java.lang.Cloneable
StructureImpl
public interface Structure
extends java.lang.Cloneable
Structure |For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_StructureChain
|Group
|Atom
The tutorial for the BioJava structure modules can be found at github.
Q: How can I get a Structure object from a PDB file?
A:
publicStructure
loadStructure(String pathToPDBFile){PDBFileReader
pdbreader = newPDBFileReader
();Structure
structure = null; try{ structure = pdbreader.getStructure(pathToPDBFile); System.out.println(structure); } catch (IOException e) { e.printStackTrace(); } return structure; }
Q: How can I calculate Phi and Psi angles of AminoAcids?
A:
public void calcPhiPsi(Structure
structure){ // get the first chain from the structureChain
chain = structure.getChain(0); // A protein chain consists of a number of groups. These can be either //AminoAcid
,Hetatom
orNucleotide
groups. // // Note: BioJava provides access to both the ATOM and SEQRES data in a PDB file. // since we are interested in doing calculations here, we only request the groups // from the ATOM records // get the Groups of the chain that are AminoAcids. Listgroups = chain.getAtomGroups(GroupType.AMINOACID); AminoAcid
a;AminoAcid
b;AminoAcid
c ; for ( int i=0; i < groups.size(); i++){ // since we requested only groups of type AMINOACID they will always be amino acids // Nucleotide and Hetatom groups will not be present in the groups list. b = (AminoAcid
)groups.get(i); double phi =360.0; double psi =360.0; if ( i > 0) { a = (AminoAcid
)groups.get(i-1) ; try { // the Calc class provides utility methods for various calculations on // structures, groups and atoms phi =Calc
.getPhi(a,b); } catch (StructureException
e){ e.printStackTrace(); phi = 360.0 ; } } if ( i < groups.size()-1) { c = (AminoAcid
)groups.get(i+1) ; try { psi =Calc
.getPsi(b,c); }catch (StructureException
e){ e.printStackTrace(); psi = 360.0 ; } } System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":" ); System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi)); }
Modifier and Type | Method | Description |
---|---|---|
void |
addChain(Chain chain) |
Add a new chain.
|
void |
addChain(Chain chain,
int modelnr) |
Add a new chain, if several models are available.
|
void |
addCompound(Compound compound) |
Add a Compound to this Structure
|
void |
addModel(java.util.List<Chain> model) |
Add a new model.
|
void |
addSSBond(Bond ssbond) |
Add a single disulfide Bond to this structure
|
Structure |
clone() |
Return an identical copy of this Structure object
|
Chain |
findChain(java.lang.String chainId) |
Request a particular chain from a structure.
|
Chain |
findChain(java.lang.String chainId,
int modelnr) |
Request a particular chain from a particular model
|
Group |
findGroup(java.lang.String chainId,
java.lang.String pdbResnum) |
Request a particular group from a structure.
|
Group |
findGroup(java.lang.String chainId,
java.lang.String pdbResnum,
int modelnr) |
Request a particular group from a structure.
|
Chain |
getChain(int pos) |
Retrieve a chain by its position within the Structure .
|
Chain |
getChain(int modelnr,
int pos) |
Retrieve a chain by its position within the Structure and model number.
|
Chain |
getChainByPDB(java.lang.String chainId) |
Request a chain by its PDB code
by default takes only the first model
|
Chain |
getChainByPDB(java.lang.String chainId,
int modelnr) |
Request a chain by its PDB code
by default takes only the first model
|
java.util.List<Chain> |
getChains() |
Retrieve all chains - if it is a NMR structure will return the chains of the first model.
|
java.util.List<Chain> |
getChains(int modelnr) |
Retrieve all chains of a model.
|
Compound |
getCompoundById(int molId) |
Request a particular compound by its molId (entity_id in mmCIF dictionary)
|
java.util.List<Compound> |
getCompounds() |
Get all the Compounds for this Structure.
|
java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> |
getConnections() |
Deprecated.
use
Atom.getBonds() instead |
PDBCrystallographicInfo |
getCrystallographicInfo() |
Get crystallographic information for this structure
|
java.util.List<DBRef> |
getDBRefs() |
Get the list of database references
|
java.util.List<Group> |
getHetGroups() |
|
java.lang.Long |
getId() |
Get the ID used by Hibernate
|
java.lang.String |
getIdentifier() |
Get a string representing this structure's contents.
|
JournalArticle |
getJournalArticle() |
Get the associated publication as defined by the JRNL records in a PDB
file.
|
java.util.List<Chain> |
getModel(int modelnr) |
Retrieve all Chains belonging to a model .
|
java.lang.String |
getName() |
Get biological name of Structure.
|
java.lang.String |
getPDBCode() |
Get PDB code of structure.
|
PDBHeader |
getPDBHeader() |
Return the header information for this PDB file
|
java.lang.String |
getPdbId() |
Deprecated.
From BioJava 4.2, use
getPDBCode() or
getStructureIdentifier().toCanonical().getPdbId() |
java.util.List<java.lang.String> |
getRanges() |
Deprecated.
From BioJava 4.2, use
getStructureIdentifier().toCanonical().getRanges() |
java.util.List<? extends ResidueRange> |
getResidueRanges() |
Deprecated.
From BioJava 4.2, use
getStructureIdentifier().toCanonical().getResidueRanges() |
java.util.List<Site> |
getSites() |
|
java.util.List<Bond> |
getSSBonds() |
Get the list of disulfide Bonds as they have been defined in the PDB files
|
StructureIdentifier |
getStructureIdentifier() |
Get an identifier corresponding to this structure
|
boolean |
hasChain(java.lang.String chainId) |
Check if a chain with the id chainId is contained in this structure.
|
boolean |
hasJournalArticle() |
Return whether or not the entry has an associated journal article
or publication.
|
boolean |
isBiologicalAssembly() |
Get flag that indicates if this structure is a biological assembly
|
boolean |
isCrystallographic() |
Test if this structure is a crystallographic structure, i.e.
|
boolean |
isNmr() |
Test if this structure is an NMR structure.
|
int |
nrModels() |
Return the number of models .
|
void |
resetModels() |
Resets all models of this Structure
|
void |
setBiologicalAssembly(boolean biologicalAssembly) |
Set a flag to indicate if this structure is a biological assembly
|
void |
setChains(int modelnr,
java.util.List<Chain> chains) |
Set the chains for a model
|
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.
|
void |
setCompounds(java.util.List<Compound> molList) |
Set the Compounds
|
void |
setConnections(java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> connections) |
Deprecated.
use
Atom.addBond(Bond) instead |
void |
setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo) |
Set crystallographic information for this structure
|
void |
setDBRefs(java.util.List<DBRef> dbrefs) |
Set the list of database references for this structure
|
void |
setId(java.lang.Long id) |
set the ID used by Hibernate
|
void |
setJournalArticle(JournalArticle journalArticle) |
Set the associated publication as defined by the JRNL records in a PDB
file.
|
void |
setModel(int position,
java.util.List<Chain> model) |
A convenience function if one wants to edit and replace the
models in a structure.
|
void |
setName(java.lang.String name) |
Set biological name of Structure .
|
void |
setNmr(boolean nmr) |
Deprecated.
|
void |
setPDBCode(java.lang.String pdb_id) |
Set PDB code of structure .
|
void |
setPDBHeader(PDBHeader header) |
Set the the header information for this PDB file
|
void |
setSites(java.util.List<Site> sites) |
|
void |
setSSBonds(java.util.List<Bond> ssbonds) |
Set the list of SSBonds for this structure
|
void |
setStructureIdentifier(StructureIdentifier structureIdentifier) |
Set the identifier corresponding to this structure
|
int |
size() |
Return number of Chains in this Structure.
|
int |
size(int modelnr) |
Return number of chains of model.
|
java.lang.String |
toMMCIF() |
Create a String that contains this Structure's contents in MMCIF file format.
|
java.lang.String |
toPDB() |
Create a String that contains this Structure's contents in PDB file format.
|
java.lang.String |
toString() |
String representation of object.
|
Structure clone()
java.lang.String toString()
toString
in class java.lang.Object
void setPDBCode(java.lang.String pdb_id)
pdb_id
- a String specifying the PDBCodegetPDBCode()
java.lang.String getPDBCode()
setPDBCode(java.lang.String)
void setName(java.lang.String name)
name
- a String specifying the biological name of the StructuregetName()
java.lang.String getName()
setName(java.lang.String)
StructureIdentifier getStructureIdentifier()
void setStructureIdentifier(StructureIdentifier structureIdentifier)
structureIdentifier
- the structureIdentifier corresponding to this structure@Deprecated void setConnections(java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> connections)
Atom.addBond(Bond)
insteadCOLUMNS 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:
connections
- a List object specifying the connectionsgetConnections()
@Deprecated java.util.List<java.util.Map<java.lang.String,java.lang.Integer>> getConnections()
Atom.getBonds()
insteadsetConnections(java.util.List<java.util.Map<java.lang.String, java.lang.Integer>>)
int size()
int size(int modelnr)
modelnr
- an int specifying the number of the Model that should be usedint nrModels()
isNmr()
.isNmr()
boolean isNmr()
nrModels()
boolean isCrystallographic()
@Deprecated void setNmr(boolean nmr)
nmr
- true to declare that this Structure has been solved by NMR.void addModel(java.util.List<Chain> model)
model
- a List object containing the Chains of the new Modelvoid setModel(int position, java.util.List<Chain> model)
position
- starting at 0model
- java.util.List<Chain> getModel(int modelnr)
modelnr
- an intgetChains(int modelnr)
java.util.List<Chain> getChains()
getModel(int modelnr)
,
getChains(int modelnr)
void setChains(java.util.List<Chain> chains)
chains
- the list of chains for this structure.setChains(int, List)
java.util.List<Chain> getChains(int modelnr)
modelnr
- an intgetModel(int)
void setChains(int modelnr, java.util.List<Chain> chains)
chains
- modelnr
- void addChain(Chain chain)
chain
- a Chain objectvoid addChain(Chain chain, int modelnr)
chain
- a Chain objectmodelnr
- an int specifying to which model the Chain should be addedChain getChain(int pos)
pos
- an int for the position in the List of Chains.Chain getChain(int modelnr, int pos)
pos
- an intmodelnr
- an intChain findChain(java.lang.String chainId) throws StructureException
chainId
- the ID of a chain that should be returnedStructureException
boolean hasChain(java.lang.String chainId)
chainId
- the name of the chainChain findChain(java.lang.String chainId, int modelnr) throws StructureException
modelnr
- the number of the model to usechainId
- the ID of a chain that should be returnedStructureException
Group findGroup(java.lang.String chainId, java.lang.String pdbResnum) throws StructureException
chainId
- the ID of the chain to usepdbResnum
- the PDB residue number of the requested groupStructureException
Group findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr) throws StructureException
chainId
- the ID of the chain to usepdbResnum
- the PDB residue number of the requested groupmodelnr
- the number of the model to useStructureException
Chain getChainByPDB(java.lang.String chainId) throws StructureException
chainId
- the chain identifierStructureException
Chain getChainByPDB(java.lang.String chainId, int modelnr) throws StructureException
chainId
- the chain identifiermodelnr
- request a particular model;StructureException
java.lang.String toPDB()
FileConvert
java.lang.String toMMCIF()
void setCompounds(java.util.List<Compound> molList)
molList
- java.util.List<Compound> getCompounds()
void addCompound(Compound compound)
void setDBRefs(java.util.List<DBRef> dbrefs)
dbrefs
- list of DBRef objectsjava.util.List<DBRef> getDBRefs()
Compound getCompoundById(int molId)
molId
- PDBHeader getPDBHeader()
boolean hasJournalArticle()
JournalArticle getJournalArticle()
void setJournalArticle(JournalArticle journalArticle)
journalArticle
- java.util.List<Bond> getSSBonds()
void setSSBonds(java.util.List<Bond> ssbonds)
ssbonds
- void addSSBond(Bond ssbond)
ssbond
- void setPDBHeader(PDBHeader header)
header
- the PDBHeader objectjava.lang.Long getId()
void setId(java.lang.Long id)
id
- void setSites(java.util.List<Site> sites)
sites
- the sites to set in the structurejava.util.List<Site> getSites()
java.util.List<Group> getHetGroups()
void setBiologicalAssembly(boolean biologicalAssembly)
biologicalAssembly
- true if biological assembly, otherwise falseboolean isBiologicalAssembly()
void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)
PDBCrystallographicInfo
- crystallographic informationPDBCrystallographicInfo getCrystallographicInfo()
void resetModels()
@Deprecated java.lang.String getPdbId()
getPDBCode()
or
getStructureIdentifier().toCanonical().getPdbId()
@Deprecated java.util.List<? extends ResidueRange> getResidueRanges()
getStructureIdentifier().toCanonical().getResidueRanges()
ResidueRanges
that this StructureIdentifier defines.
This is a unique representation.@Deprecated java.util.List<java.lang.String> getRanges()
getStructureIdentifier().toCanonical().getRanges()
getRanges().get(0): 'A' getRanges().get(1): 'B_5-100'This is a unique representation.
java.lang.String getIdentifier()
getStructureIdentifier()
.getIdentifier(), which should give
the string originally used to create the structure
getName()
getPDBCode()
with a heuristic description
of the residue ranges, in SubstructureIdentifier
format.
SubstructureIdentifier
-format string describing the residue ranges in this structuregetPDBCode()