org.biojava.bio.structure
Interface Group

All Known Subinterfaces:

AminoAcid

All Known Implementing Classes:

AminoAcidImpl, HetatomImpl, NucleotideImpl

public interface Group

This is the datastructure for a single Group of atoms. A protein sequence (Chain in PDB file) is represented as a list of this kind of objects. Groups can be of type "amino","hetatm","nucleotide". There are corresponding classes for each of this type which implement interface Group.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Horvath Tamas

See Also:

HetatomImpl, AminoAcidImpl, NucleotideImpl

Method Summary

void	addAtom(Atom atom) add an atom to this group.
void	clearAtoms() remove all atoms from this group
Object	clone() returns and identical copy of this Group object .
Atom	getAtom(int position) get at atom by position.
Atom	getAtom(String name) get an atom throws StructureException if atom not found.
List	getAtoms() get list of atoms.
Chain	getParent() Returns the parent Chain of the Group
String	getPDBCode() return the PDBcode (residue number) of this group.
String	getPDBName() set the PDB 3 character name for this group.
Map	getProperties() return properties.
Object	getProperty(String key) get a single property .
String	getType() get Type of group, e.g.
boolean	has3D() returns true or false, depending if this group has 3D coordinates or not.
boolean	hasAminoAtoms() calculate if a groups has all atoms required for an amino acid.
boolean	hasAtom(String name) returns flag whether a particular atom is existing within this group .
Iterator	iterator() get an Atom Iterator.
void	setParent(Chain parent) Set the back-reference (to its parent Chain)
void	setPDBCode(String pdbcode) Specifies the PDBCode value.
void	setPDBFlag(boolean flag) flag if group has 3D data .
void	setPDBName(String s) get the PDB 3 character name for this group.
void	setProperties(Map properties) properties of this amino acid.
void	setProperty(String key, Object value) set a single property .
int	size() getnumber of atoms.

Method Detail

getPDBCode

String getPDBCode()

return the PDBcode (residue number) of this group.

Returns:

a String representing the PDBCode value

See Also:

setPDBCode(java.lang.String)

setPDBCode

void setPDBCode(String pdbcode)

Specifies the PDBCode value.

Parameters:

pdbcode - a String specifying the PDBCode value

See Also:

getPDBCode()

size

int size()

getnumber of atoms.

Returns:

number of atoms of this Group

has3D

boolean has3D()

returns true or false, depending if this group has 3D coordinates or not.

Returns:

true if Group has 3D coordinates

setPDBFlag

void setPDBFlag(boolean flag)

flag if group has 3D data .

Parameters:

flag - true to set flag that this Group has 3D coordinates

getType

String getType()

get Type of group, e.g. amino, hetatom, nucleotide.

Returns:

a String representing the type value

addAtom

void addAtom(Atom atom)

add an atom to this group.

Parameters:

atom - an Atom object

getAtoms

List getAtoms()

get list of atoms.

Returns:

an List object representing the atoms

clearAtoms

void clearAtoms()

remove all atoms from this group

getAtom

Atom getAtom(String name)
             throws StructureException

get an atom throws StructureException if atom not found.

Parameters:

name - a String

Returns:

an Atom object

Throws:

StructureException - ...

getAtom

Atom getAtom(int position)
             throws StructureException

get at atom by position.

Parameters:

position - an int

Returns:

an Atom object

Throws:

StructureException - ...

hasAtom

boolean hasAtom(String name)

returns flag whether a particular atom is existing within this group .

Parameters:

name - a String ...

Returns:

true if Atom with name is existing within this group

getPDBName

String getPDBName()

set the PDB 3 character name for this group.

Returns:

a String representing the PDBName value

See Also:

setPDBName(java.lang.String)

setPDBName

void setPDBName(String s)
                throws PDBParseException

get the PDB 3 character name for this group.

Parameters:

s - a String specifying the PDBName value

Throws:

PDBParseException - ...

See Also:

getPDBName()

hasAminoAtoms

boolean hasAminoAtoms()

calculate if a groups has all atoms required for an amino acid. this allows to include chemically modified amino acids that are labeled hetatoms into some computations ... the usual way to identify if a group is an amino acid is getType() !

amino atoms are : N, CA, C, O, CB GLY does not have CB (unless we would calculate some artificially

Example: 1DW9 chain A first group is a Selenomethionine, provided as HETATM, but here returns true.

     HETATM    1  N   MSE A   1      11.720  20.973   1.584  0.00  0.00           N
     HETATM    2  CA  MSE A   1      10.381  20.548   1.139  0.00  0.00           C
     HETATM    3  C   MSE A   1       9.637  20.037   2.398  0.00  0.00           C
     HETATM    4  O   MSE A   1      10.198  19.156   2.985  0.00  0.00           O
     HETATM    5  CB  MSE A   1      10.407  19.441   0.088  0.00  0.00           C
     

Returns:

true if all Atoms required for an AminoAcid are available (N, CA, C, O, CB)

See Also:

getType()

setProperties

void setProperties(Map properties)

properties of this amino acid. currerntly available properties. are: phi psi

Parameters:

properties - a Map object specifying the properties value

See Also:

getProperties()

getProperties

Map getProperties()

return properties.

Returns:

a HashMap object representing the properties value

See Also:

setProperties(java.util.Map)

setProperty

void setProperty(String key,
                 Object value)

set a single property .

Parameters:

key - a String

value - an Object

See Also:

getProperty(java.lang.String)

getProperty

Object getProperty(String key)

get a single property .

Parameters:

key - a String

Returns:

an Object

See Also:

setProperty(java.lang.String, java.lang.Object)

iterator

Iterator iterator()

get an Atom Iterator.

Returns:

an Iterator object

clone

Object clone()

returns and identical copy of this Group object .

Returns:

and identical copy of this Group object

setParent

void setParent(Chain parent)

Set the back-reference (to its parent Chain)

Parameters:

parent - a WeakReference to the parent Chain

getParent

Chain getParent()

Returns the parent Chain of the Group

Returns:

Chain the Chain object that contains the Group