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java.lang.Objectorg.biojava.bio.structure.StructureImpl
public class StructureImpl
Implementation of a PDB Structure. This class provides the data contained in a PDB file. to get structure objects from different sources see io package.
Constructor Summary | |
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StructureImpl()
Constructs a StructureImpl object. |
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StructureImpl(Chain c)
construct a Structure object that contains a particular chain |
|
StructureImpl(Group g)
construct a Structure object that only contains a single group |
Method Summary | |
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void |
addChain(Chain chain)
add a new chain. |
void |
addChain(Chain chain,
int modelnr)
add a new chain, if several models are available. |
void |
addModel(List model)
add a new model. |
Object |
clone()
returns an identical copy of this structure . |
Chain |
findChain(String chainId)
request a particular chain from a structure. |
Chain |
findChain(String chainId,
int modelnr)
request a particular chain from a particular model |
Group |
findGroup(String chainName,
String pdbResnum)
request a particular group from a structure. |
Group |
findGroup(String chainId,
String pdbResnum,
int modelnr)
request a particular group from a structure. |
Chain |
getChain(int number)
retrieve a chain by it's position within the Structure. |
Chain |
getChain(int modelnr,
int number)
retrieve a chain by it's position within the Structure and model number. |
Chain |
getChainByPDB(String chainId)
request a chain by it's PDB code by default takes only the first model |
Chain |
getChainByPDB(String chainId,
int modelnr)
request a chain by it's PDB code by default takes only the first model |
List |
getChains(int modelnr)
retrieve all chains of a model. |
List |
getConnections()
Returns the connections value. |
Map |
getHeader()
get Header data. |
List |
getModel(int modelnr)
retrieve all Chains belonging to a model . |
String |
getName()
get biological name of Structure. |
String |
getPDBCode()
get PDB code of structure . |
boolean |
hasChain(String chainId)
check if a chain with the id chainId is contained in this structure. |
boolean |
isNmr()
is this structure an nmr structure ? |
int |
nrModels()
return number of models. |
void |
setConnections(List conns)
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file: |
void |
setHeader(Map h)
set the Header data. |
void |
setName(String nam)
set biological name of Structure. |
void |
setNmr(boolean nmr)
set NMR flag. |
void |
setPDBCode(String pdb_id_)
set PDB code of structure . |
int |
size()
return number of chains , if NMR return number of chains of first model . |
int |
size(int modelnr)
return number of chains of model. |
String |
toPDB()
create a String that contains the contents of a PDB file. |
String |
toString()
string representation. |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public StructureImpl()
public StructureImpl(Group g)
g
- public StructureImpl(Chain c)
c
- Method Detail |
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public Object clone()
clone
in interface Structure
clone
in class Object
public Group findGroup(String chainId, String pdbResnum, int modelnr) throws StructureException
Structure
findGroup
in interface Structure
chainId
- the ID of the chain to usepdbResnum
- the PDB residue number of the requested groupmodelnr
- the number of the model to use
StructureException
public Group findGroup(String chainName, String pdbResnum) throws StructureException
Structure
findGroup
in interface Structure
chainName
- the ID of the chain to usepdbResnum
- the PDB residue number of the requested group
StructureException
public Chain findChain(String chainId, int modelnr) throws StructureException
Structure
findChain
in interface Structure
chainId
- the ID of a chain that should be returnedmodelnr
- the number of the model to use
StructureException
public Chain findChain(String chainId) throws StructureException
Structure
findChain
in interface Structure
chainId
- the ID of a chain that should be returned
StructureException
public void setPDBCode(String pdb_id_)
setPDBCode
in interface Structure
pdb_id_
- a String specifying the PDBCodegetPDBCode()
public String getPDBCode()
getPDBCode
in interface Structure
setPDBCode(java.lang.String)
public void setName(String nam)
setName
in interface Structure
nam
- a String specifying the biological name of the StructuregetName()
public String getName()
getName
in interface Structure
setName(java.lang.String)
public void setHeader(Map h)
setHeader
in interface Structure
h
- a Map object specifying the headergetHeader()
public Map getHeader()
getHeader
in interface Structure
setHeader(java.util.Map)
public void setConnections(List conns)
Structure
COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "CONECT" 7 - 11 Integer serial Atom serial number 12 - 16 Integer serial Serial number of bonded atom 17 - 21 Integer serial Serial number of bonded atom 22 - 26 Integer serial Serial number of bonded atom 27 - 31 Integer serial Serial number of bonded atom 32 - 36 Integer serial Serial number of hydrogen bonded atom 37 - 41 Integer serial Serial number of hydrogen bonded atom 42 - 46 Integer serial Serial number of salt bridged atom 47 - 51 Integer serial Serial number of hydrogen bonded atom 52 - 56 Integer serial Serial number of hydrogen bonded atom 57 - 61 Integer serial Serial number of salt bridged atomthe HashMap for a single CONECT line contains the following fields:
setConnections
in interface Structure
conns
- a List object specifying the connectionsinterface.
public List getConnections()
getConnections
in interface Structure
interface
,
setConnections(java.util.List)
public void addChain(Chain chain)
addChain
in interface Structure
chain
- a Chain objectpublic void addChain(Chain chain, int modelnr)
addChain
in interface Structure
chain
- a Chain objectmodelnr
- an int specifying to which model the Chain should be addedpublic Chain getChain(int number)
getChain
in interface Structure
number
- an int
public Chain getChain(int modelnr, int number)
getChain
in interface Structure
modelnr
- an intnumber
- an int
public void addModel(List model)
addModel
in interface Structure
model
- a List object containing the Chains of the new Modelpublic String toString()
toString
in interface Structure
toString
in class Object
public int size()
size
in interface Structure
public int size(int modelnr)
size
in interface Structure
modelnr
- an int specifying the number of the Model that should be used
public int nrModels()
nrModels
in interface Structure
public boolean isNmr()
isNmr
in interface Structure
public void setNmr(boolean nmr)
Structure
setNmr
in interface Structure
nmr
- true to declare that this Structure has been solved by NMR.public List getChains(int modelnr)
getChains
in interface Structure
modelnr
- an int
Structure.getModel(int)
public List getModel(int modelnr)
getModel
in interface Structure
modelnr
- an int
Structure.getChains(int)
public Chain getChainByPDB(String chainId, int modelnr) throws StructureException
Structure
getChainByPDB
in interface Structure
chainId
- the chain identifiermodelnr
- request a particular model;
StructureException
public Chain getChainByPDB(String chainId) throws StructureException
Structure
getChainByPDB
in interface Structure
chainId
- the chain identifier
StructureException
public String toPDB()
toPDB
in interface Structure
public boolean hasChain(String chainId)
Structure
hasChain
in interface Structure
chainId
- the name of the chain
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