org.biojava.bio.structure
Interface Structure

All Known Implementing Classes:

StructureImpl

public interface Structure

Interface for a structure object. Provides access to the data of a PDB file.

Q: How can I get a Structure object from a PDB file?

A:

 String filename =  "path/to/pdbfile.ent" ;

 PDBFileReader pdbreader = new PDBFileReader();

 try{
        Structure struc = pdbreader.getStructure(filename);
        System.out.println(struc);
 } catch (Exception e) {
        e.printStackTrace();
 }
 

Q: How can I calculate Phi and Psi angles of the AminoAcids?

A:

        ArrayList chains = (ArrayList)struc.getModel(0);
        Chain tmpchn  = (Chain)chains.get(0) ;
        ArrayList aminos = tmpchn.getGroups("amino");

        AminoAcid a;
        AminoAcid b;
        AminoAcid c ;

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

            b = (AminoAcid)aminos.get(i);
            double phi =360.0;
            double psi =360.0;

            if ( i > 0) {
                a = (AminoAcid)aminos.get(i-1) ;
                try {
                    phi = Calc.getPhi(a,b);                                
                } catch (StructureException e){             
                    e.printStackTrace();
                    phi = 360.0 ;
                }
            }
            if ( i < aminos.size()-1) {
                c = (AminoAcid)aminos.get(i+1) ;
                try {
                    psi = Calc.getPsi(b,c);
                }catch (StructureException e){
                    e.printStackTrace();
                    psi = 360.0 ;
                }
            }

            String str = b.getPDBCode() + " " + b.getPDBName() + ":"  ;
            str += "\tphi: " + phi + "\tpsi: " + psi;
            System.out.println(str);

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 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 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	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() test if this structure is an nmr structure.
int	nrModels() return number of models .
void	setConnections(List connections) 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 name) 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 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

Object clone()

returns an identical copy of this structure .

Returns:

an identical 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 h)

set the Header data .

Parameters:

h - a Map object specifying the header

See Also:

getHeader()

getHeader

Map getHeader()

get Header data .

Returns:

a Map object representing the header value

See Also:

setHeader(java.util.Map)

setConnections

void setConnections(List 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 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 model)

add a new model.

Parameters:

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

getModel

List 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)

getChains

List 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)

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