org.biojava.bio.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

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("amino");

                AminoAcid a;
                AminoAcid b;
                AminoAcid c ;

                for ( int i=0; i < groups.size(); i++){

                        // since we requested only groups of type "amino" 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

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<Chain> model) add a new model.
void	addSSBond(SSBond ssbond) add a single SSBond to this structure
Structure	clone() returns 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 it's position within the Structure .
Chain	getChain(int pos, int modelnr) 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<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(String molId) request a particular compound by its id
List<Compound>	getCompounds() get all the Compounds that are defined in the PDB Header
List<Map<String,Integer>>	getConnections() Returns the connections value.
List<DBRef>	getDBRefs() get the list of database references
Map<String,Object>	getHeader() Deprecated. use getPDBHeader instead
Long	getId() get the ID used by Hibernate
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
List<SSBond>	getSSBonds() get the list of SSBonds as they have been defined in the PDB files
boolean	hasChain(String chainId) check if a chain with the id chainId is contained in this structure.
boolean	isNmr() test if this structure is an nmr structure.
int	nrModels() return number of models .
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 compounts
void	setConnections(List<Map<String,Integer>> connections) sets/gets an List of Maps which corresponds to the CONECT lines in the PDB file:
void	setDBRefs(List<DBRef> dbrefs) set the list of database references for this structure
void	setHeader(Map<String,Object> h) set the Header data .
void	setId(Long id) set the ID used by Hibernate
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) set NMR flag.
void	setPDBCode(String pdb_id) set PDB code of structure .
void	setPDBHeader(PDBHeader header) the the header information for this PDB file
void	setSSBonds(List<SSBond> ssbonds) set the list of SSBonds for this structure
int	size() return number of Chains in this Structure.
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 of object.

Method Detail

clone

Structure clone()

returns 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)

setHeader

void setHeader(Map<String,Object> h)

set the Header data .

Parameters:

h - a Map object specifying the header

See Also:

getHeader()

getHeader

Map<String,Object> getHeader()

Deprecated. use getPDBHeader instead

get Header data .

Returns:

a Map object representing the header value

See Also:

setHeader(java.util.Map), getPDBHeader()

setConnections

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

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

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

Returns the connections value.

Returns:

a List object representing the connections value

See Also:

setConnections(java.util.List>)

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 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 @see isNMR , since this is based on the info in the PDB file header.

Returns:

an int representing the number of models in this Structure

isNmr

boolean isNmr()

test if this structure is an nmr structure.

Returns:

true if this Structure has been resolved by NMR

setNmr

void setNmr(boolean nmr)

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 it's position within the Structure .

Parameters:

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

Returns:

a Chain object

getChain

Chain getChain(int pos,
               int modelnr)

retrieve a chain by it's 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 it's 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 it's 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 the contents of a PDB file .

Returns:

a String that looks like a PDB file

See Also:

FileConvert

setCompounds

void setCompounds(List<Compound> molList)

set the compounts

Parameters:

molList -

getCompounds

List<Compound> getCompounds()

get all the Compounds that are defined in the PDB Header

Returns:

a list of compound

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(String molId)

request a particular compound by its id

Parameters:

molId -

Returns:

a compound

getPDBHeader

PDBHeader getPDBHeader()

return the header information for this PDB file

Returns:

the PDBHeader object

getSSBonds

List<SSBond> getSSBonds()

get the list of SSBonds as they have been defined in the PDB files

Returns:

a list of SSBonds

setSSBonds

void setSSBonds(List<SSBond> ssbonds)

set the list of SSBonds for this structure

Parameters:

ssbonds -

addSSBond

void addSSBond(SSBond ssbond)

add a single SSBond to this structure

Parameters:

ssbond -

setPDBHeader

void setPDBHeader(PDBHeader header)

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 -