pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit
Class Peptide

java.lang.Object
  pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.Peptide

public class Peptide
extends java.lang.Object

Fully described polipeptide chain with aminoacids.

Field Summary

private char	id chain id, due to PDB file
private int	index internal enumerator of aacids, also length of the peptide chain
private float	maxabsdeviation
private float	maxavgdihedralangle
private float	maxdeviation
private float	maxlnradius
private float	minabsdeviation
private float	minavgdihedralangle
private float	mindeviation
private float	minlnradius
private boolean	peptide if one day we would like to read complexes with e.g aacids
private java.util.List<Aminoacid>	residues list of aminoacids in the chain
private float	xmax
private float	xmin
private float	ymax
private float	ymin
private float	zmax
private float	zmin

Constructor Summary

Peptide(char id)
Creates a new instance of Peptide

Method Summary

void	appendAmino(java.lang.String residuename, java.lang.String residuenum, java.util.Map AtomCoords) Appends an aminoacid of known coordinates to the chain.
void	calculateAbsDeviations()
void	calculateDeviations()
void	calculatePeptideBondPlanesDihedral()
void	estimateCurvatures()
float	getBoundXmax()
float	getBoundXmin()
float	getBoundYmax()
float	getBoundYmin()
float	getBoundZmax()
float	getBoundZmin()
char	getId()
int	getIndexOf(Aminoacid aa)
float	getMaxAbsDeviation()
float	getMaxAvgDihedralAngle()
float	getMaxDeviation()
float	getMaxLnRadius()
float	getMinAbsDeviation()
float	getMinAvgDihedralAngle()
float	getMinDeviation()
float	getMinLnRadius()
Aminoacid	getResidue(int position)
java.util.List<Aminoacid>	getResidues()
int	length()
void	setBounds(float xmin, float xmax, float ymin, float ymax, float zmin, float zmax)
void	setId(char id)

Methods inherited from class java.lang.Object

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

Field Detail

peptide

private boolean peptide

if one day we would like to read complexes with e.g aacids

id

private char id

chain id, due to PDB file

index

private int index

internal enumerator of aacids, also length of the peptide chain

residues

private java.util.List<Aminoacid> residues

list of aminoacids in the chain

minlnradius

private float minlnradius

maxlnradius

private float maxlnradius

minavgdihedralangle

private float minavgdihedralangle

maxavgdihedralangle

private float maxavgdihedralangle

mindeviation

private float mindeviation

maxdeviation

private float maxdeviation

minabsdeviation

private float minabsdeviation

maxabsdeviation

private float maxabsdeviation

xmin

private float xmin

xmax

private float xmax

ymin

private float ymin

ymax

private float ymax

zmin

private float zmin

zmax

private float zmax

Constructor Detail

Peptide

public Peptide(char id)

Creates a new instance of Peptide

Method Detail

appendAmino

public void appendAmino(java.lang.String residuename,
                        java.lang.String residuenum,
                        java.util.Map AtomCoords)

Appends an aminoacid of known coordinates to the chain.

Parameters:

residuename - literal name of the residue being appended

residuenum - sequential number (or subnumber like 105A)

AtomCoords - HashMap of [String atomname => Atom coordinates] pairs

estimateCurvatures

public void estimateCurvatures()

calculatePeptideBondPlanesDihedral

public void calculatePeptideBondPlanesDihedral()

calculateDeviations

public void calculateDeviations()

calculateAbsDeviations

public void calculateAbsDeviations()

getResidue

public Aminoacid getResidue(int position)

getId

public char getId()

setId

public void setId(char id)

getResidues

public java.util.List<Aminoacid> getResidues()

length

public int length()

getIndexOf

public int getIndexOf(Aminoacid aa)

setBounds

public void setBounds(float xmin,
                      float xmax,
                      float ymin,
                      float ymax,
                      float zmin,
                      float zmax)

getBoundXmin

public float getBoundXmin()

getBoundXmax

public float getBoundXmax()

getBoundYmin

public float getBoundYmin()

getBoundYmax

public float getBoundYmax()

getBoundZmin

public float getBoundZmin()

getBoundZmax

public float getBoundZmax()

getMinLnRadius

public float getMinLnRadius()

getMaxLnRadius

public float getMaxLnRadius()

getMinAvgDihedralAngle

public float getMinAvgDihedralAngle()

getMaxAvgDihedralAngle

public float getMaxAvgDihedralAngle()

getMinDeviation

public float getMinDeviation()

getMaxDeviation

public float getMaxDeviation()

getMinAbsDeviation

public float getMinAbsDeviation()

getMaxAbsDeviation

public float getMaxAbsDeviation()