Modifier and Type | Field and Description |
---|---|
static java.lang.String |
DEFAULT_CHAIN_ID
The default chain identifier is an empty space.
|
Constructor and Description |
---|
ChainImpl()
Constructs a ChainImpl object.
|
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.
|
java.lang.Object |
clone()
Returns an identical copy of this Chain .
|
Annotation |
getAnnotation()
get/set the Annotation of a Chain.
|
Group |
getAtomGroup(int position)
return the group at position .
|
java.util.List<Group> |
getAtomGroups()
Return all groups that have been specified in the ATOM section of this chain .
|
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.
|
int |
getAtomLength()
Return the number of Groups in the ATOM records of the chain.
|
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.
|
Group |
getGroup(int position)
Deprecated.
use getAtomGroup or getSeqResGroup instead
|
Group |
getGroupByPDB(java.lang.String pdbresnum)
get a group by its PDB residue numbering.
|
java.util.List<Group> |
getGroups()
Deprecated.
use getAtomGroups instead
|
java.util.List<Group> |
getGroups(java.lang.String type)
Deprecated.
use getAtomGroups instead
|
Group[] |
getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd)
Get all groups that are located between two PDB residue numbers.
|
Group[] |
getGroupsByPDB(java.lang.String pdbresnumStart,
java.lang.String pdbresnumEnd,
boolean ignoreMissing)
Get all groups that are located between two PDB residue numbers.
|
Compound |
getHeader()
Returns the Header ( a Compound object) for this chain.
|
java.lang.Long |
getId()
Get the ID used by Hibernate.
|
int |
getLength()
Deprecated.
use getAtomLength instead
|
int |
getLengthAminos()
returns the length of the AminoAcids in the ATOM records of this chain.
|
java.lang.String |
getName()
get and set the name of this chain (Chain id in PDB file ).
|
Structure |
getParent()
Returns the parent Structure of this chain.
|
Group |
getSeqResGroup(int position)
return the Group at position X.
|
java.util.List<Group> |
getSeqResGroups()
Return all groups of this chain.
|
java.util.List<Group> |
getSeqResGroups(java.lang.String type)
Return a List of all groups of a special type (e.g.
|
int |
getSeqResLength()
Returns the number of groups in the SEQRES records of the chain.
|
java.lang.String |
getSeqResSequence()
Get the sequence for all amino acids as it is specified in the SEQRES residues.
|
java.lang.String |
getSequence()
Deprecated.
use getAtomSequence instead
|
java.lang.String |
getSwissprotId()
get the Swissprot id of this chains .
|
void |
setAnnotation(Annotation anno)
get/set the Annotation of a Chain.
|
void |
setAtomGroups(java.util.List<Group> groups)
Set all groups that have been specified in the ATOM section of this chain .
|
void |
setHeader(Compound mol)
Set the Header from the PDB file.
|
void |
setId(java.lang.Long id)
Set the ID used by Hibernate.
|
void |
setName(java.lang.String nam)
get and set the name of this chain (Chain id in PDB file ).
|
void |
setParent(Structure parent)
Set the back-reference to its parent Structure.
|
void |
setSeqResGroups(java.util.List<Group> groups)
Set the list of SeqResGroups for this chain.
|
void |
setSwissprotId(java.lang.String sp_id)
set the Swissprot id of this chains .
|
java.lang.String |
toString()
String representation.
|
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 setAnnotation(Annotation anno)
setAnnotation
in interface Chain
anno
- the Annotation to be provided.Chain.getAnnotation()
public Annotation getAnnotation()
getAnnotation
in interface Chain
Chain.setAnnotation(Annotation)
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 getGroupByPDB(java.lang.String pdbresnum) throws StructureException
Chain
getGroupByPDB
in interface Chain
pdbresnum
- 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 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)
public java.lang.String getName()
getName
in interface Chain
setName(java.lang.String)
public java.lang.String toString()
public Sequence getBJSequence() throws IllegalSymbolException
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