org.biojava.bio.structure
Class Hetatom

java.lang.Object
  org.biojava.bio.structure.Hetatom

All Implemented Interfaces:

Group

Direct Known Subclasses:

AminoAcid, Nucleotide

public class Hetatom

extends Object

implements Group

Generic Implementation of a Group interface. AminoAcid and Nucleotide are closely related classes.

See Also:

AminoAcid, Nucleotide

Field Summary

static String

type

Constructor Summary

Hetatom()

Method Summary

void	addAtom(Atom atom) add an atom to this group
Atom	getAtom(int position) return an atom by its position in the internal ArrayList
Atom	getAtom(String name) get an Atom or null, if Atom not in this group
ArrayList	getAtoms() get all atoms of this group
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) test is an Atom with name is existing
void	setPDBCode(String pdb)
void	setPDBFlag(boolean flag) flag if group has 3D data
void	setPDBName(String s) set three character name of Amino acid
void	setProperties(HashMap props) properties of this amino acid.
void	setProperty(String key, Object value) set a single property
int	size() getnumber of atoms
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

type

public static String type

Constructor Detail

Hetatom

public Hetatom()

Method Detail

has3D

public boolean has3D()

Description copied from interface: Group

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

Specified by:

has3D in interface Group

setPDBFlag

public void setPDBFlag(boolean flag)

Description copied from interface: Group

flag if group has 3D data

Specified by:

setPDBFlag in interface Group

getPDBCode

public String getPDBCode()

Description copied from interface: Group

return the PDBcode of this amino acid

Specified by:

getPDBCode in interface Group

setPDBCode

public void setPDBCode(String pdb)

Specified by:

setPDBCode in interface Group

setPDBName

public void setPDBName(String s)
                throws PDBParseException

set three character name of Amino acid

Specified by:

setPDBName in interface Group

Throws:

PDBParseException

getPDBName

public String getPDBName()

Description copied from interface: Group

set the PDB 3 character name for this group

Specified by:

getPDBName in interface Group

addAtom

public void addAtom(Atom atom)

add an atom to this group

Specified by:

addAtom in interface Group

size

public int size()

Description copied from interface: Group

getnumber of atoms

Specified by:

size in interface Group

getAtoms

public ArrayList getAtoms()

get all atoms of this group

Specified by:

getAtoms in interface Group

getAtom

public Atom getAtom(String name)
             throws StructureException

get an Atom or null, if Atom not in this group

Specified by:

getAtom in interface Group

Throws:

StructureException

getAtom

public Atom getAtom(int position)
             throws StructureException

return an atom by its position in the internal ArrayList

Specified by:

getAtom in interface Group

Throws:

StructureException

hasAtom

public boolean hasAtom(String name)

test is an Atom with name is existing

Specified by:

hasAtom in interface Group

getType

public String getType()

Description copied from interface: Group

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

Specified by:

getType in interface Group

toString

public String toString()

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() !

Specified by:

hasAminoAtoms in interface Group

See Also:

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

if this method call is performed too often, it should become a private method and set a flag ...

setProperties

public void setProperties(HashMap props)

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

Specified by:

setProperties in interface Group

getProperties

public HashMap getProperties()

return properties. @see setProperties()

Specified by:

getProperties in interface Group

setProperty

public void setProperty(String key,
                        Object value)

set a single property

Specified by:

setProperty in interface Group

getProperty

public Object getProperty(String key)

get a single property

Specified by:

getProperty in interface Group