org.biojava.bio.structure
Interface Group

All Known Implementing Classes:

Hetatom

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.

See Also:

Hetatom, AminoAcid, Nucleotide

Method Summary

void	addAtom(Atom atom) add an atom to this group
Atom	getAtom(int position) get at atom by position
Atom	getAtom(String name) get an atom throws StructureException if atom not found
ArrayList	getAtoms() get list of atoms
String	getPDBCode() return the PDBcode of this amino acid
String	getPDBName() set the PDB 3 character name for this group
HashMap	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 this allows to include chemically modified amino acids that are labeled hetatoms into some computations ...
boolean	hasAtom(String name) returns flag whether a particular atom is existing within this group
void	setPDBCode(String pdbcode)
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(HashMap properties) properties of this amino acid.
void	setProperty(String key, Object value) set a single property
int	size() getnumber of atoms

Method Detail

getPDBCode

public String getPDBCode()

return the PDBcode of this amino acid

setPDBCode

public void setPDBCode(String pdbcode)

size

public int size()

getnumber of atoms

has3D

public boolean has3D()

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

setPDBFlag

public void setPDBFlag(boolean flag)

flag if group has 3D data

getType

public String getType()

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

addAtom

public void addAtom(Atom atom)

add an atom to this group

getAtoms

public ArrayList getAtoms()

get list of atoms

getAtom

public Atom getAtom(String name)
             throws StructureException

get an atom throws StructureException if atom not found

Throws:

StructureException

getAtom

public Atom getAtom(int position)
             throws StructureException

get at atom by position

Throws:

StructureException

hasAtom

public boolean hasAtom(String name)

returns flag whether a particular atom is existing within this group

getPDBName

public String getPDBName()

set the PDB 3 character name for this group

setPDBName

public void setPDBName(String s)
                throws PDBParseException

get the PDB 3 character name for this group

Throws:

PDBParseException

hasAminoAtoms

public 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() !

See Also:

getType()

setProperties

public void setProperties(HashMap properties)

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

getProperties

public HashMap getProperties()

return properties. @see setProperties()

setProperty

public void setProperty(String key,
                        Object value)

set a single property

getProperty

public Object getProperty(String key)

get a single property