Module pdb

Package de.grogra.ext.pdb.model

Class AminoAcid

java.lang.Object

de.grogra.ext.pdb.model.AminoAcid

public class AminoAcid
extends Object

Author:

fdill Respresenting amino acids. The amino acid holds its atoms.

Field Summary

Fields

Modifier and Type	Field	Description
static int	numberOfAcids

Constructor Summary

Constructors

Constructor	Description
AminoAcid(String name, int resSeqNr)	By every creation a counter is incremented.

Method Summary

Modifier and Type	Method	Description
void	addAtom(Atom atom)	Adds an atom to this amino acid
Vector	getAtoms()
String	getName()
int	getResSeqNr()
void	setAtoms(Vector vector)
void	setName(String string)
void	setResSeqNr(int i)
void	validate()	Compares the actual vector of atoms with a reference vector from the HashMap which is initialized in the constructor.

Methods inherited from class java.lang.Object

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

Field Details

numberOfAcids

public static int numberOfAcids

Constructor Details

AminoAcid

public AminoAcid(String name,
 int resSeqNr)

By every creation a counter is incremented.

Parameters:

chainId - - a field of the pdb file

name - - the name of the atom

resSeqNr - - a unique identifier for the amino acid

Method Details

getAtoms

public Vector getAtoms()

Returns:

getName

public String getName()

Returns:

setAtoms

public void setAtoms(Vector vector)

Parameters:

vector -

setName

public void setName(String string)

Parameters:

string -

addAtom

public void addAtom(Atom atom)

Adds an atom to this amino acid

Parameters:

atom -

validate

public void validate()

Compares the actual vector of atoms with a reference vector from the HashMap which is initialized in the constructor. If they are not equal a text output is generated.

getResSeqNr

public int getResSeqNr()

Returns:

setResSeqNr

public void setResSeqNr(int i)

Parameters:

i -