public class StructureImpl extends java.lang.Object implements Structure
Constructor and Description |
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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
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StructureImpl(Group g)
construct a Structure object that only contains a single group
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Modifier and Type | Method and Description |
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void |
addChain(Chain chain)
add a new chain.
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void |
addChain(Chain chain,
int modelnr)
add a new chain, if several models are available.
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void |
addModel(java.util.List<Chain> model)
add a new model.
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void |
addSSBond(SSBond ssbond)
add a single SSBond to this structure
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Structure |
clone()
returns an identical copy of this structure .
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Chain |
findChain(java.lang.String chainId)
request a particular chain from a structure.
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Chain |
findChain(java.lang.String chainId,
int modelnr)
request a particular chain from a particular model
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Group |
findGroup(java.lang.String chainName,
java.lang.String pdbResnum)
request a particular group from a structure.
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Group |
findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr)
request a particular group from a structure.
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Chain |
getChain(int number)
retrieve a chain by it's position within the Structure.
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Chain |
getChain(int modelnr,
int number)
retrieve a chain by it's position within the Structure and model number.
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Chain |
getChainByPDB(java.lang.String chainId)
request a chain by it's PDB code
by default takes only the first model
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Chain |
getChainByPDB(java.lang.String chainId,
int modelnr)
request a chain by it's PDB code
by default takes only the first model
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java.util.List<Chain> |
getChains()
retrieve all chains - if it is a NMR structure will return the chains of the first model.
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java.util.List<Chain> |
getChains(int modelnr)
retrieve all chains of a model.
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Compound |
getCompoundById(java.lang.String molId)
request a particular compound by its id
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java.util.List<Compound> |
getCompounds()
get all the Compounds that are defined in the PDB Header
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java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> |
getConnections()
Returns the connections value.
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java.util.List<DBRef> |
getDBRefs()
get the list of database references
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java.util.Map<java.lang.String,java.lang.Object> |
getHeader()
get Header data.
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java.lang.Long |
getId()
get the ID used by Hibernate
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JournalArticle |
getJournalArticle()
get the associated publication as defined by the JRNL records in a PDB
file.
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java.util.List<Chain> |
getModel(int modelnr)
retrieve all Chains belonging to a model .
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java.lang.String |
getName()
get biological name of Structure.
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java.lang.String |
getPDBCode()
get PDB code of structure .
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PDBHeader |
getPDBHeader()
return the header information for this PDB file
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java.util.List<SSBond> |
getSSBonds()
get the list of SSBonds as they have been defined in the PDB files
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boolean |
hasChain(java.lang.String chainId)
check if a chain with the id chainId is contained in this structure.
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boolean |
hasJournalArticle()
Return whether or not the entry has an associated journal article
or publication.
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boolean |
isNmr()
is this structure an nmr structure ?
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int |
nrModels()
return number of models.
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void |
setChains(int modelnr,
java.util.List<Chain> chains)
set the chains for a model
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void |
setChains(java.util.List<Chain> chains)
set the chains of a structure, if this is a NMR structure,
this will only set model 0.
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void |
setCompounds(java.util.List<Compound> molList)
set the compounts
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void |
setConnections(java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> conns)
sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
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void |
setDBRefs(java.util.List<DBRef> dbrefs)
set the list of database references for this structure
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void |
setHeader(java.util.Map<java.lang.String,java.lang.Object> h)
set the Header data.
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void |
setId(java.lang.Long id)
set the ID used by Hibernate
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void |
setJournalArticle(JournalArticle journalArticle)
set the associated publication as defined by the JRNL records in a PDB
file.
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void |
setModel(int position,
java.util.List<Chain> model)
a convenience function if one wants to edit and replace the
models in a structure.
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void |
setName(java.lang.String nam)
set biological name of Structure.
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void |
setNmr(boolean nmr)
set NMR flag.
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void |
setPDBCode(java.lang.String pdb_id_)
set PDB code of structure .
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void |
setPDBHeader(PDBHeader pdbHeader)
the the header information for this PDB file
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void |
setSSBonds(java.util.List<SSBond> ssbonds)
set the list of SSBonds for this structure
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int |
size()
return number of chains , if NMR return number of chains of first model .
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int |
size(int modelnr)
return number of chains of model.
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java.lang.String |
toPDB()
create a String that contains the contents of a PDB file.
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java.lang.String |
toString()
string representation.
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public StructureImpl()
public StructureImpl(Group g)
g
- public StructureImpl(Chain c)
c
- public java.lang.Long getId()
public void setId(java.lang.Long id)
public Structure clone()
public Group findGroup(java.lang.String chainId, java.lang.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 useStructureException
public Group findGroup(java.lang.String chainName, java.lang.String pdbResnum) throws StructureException
Structure
findGroup
in interface Structure
chainName
- the ID of the chain to usepdbResnum
- the PDB residue number of the requested groupStructureException
public Chain findChain(java.lang.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 useStructureException
public Chain findChain(java.lang.String chainId) throws StructureException
Structure
findChain
in interface Structure
chainId
- the ID of a chain that should be returnedStructureException
public void setPDBCode(java.lang.String pdb_id_)
setPDBCode
in interface Structure
pdb_id_
- a String specifying the PDBCodegetPDBCode()
public java.lang.String getPDBCode()
getPDBCode
in interface Structure
setPDBCode(java.lang.String)
public void setName(java.lang.String nam)
public java.lang.String getName()
getName
in interface Structure
setName(java.lang.String)
public void setHeader(java.util.Map<java.lang.String,java.lang.Object> h)
setHeader
in interface Structure
h
- a Map object specifying the headergetHeader()
public java.util.Map<java.lang.String,java.lang.Object> getHeader()
getHeader
in interface Structure
setHeader(java.util.Map<java.lang.String, java.lang.Object>)
public void setConnections(java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> 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 java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> getConnections()
getConnections
in interface Structure
interface
,
setConnections(java.util.List<java.util.Map<java.lang.String, java.lang.Integer>>)
public void addChain(Chain chain)
public void addChain(Chain chain, int modelnr)
public Chain getChain(int number)
public Chain getChain(int modelnr, int number)
public void addModel(java.util.List<Chain> model)
public void setChains(java.util.List<Chain> chains)
Structure
setChains
in interface Structure
chains
- the list of chains for this structure.Structure.setChains(int, List)
public void setModel(int position, java.util.List<Chain> model)
Structure
public java.lang.String toString()
public int size()
public int size(int modelnr)
public int nrModels()
public boolean isNmr()
public void setNmr(boolean nmr)
Structure
public java.util.List<Chain> getChains(int modelnr)
getChains
in interface Structure
modelnr
- an intStructure.getModel(int)
public java.util.List<Chain> getChains()
Structure
getChains
in interface Structure
Structure.getModel(int modelnr)
,
Structure.getChains(int modelnr)
public void setChains(int modelnr, java.util.List<Chain> chains)
Structure
public java.util.List<Chain> getModel(int modelnr)
getModel
in interface Structure
modelnr
- an intStructure.getChains(int modelnr)
public Chain getChainByPDB(java.lang.String chainId, int modelnr) throws StructureException
Structure
getChainByPDB
in interface Structure
chainId
- the chain identifiermodelnr
- request a particular model;StructureException
public Chain getChainByPDB(java.lang.String chainId) throws StructureException
Structure
getChainByPDB
in interface Structure
chainId
- the chain identifierStructureException
public java.lang.String toPDB()
toPDB
in interface Structure
FileConvert
public boolean hasChain(java.lang.String chainId)
Structure
public void setCompounds(java.util.List<Compound> molList)
Structure
setCompounds
in interface Structure
public java.util.List<Compound> getCompounds()
Structure
getCompounds
in interface Structure
public Compound getCompoundById(java.lang.String molId)
Structure
getCompoundById
in interface Structure
public java.util.List<DBRef> getDBRefs()
Structure
public void setDBRefs(java.util.List<DBRef> dbrefs)
Structure
public PDBHeader getPDBHeader()
Structure
getPDBHeader
in interface Structure
public void setPDBHeader(PDBHeader pdbHeader)
Structure
setPDBHeader
in interface Structure
pdbHeader
- the PDBHeader objectpublic java.util.List<SSBond> getSSBonds()
getSSBonds
in interface Structure
public void setSSBonds(java.util.List<SSBond> ssbonds)
setSSBonds
in interface Structure
ssbonds
- public void addSSBond(SSBond ssbond)
public boolean hasJournalArticle()
hasJournalArticle
in interface Structure
public JournalArticle getJournalArticle()
getJournalArticle
in interface Structure
public void setJournalArticle(JournalArticle journalArticle)
setJournalArticle
in interface Structure
journalArticle
- the article