Module pdb

Package de.grogra.ext.pdb.model

Class Protein

java.lang.Object

de.grogra.ext.pdb.model.Protein

All Implemented Interfaces:

IProtein

public class Protein
extends Object
implements IProtein

Author:

fdill, mdube The protein contains the sequences as a vector. It also provides a text output. RH20060629 changed variable name 'enum' to 'e' to avoid problems with java 1.5

Constructor Summary

Constructors

Constructor	Description
Protein()
Protein(String proteinName)

Method Summary

Modifier and Type	Method	Description
void	addAminoSequence(AminoSequence sequence)
String	getAcidName(int sequence, int acid)
Vector	getAminoSequences()
String	getAtomName(int sequence, int acid, int atom)
String	getElement(int sequence, int acid, int atom)
String	getName()
int	getNumberOfAcids(int sequence)
int	getNumberOfAtoms(int sequence, int acid)
int	getNumberOfSequences()
int	getResSeqNr(int sequence, int acid)
float	getXCoord(int sequence, int acid, int atom)
float	getYCoord(int sequence, int acid, int atom)
float	getZCoord(int sequence, int acid, int atom)
void	textOutput()	text output for testing

Methods inherited from class java.lang.Object

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

Constructor Details

Protein

public Protein(String proteinName)

Parameters:

proteinName - - the name of the protein

Protein

public Protein()

Method Details

addAminoSequence

public void addAminoSequence(AminoSequence sequence)

Parameters:

sequence - - a sequence to be added to this protein

textOutput

public void textOutput()

text output for testing

getAminoSequences

public Vector getAminoSequences()

Returns:

- a vector containing the amino sequences of the type @link AminoSequence of this protein

getName

public String getName()

Returns:

- the name of the protein

getAcidName

public String getAcidName(int sequence,
 int acid)

Specified by:

getAcidName in interface IProtein

See Also:

• IProtein.getAcidName(int, int)

getResSeqNr

public int getResSeqNr(int sequence,
 int acid)

Specified by:

getResSeqNr in interface IProtein

See Also:

• IProtein.getResSeqNr(int, int)

getXCoord

public float getXCoord(int sequence,
 int acid,
 int atom)

Specified by:

getXCoord in interface IProtein

See Also:

• IProtein.getXCoord(int, int, int)

getYCoord

public float getYCoord(int sequence,
 int acid,
 int atom)

Specified by:

getYCoord in interface IProtein

See Also:

• IProtein.getYCoord(int, int, int)

getZCoord

public float getZCoord(int sequence,
 int acid,
 int atom)

Specified by:

getZCoord in interface IProtein

See Also:

• IProtein.getZCoord(int, int, int)

getElement

public String getElement(int sequence,
 int acid,
 int atom)

Specified by:

getElement in interface IProtein

See Also:

• IProtein.getElement(int, int, int)

getAtomName

public String getAtomName(int sequence,
 int acid,
 int atom)

Specified by:

getAtomName in interface IProtein

See Also:

• IProtein.getAtomName(int, int, int)

getNumberOfSequences

public int getNumberOfSequences()

Specified by:

getNumberOfSequences in interface IProtein

See Also:

• IProtein.getNumberOfSequences()

getNumberOfAcids

public int getNumberOfAcids(int sequence)

Specified by:

getNumberOfAcids in interface IProtein

See Also:

• IProtein.getNumberOfAcids(int)

getNumberOfAtoms

public int getNumberOfAtoms(int sequence,
 int acid)

Specified by:

getNumberOfAtoms in interface IProtein

See Also:

• IProtein.getNumberOfAtoms(int, int)