meshi.applications.prediction.beautify
Class BeautifyAttribute

java.lang.Object
  meshi.applications.prediction.beautify.BeautifyAttribute

All Implemented Interfaces:

MeshiAttribute

public class BeautifyAttribute
extends java.lang.Object
implements MeshiAttribute

Field Summary

private boolean	loop
private boolean	problematic
private java.lang.String	problematicComment
private Residue	problematicNeighbor
private boolean	visible

Fields inherited from interface meshi.util.MeshiAttribute

BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE

Constructor Summary

BeautifyAttribute()

Method Summary

static void	addTo(Protein protein)
static void	copy(ResidueAlignment residueAlignment)
static void	copy(Residue source, Residue target)
static BeautifyAttribute	getBeautifyAttribute(Residue residue)
boolean	hasProblematicNeighbor()
static boolean	hasProblematicNeighbor(Residue residue)
boolean	isLoop()
static boolean	isLoop(Residue residue)
boolean	isProblematic()
static boolean	isProblematic(Residue residue)
static boolean	isProblematicOrHasProblematicNeighbor(Residue residue)
static boolean	isProblematicOrLoop(Residue residue)
static boolean	isVisible(Residue residue)
int	key()
java.lang.String	problematicComment()
static java.lang.String	problematicComment(Residue residue)
Residue	problematicNeighbor()
static Residue	problematicNeighbor(Residue residue)
void	setLoop(boolean flag)
static void	setLoop(Residue residue, boolean flag)
void	setProblematic(boolean flag, java.lang.String comment)
static void	setProblematic(Residue residue, boolean flag, java.lang.String comment)
void	setProblematicNeighbor(Residue neighbor)
static void	setProblematicNeighbor(Residue residue, Residue neighbor)
static void	setVisible(Residue residue)
java.lang.String	toSrtring()

Methods inherited from class java.lang.Object

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

Field Detail

loop

private boolean loop

problematic

private boolean problematic

visible

private boolean visible

problematicComment

private java.lang.String problematicComment

problematicNeighbor

private Residue problematicNeighbor

Constructor Detail

BeautifyAttribute

public BeautifyAttribute()

Method Detail

setLoop

public void setLoop(boolean flag)

isLoop

public boolean isLoop()

setLoop

public static void setLoop(Residue residue,
                           boolean flag)

isLoop

public static boolean isLoop(Residue residue)

setProblematic

public void setProblematic(boolean flag,
                           java.lang.String comment)

isProblematic

public boolean isProblematic()

problematicComment

public java.lang.String problematicComment()

setProblematic

public static void setProblematic(Residue residue,
                                  boolean flag,
                                  java.lang.String comment)

isProblematic

public static boolean isProblematic(Residue residue)

problematicComment

public static java.lang.String problematicComment(Residue residue)

isVisible

public static boolean isVisible(Residue residue)

setVisible

public static void setVisible(Residue residue)

setProblematicNeighbor

public void setProblematicNeighbor(Residue neighbor)

hasProblematicNeighbor

public boolean hasProblematicNeighbor()

problematicNeighbor

public Residue problematicNeighbor()

setProblematicNeighbor

public static void setProblematicNeighbor(Residue residue,
                                          Residue neighbor)

hasProblematicNeighbor

public static boolean hasProblematicNeighbor(Residue residue)

problematicNeighbor

public static Residue problematicNeighbor(Residue residue)

isProblematicOrHasProblematicNeighbor

public static boolean isProblematicOrHasProblematicNeighbor(Residue residue)

isProblematicOrLoop

public static boolean isProblematicOrLoop(Residue residue)

copy

public static void copy(Residue source,
                        Residue target)

copy

public static void copy(ResidueAlignment residueAlignment)

addTo

public static void addTo(Protein protein)

getBeautifyAttribute

public static BeautifyAttribute getBeautifyAttribute(Residue residue)

toSrtring

public java.lang.String toSrtring()

key

public int key()

Specified by:

key in interface MeshiAttribute