org.biojava.nbio.structure

Interface Structure

All Superinterfaces:

Cloneable

All Known Implementing Classes:

StructureImpl

public interface Structure
extends Cloneable

Interface for a structure object. Provides access to the data of a PDB file. A structure object allows to access the PDB header information as well as to the data from the ATOM records. The header information is currently available through the following objects:

• PDBHeader
• DBRef
• Compound

The structure object provides access to the data from the ATOM records through a hierarchy of sub-object:

 Structure
         |
         Chain
             |
             Group
                 |
                 Atom
 

For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure

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:

 public Structure loadStructure(String pathToPDBFile){
                PDBFileReader pdbreader = new PDBFileReader();

                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 structure

                Chain chain  = structure.getChain(0);

                // A protein chain consists of a number of groups. These can be either
                // AminoAcid, Hetatom or Nucleotide 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.
                List groups = 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));

                }
 

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

Method Summary

Methods

Modifier and Type	Method and 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(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(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 chainId, 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 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(String chainId) Request a chain by its PDB code by default takes only the first model
Chain	getChainByPDB(String chainId, int modelnr) Request a chain by its PDB code by default takes only the first model
List<Chain>	getChains() Retrieve all chains - if it is a NMR structure will return the chains of the first model.
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)
List<Compound>	getCompounds() Get all the Compounds for this Structure.
List<Map<String,Integer>>	getConnections() Deprecated. use Atom.getBonds() instead
PDBCrystallographicInfo	getCrystallographicInfo() Get crystallographic information for this structure
List<DBRef>	getDBRefs() Get the list of database references
List<Group>	getHetGroups()
Long	getId() Get the ID used by Hibernate
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.
List<Chain>	getModel(int modelnr) Retrieve all Chains belonging to a model .
String	getName() Get biological name of Structure.
String	getPDBCode() Get PDB code of structure.
PDBHeader	getPDBHeader() Return the header information for this PDB file
String	getPdbId() Deprecated. From BioJava 4.2, use getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()
List<String>	getRanges() Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()
List<? extends ResidueRange>	getResidueRanges() Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()
List<Site>	getSites()
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(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, List<Chain> chains) Set the chains for a model
void	setChains(List<Chain> chains) Set the chains of a structure, if this is a NMR structure, this will only set model 0.
void	setCompounds(List<Compound> molList) Set the Compounds
void	setConnections(List<Map<String,Integer>> connections) Deprecated. use Atom.addBond(Bond) instead
void	setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo) Set crystallographic information for this structure
void	setDBRefs(List<DBRef> dbrefs) Set the list of database references for this structure
void	setId(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, List<Chain> model) A convenience function if one wants to edit and replace the models in a structure.
void	setName(String name) Set biological name of Structure .
void	setNmr(boolean nmr) Deprecated.
void	setPDBCode(String pdb_id) Set PDB code of structure .
void	setPDBHeader(PDBHeader header) Set the the header information for this PDB file
void	setSites(List<Site> sites)
void	setSSBonds(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.
String	toMMCIF() Create a String that contains this Structure's contents in MMCIF file format.
String	toPDB() Create a String that contains this Structure's contents in PDB file format.
String	toString() String representation of object.

Method Detail

clone

Structure clone()

Return an identical copy of this Structure object

Returns:

identical copy of this Structure object

toString

String toString()

String representation of object.

Overrides:

toString in class Object

setPDBCode

void setPDBCode(String pdb_id)

Set PDB code of structure .

Parameters:

pdb_id - a String specifying the PDBCode

See Also:

getPDBCode()

getPDBCode

String getPDBCode()

Get PDB code of structure.

Returns:

a String representing the PDBCode value

See Also:

setPDBCode(java.lang.String)

setName

void setName(String name)

Set biological name of Structure .

Parameters:

name - a String specifying the biological name of the Structure

See Also:

getName()

getName

String getName()

Get biological name of Structure.

Returns:

a String representing the biological name of the Structure

See Also:

setName(java.lang.String)

getStructureIdentifier

StructureIdentifier getStructureIdentifier()

Get an identifier corresponding to this structure

Returns:

The StructureIdentifier used to create this structure

setStructureIdentifier

void setStructureIdentifier(StructureIdentifier structureIdentifier)

Set the identifier corresponding to this structure

Parameters:

structureIdentifier - the structureIdentifier corresponding to this structure

setConnections

@Deprecated
void setConnections(List<Map<String,Integer>> connections)

Deprecated. use Atom.addBond(Bond) instead

sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:

           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
           atom
           

the HashMap for a single CONECT line contains the following fields:

atomserial (mandatory) : Atom serial number bond1 .. bond4 (optional): Serial number of bonded atom hydrogen1 .. hydrogen4 (optional):Serial number of hydrogen bonded atom salt1 .. salt2 (optional): Serial number of salt bridged atom

Parameters:

connections - a List object specifying the connections

See Also:

getConnections()

getConnections

@Deprecated
List<Map<String,Integer>> getConnections()

Deprecated. use Atom.getBonds() instead

Return the connections value.

Returns:

a List object representing the connections value

See Also:

setConnections(java.util.List<java.util.Map<java.lang.String, java.lang.Integer>>)

size

int size()

Return number of Chains in this Structure.

Returns:

an int representing the number of Chains in this Structure

size

int size(int modelnr)

Return number of chains of model.

Parameters:

modelnr - an int specifying the number of the Model that should be used

Returns:

an int representing the number of Chains in this Model

nrModels

int nrModels()

Return the number of models . In this implementation also XRAY structures have "1 model", since model is the container for the chains. to test if a Structure is an NMR structure use isNmr().

Returns:

an int representing the number of models in this Structure

See Also:

isNmr()

isNmr

boolean isNmr()

Test if this structure is an NMR structure.

Returns:

true if this Structure has been solved by NMR

See Also:

nrModels()

isCrystallographic

boolean isCrystallographic()

Test if this structure is a crystallographic structure, i.e. it is an asymmetric unit from which it is possible to reconstruct the crystal lattice given cell parameters and space group.

Returns:

true if crystallographic, false otherwise

setNmr

@Deprecated
void setNmr(boolean nmr)

Deprecated.

set NMR flag.

Parameters:

nmr - true to declare that this Structure has been solved by NMR.

addModel

void addModel(List<Chain> model)

Add a new model.

Parameters:

model - a List object containing the Chains of the new Model

setModel

void setModel(int position,
            List<Chain> model)

A convenience function if one wants to edit and replace the models in a structure. Allows to set (replace) the model at position with the new List of Chains.

Parameters:

position - starting at 0

model -

getModel

List<Chain> getModel(int modelnr)

Retrieve all Chains belonging to a model .

Parameters:

modelnr - an int

Returns:

a List object containing the Chains of Model nr. modelnr

See Also:

getChains(int modelnr)

getChains

List<Chain> getChains()

Retrieve all chains - if it is a NMR structure will return the chains of the first model. This is the same as getChains(0);

Returns:

a List object containing the Chains of Model nr. modelnr

See Also:

getModel(int modelnr), getChains(int modelnr)

setChains

void setChains(List<Chain> chains)

Set the chains of a structure, if this is a NMR structure, this will only set model 0.

Parameters:

chains - the list of chains for this structure.

See Also:

setChains(int, List)

getChains

List<Chain> getChains(int modelnr)

Retrieve all chains of a model.

Parameters:

modelnr - an int

Returns:

a List object containing the Chains of Model nr. modelnr

See Also:

getModel(int)

setChains

void setChains(int modelnr,
             List<Chain> chains)

Set the chains for a model

Parameters:

chains -

modelnr -

addChain

void addChain(Chain chain)

Add a new chain.

Parameters:

chain - a Chain object

addChain

void addChain(Chain chain,
            int modelnr)

Add a new chain, if several models are available.

Parameters:

chain - a Chain object

modelnr - an int specifying to which model the Chain should be added

getChain

Chain getChain(int pos)

Retrieve a chain by its position within the Structure .

Parameters:

pos - an int for the position in the List of Chains.

Returns:

a Chain object

getChain

Chain getChain(int modelnr,
             int pos)

Retrieve a chain by its position within the Structure and model number.

Parameters:

pos - an int

modelnr - an int

Returns:

a Chain object

findChain

Chain findChain(String chainId)
                throws StructureException

Request a particular chain from a structure. by default considers only the first model.

Parameters:

chainId - the ID of a chain that should be returned

Returns:

Chain the requested chain

Throws:

StructureException

hasChain

boolean hasChain(String chainId)

Check if a chain with the id chainId is contained in this structure.

Parameters:

chainId - the name of the chain

Returns:

true if a chain with the id (name) chainId is found

findChain

Chain findChain(String chainId,
              int modelnr)
                throws StructureException

Request a particular chain from a particular model

Parameters:

modelnr - the number of the model to use

chainId - the ID of a chain that should be returned

Returns:

Chain the requested chain

Throws:

StructureException

findGroup

Group findGroup(String chainId,
              String pdbResnum)
                throws StructureException

Request a particular group from a structure. by default considers only the first model in the structure.

Parameters:

chainId - the ID of the chain to use

pdbResnum - the PDB residue number of the requested group

Returns:

Group the requested Group

Throws:

StructureException

findGroup

Group findGroup(String chainId,
              String pdbResnum,
              int modelnr)
                throws StructureException

Request a particular group from a structure. considers only model nr X. count starts with 0.

Parameters:

chainId - the ID of the chain to use

pdbResnum - the PDB residue number of the requested group

modelnr - the number of the model to use

Returns:

Group the requested Group

Throws:

StructureException

getChainByPDB

Chain getChainByPDB(String chainId)
                    throws StructureException

Request a chain by its PDB code by default takes only the first model

Parameters:

chainId - the chain identifier

Returns:

the Chain that matches the chainID

Throws:

StructureException

getChainByPDB

Chain getChainByPDB(String chainId,
                  int modelnr)
                    throws StructureException

Request a chain by its PDB code by default takes only the first model

Parameters:

chainId - the chain identifier

modelnr - request a particular model;

Returns:

the Chain that matches the chainID in the model

Throws:

StructureException

toPDB

String toPDB()

Create a String that contains this Structure's contents in PDB file format.

Returns:

a String that looks like a PDB file

See Also:

FileConvert

toMMCIF

String toMMCIF()

Create a String that contains this Structure's contents in MMCIF file format.

Returns:

setCompounds

void setCompounds(List<Compound> molList)

Set the Compounds

Parameters:

molList -

getCompounds

List<Compound> getCompounds()

Get all the Compounds for this Structure. Compounds are called Entities in mmCIF dictionary.

Returns:

a list of Compounds

addCompound

void addCompound(Compound compound)

Add a Compound to this Structure

setDBRefs

void setDBRefs(List<DBRef> dbrefs)

Set the list of database references for this structure

Parameters:

dbrefs - list of DBRef objects

getDBRefs

List<DBRef> getDBRefs()

Get the list of database references

Returns:

list of DBRef objects

getCompoundById

Compound getCompoundById(int molId)

Request a particular compound by its molId (entity_id in mmCIF dictionary)

Parameters:

molId -

Returns:

a compound

getPDBHeader

PDBHeader getPDBHeader()

Return the header information for this PDB file

Returns:

the PDBHeader object

hasJournalArticle

boolean hasJournalArticle()

Return whether or not the entry has an associated journal article or publication. The JRNL section is not mandatory and thus may not be present.

Returns:

flag if a JournalArticle has been found.

getJournalArticle

JournalArticle getJournalArticle()

Get the associated publication as defined by the JRNL records in a PDB file.

Returns:

a JournalArticle

setJournalArticle

void setJournalArticle(JournalArticle journalArticle)

Set the associated publication as defined by the JRNL records in a PDB file.

Parameters:

journalArticle -

getSSBonds

List<Bond> getSSBonds()

Get the list of disulfide Bonds as they have been defined in the PDB files

Returns:

a list of Bonds

setSSBonds

void setSSBonds(List<Bond> ssbonds)

Set the list of SSBonds for this structure

Parameters:

ssbonds -

addSSBond

void addSSBond(Bond ssbond)

Add a single disulfide Bond to this structure

Parameters:

ssbond -

setPDBHeader

void setPDBHeader(PDBHeader header)

Set the the header information for this PDB file

Parameters:

header - the PDBHeader object

getId

Long getId()

Get the ID used by Hibernate

Returns:

the ID used by Hibernate

setId

void setId(Long id)

set the ID used by Hibernate

Parameters:

id -

setSites

void setSites(List<Site> sites)

Parameters:

sites - the sites to set in the structure

getSites

List<Site> getSites()

Returns:

the sites contained in this structure

getHetGroups

List<Group> getHetGroups()

setBiologicalAssembly

void setBiologicalAssembly(boolean biologicalAssembly)

Set a flag to indicate if this structure is a biological assembly

Parameters:

biologicalAssembly - true if biological assembly, otherwise false

Since:

3.2

isBiologicalAssembly

boolean isBiologicalAssembly()

Get flag that indicates if this structure is a biological assembly

Returns:

true if biological assembly, otherwise false

Since:

3.2

setCrystallographicInfo

void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo)

Set crystallographic information for this structure

Parameters:

PDBCrystallographicInfo - crystallographic information

Since:

3.2

getCrystallographicInfo

PDBCrystallographicInfo getCrystallographicInfo()

Get crystallographic information for this structure

Returns:

PDBCrystallographicInfo crystallographic information

Since:

3.2

resetModels

void resetModels()

Resets all models of this Structure

Since:

4.0.1

getPdbId

@Deprecated
String getPdbId()

Deprecated. From BioJava 4.2, use getPDBCode() or getStructureIdentifier().toCanonical().getPdbId()

Returns the PDB identifier associated with this StructureIdentifier.

getResidueRanges

@Deprecated
List<? extends ResidueRange> getResidueRanges()

Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getResidueRanges()

Returns the list of ResidueRanges that this StructureIdentifier defines. This is a unique representation.

getRanges

@Deprecated
List<String> getRanges()

Deprecated. From BioJava 4.2, use getStructureIdentifier().toCanonical().getRanges()

Returns a list of residue ranges. For example:

 getRanges().get(0): 'A'
 getRanges().get(1): 'B_5-100'
 

This is a unique representation.

getIdentifier

String getIdentifier()

Get a string representing this structure's contents. The following places are searched for a non-null value, with the first being returned:

1. getStructureIdentifier().getIdentifier(), which should give the string originally used to create the structure
2. getName()
3. A combination of getPDBCode() with a heuristic description of the residue ranges, in SubstructureIdentifier format.

Returns:

A SubstructureIdentifier-format string describing the residue ranges in this structure

Since:

The behavior of this method changed in BioJava 4.2. Previously it returned the same value as getPDBCode()