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java.lang.Objectorg.biojava.bio.structure.ChainImpl
public class ChainImpl
A Chain in a PDB file. It contains several groups which can be of
one of the types defined in the GroupType
constants.
Field Summary | |
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static String |
DEFAULT_CHAIN_ID
The default chain identifier is an empty space. |
Constructor Summary | |
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ChainImpl()
Constructs a ChainImpl object. |
Method Summary | |
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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 position . |
List<Group> |
getAtomGroups()
Return all groups that have been specified in the ATOM section of this chain . |
List<Group> |
getAtomGroups(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. |
List<Group> |
getAtomLigands()
Get all groups that are not polymer groups and that are not solvent groups. |
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. |
String |
getChainID()
get and set the name of this chain (Chain id in PDB file ). |
Group |
getGroup(int position)
Deprecated. use getAtomGroup or getSeqResGroup instead |
Group |
getGroupByPDB(ResidueNumber resNum)
Get a group by its PDB residue numbering. |
Group |
getGroupByPDB(String pdbresnum)
get a group by its PDB residue numbering. |
List<Group> |
getGroups()
Deprecated. use getAtomGroups instead |
List<Group> |
getGroups(String type)
Deprecated. use getAtomGroups instead |
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. |
Group[] |
getGroupsByPDB(String pdbresnumStart,
String pdbresnumEnd)
Get all groups that are located between two PDB residue numbers. |
Group[] |
getGroupsByPDB(String pdbresnumStart,
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. |
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. |
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. |
List<Group> |
getSeqResGroups()
Return all groups of this chain. |
List<Group> |
getSeqResGroups(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. |
String |
getSeqResSequence()
Get the sequence for all amino acids as it is specified in the SEQRES residues. |
String |
getSequence()
Deprecated. use getAtomSequence instead |
String |
getSwissprotId()
get the Swissprot id of this chains . |
void |
setAtomGroups(List<Group> groups)
Set all groups that have been specified in the ATOM section of this chain . |
void |
setChainID(String nam)
get and set the name of this chain (Chain id in PDB file ). |
void |
setHeader(Compound mol)
Set the Header from the PDB file. |
void |
setId(Long id)
Set the ID used by Hibernate. |
void |
setName(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(List<Group> groups)
Set the list of SeqResGroups for this chain. |
void |
setSwissprotId(String sp_id)
set the Swissprot id of this chains . |
String |
toString()
String representation. |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static String DEFAULT_CHAIN_ID
Constructor Detail |
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public ChainImpl()
Method Detail |
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public Long getId()
getId
in interface Chain
Chain.setId(Long)
public void setId(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 Object clone()
clone
in interface Chain
clone
in class Object
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(String sp_id)
setSwissprotId
in interface Chain
sp_id
- a String specifying the swissprot id valuegetSwissprotId()
public String getSwissprotId()
getSwissprotId
in interface Chain
setSwissprotId(java.lang.String)
public void addGroup(Group group)
addGroup
in interface Chain
group
- a Group objectpublic Group getGroup(int position)
getGroup
in interface Chain
position
- an int
Chain.getAtomGroup(int)
,
Chain.getSeqResGroup(int)
public Group getAtomGroup(int position)
getAtomGroup
in interface Chain
position
- an int
public List<Group> getGroups(String type)
GroupType
constants.
getGroups
in interface Chain
type
- a String
public List<Group> getAtomGroups(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
constants
Chain.setAtomGroups(List)
public List<Group> getGroups()
getGroups
in interface Chain
public List<Group> getAtomGroups()
getAtomGroups
in interface Chain
Chain.setAtomGroups(List)
public void setAtomGroups(List<Group> groups)
setAtomGroups
in interface Chain
groups
- a List object representing the Groups of this Chain.Chain.getAtomGroups()
public Group[] getGroupsByPDB(String pdbresnumStart, 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(String pdbresnum) throws StructureException
getGroupByPDB
in interface Chain
pdbresnum
- the PDB residue number of the group
StructureException
public Group getGroupByPDB(ResidueNumber resNum) throws StructureException
getGroupByPDB
in interface Chain
resNum
- the PDB residue number of the group
StructureException
public Group[] getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd) throws StructureException
getGroupsByPDB
in interface Chain
pdbresnumStart
- PDB residue number of startpdbresnumEnd
- PDB residue number of end
StructureException
public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end) throws StructureException
getGroupsByPDB
in interface Chain
start
- PDB residue number of startend
- PDB residue number of end
StructureException
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(String nam)
Chain
setName
in interface Chain
nam
- a String specifying the name valueChain.getName()
public String getName()
Chain
getName
in interface Chain
Chain.setName(java.lang.String)
public void setChainID(String nam)
setChainID
in interface Chain
nam
- a String specifying the name valuegetChainID()
public String getChainID()
getChainID
in interface Chain
setName(java.lang.String)
public String toString()
toString
in interface Chain
toString
in class Object
public Sequence<?> getBJSequence()
getBJSequence
in interface Chain
IllegalSymbolException
public String getSequence()
getSequence
in interface Chain
getAtomSequence()
,
getSeqResSequence()
public String getAtomSequence()
getAtomSequence
in interface Chain
Chain.getSeqResSequence()
public String getSeqResSequence()
getSeqResSequence
in interface Chain
Chain.getAtomSequence()
public Group getSeqResGroup(int position)
getSeqResGroup
in interface Chain
position
- an int
public List<Group> getSeqResGroups(String type)
getSeqResGroups
in interface Chain
type
- a String
Chain.setSeqResGroups(List)
public List<Group> getSeqResGroups()
getSeqResGroups
in interface Chain
Chain.setSeqResGroups(List)
public void setSeqResGroups(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 List<Group> getAtomLigands()
getAtomLigands
in interface Chain
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