupsByPDB(ResidueNumber start,
ResidueNumber end)
Get all groups that are located between two PDB residue numbers.
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Group[] |
getGroupsByPDB(ResidueNumber start,
ResidueNumber end,
boolean ignoreMissing)
Get all groups that are located between two PDB residue numbers.
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Group[] |
getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd)
Get all groups that are located between two PDB residue numbers.
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Group[] |
getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd,
boolean ignoreMissing)
Get all groups that are located between two PDB residue numbers.
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Compound |
getHeader()
Returns the Header ( a Compound object) for this chain.
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java.lang.Long |
getId()
Get the ID used by Hibernate.
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int |
getLength()
Deprecated.
use getAtomLength instead
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int |
getLengthAminos()
returns the length of the AminoAcids in the ATOM records of this chain.
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java.lang.String |
getName()
get and set the name of this chain (Chain id in PDB file ).
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Structure |
getParent()
Returns the parent Structure of this chain.
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Group |
getSeqResGroup(int position)
return the Group at position X.
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java.util.List<Group> |
getSeqResGroups()
Return all groups of this chain.
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java.util.List<Group> |
getSeqResGroups(java.lang.String type)
Return a List of all groups of a special type (e.g.
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int |
getSeqResLength()
Returns the number of groups in the SEQRES records of the chain.
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java.lang.String |
getSeqResSequence()
Get the sequence for all amino acids as it is specified in the SEQRES residues.
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java.lang.String |
getSequence()
Deprecated.
use getAtomSequence instead
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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 that have been specified in the ATOM section of this chain .
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void |
setChainID(java.lang.String nam)
get and set the name of this chain (Chain id in PDB file ).
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void |
setHeader(Compound mol)
Set the Header from the PDB file.
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void |
setId(java.lang.Long id)
Set the ID used by Hibernate.
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void |
setName(java.lang.String nam)
get and set the name of this chain (Chain id in PDB file ).
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void |
setParent(Structure parent)
Set the back-reference to its parent Structure.
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void |
setSeqResGroups(java.util.List<Group> groups)
Set the list of SeqResGroups for this chain.
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void |
setSwissprotId(java.lang.String sp_id)
set the Swissprot id of this chains .
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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 setHeader(Compound mol)
setHeader
in interface Chain
mol
- the Compound that contains the header information for this chainChain.getHeader()
public Compound getHeader()
getHeader
in interface Chain
Chain.setHeader(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 getGroup(int position)
getGroup
in interface Chain
position
- an intChain.getAtomGroup(int)
,
Chain.getSeqResGroup(int)
public Group getAtomGroup(int position)
getAtomGroup
in interface Chain
position
- an intpublic java.util.List<Group> getGroups(java.lang.String type)
GroupType
constants.public java.util.List<Group> getAtomGroups(java.lang.String type)
getAtomGroups
in interface Chain
type
- the type of the groups to return. Can be one of the 3 types defined in the GroupType
constantsChain.setAtomGroups(List)
public java.util.List<Group> getGroups()
public java.util.List<Group> getAtomGroups()
getAtomGroups
in interface Chain
Chain.setAtomGroups(List)
public void setAtomGroups(java.util.List<Group> groups)
setAtomGroups
in interface Chain
groups
- a List object representing the Groups of this Chain.Chain.getAtomGroups()
public Group[] getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd, boolean ignoreMissing) throws StructureException
getGroupsByPDB
in interface Chain
pdbresnumStart
- PDB residue number of startpdbresnumEnd
- PDB residue number of endignoreMissing
- ignore missing groups in this range.StructureException
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(java.lang.String pdbresnum) throws StructureException
getGroupByPDB
in interface Chain
pdbresnum
- the PDB residue number of the groupStructureException
public Group getGroupByPDB(ResidueNumber resNum) throws StructureException
getGroupByPDB
in interface Chain
resNum
- the PDB residue number of the groupStructureException
public Group[] getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd) throws StructureException
getGroupsByPDB
in interface Chain
pdbresnumStart
- PDB residue number of startpdbresnumEnd
- PDB residue number of endStructureException
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 getLength()
Chain
getLength
in interface Chain
Chain.getAtomLength()
,
Chain.getSeqResLength()
public int getLengthAminos()
getLengthAminos
in interface Chain
public int getSeqResLength()
Chain
getSeqResLength
in interface Chain
public void setName(java.lang.String nam)
Chain
setName
in interface Chain
nam
- a String specifying the name valueChain.getName()
public java.lang.String getName()
Chain
getName
in interface Chain
Chain.setName(java.lang.String)
public void setChainID(java.lang.String nam)
setChainID
in interface Chain
nam
- a String specifying the name valuegetChainID()
public java.lang.String getChainID()
getChainID
in interface Chain
setName(java.lang.String)
public java.lang.String toString()
public Sequence<?> getBJSequence()
getBJSequence
in interface Chain
IllegalSymbolException
public java.lang.String getSequence()
getSequence
in interface Chain
getAtomSequence()
,
getSeqResSequence()
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 intpublic java.util.List<Group> getSeqResGroups(java.lang.String type)
getSeqResGroups
in interface Chain
type
- a StringChain.setSeqResGroups(List)
public java.util.List<Group> getSeqResGroups()
getSeqResGroups
in interface Chain
Chain.setSeqResGroups(List)
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()
public int getAtomLength()
getAtomLength
in interface Chain
public java.util.List<Group> getAtomLigands()
getAtomLigands
in interface Chain