meshi.energy.hydrogenBondsPairs
Class PairOfHydrogenBondsElements

java.lang.Object
  meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements

public class PairOfHydrogenBondsElements
extends java.lang.Object

Field Summary

private AtomList	atoms
private boolean	betaPair
protected Atom	hAtom1
protected Atom	hAtom2
private static int	HB_PAIR_CAPACITY
private boolean	helixPair
protected int	hhSeqDistance
protected Distance	HOelement1
protected Distance	HOelement2
protected int	hoSeqDistance
protected boolean	lookAtThisPair
int	MAX_INER_SEQ_DISTANCE
int	MAX_SEQ_PAIRS_DISTANCE
protected Atom	oAtom1
protected Atom	oAtom2
protected int	ohSeqDistance
private boolean	oneBetta
private boolean	oneHelix
protected int	ooSeqDistance
private double	pairFactor
private double	pairValue
protected int	seqDistance1
protected int	seqDistance2

Constructor Summary

PairOfHydrogenBondsElements()

PairOfHydrogenBondsElements(Distance _HOelement1, Distance _HOelement2)

PairOfHydrogenBondsElements(PairOfHydrogenBondsElements pair)

Method Summary

AtomList	atoms()
double	getPairValue()
Atom	hAtom(Distance atomPair)
boolean	helixPair(Distance atomPair)
boolean	helixSheetPair(Distance atomPair)
int	hhSeqDistance()
Distance	HOelement1()
Distance	HOelement2()
int	hoSeqDistance()
boolean	isBetaPair()
boolean	isHelixPair()
boolean	isOneBetta()
boolean	isOneHelix()
Atom	oAtom(Distance atomPair)
int	ohSeqDistance()
int	ooSeqDistance()
int	seqDistance1()
int	seqDistance2()
void	set(Distance _HOelement1, Distance _HOelement2)
void	setPairFactor(double pairFactor)
void	setPairValue(double pairValue)
boolean	sheetPair(Distance atomPair)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

HOelement1

protected Distance HOelement1

HOelement2

protected Distance HOelement2

seqDistance1

protected int seqDistance1

seqDistance2

protected int seqDistance2

ooSeqDistance

protected int ooSeqDistance

hhSeqDistance

protected int hhSeqDistance

ohSeqDistance

protected int ohSeqDistance

hoSeqDistance

protected int hoSeqDistance

MAX_INER_SEQ_DISTANCE

public final int MAX_INER_SEQ_DISTANCE

See Also:

Constant Field Values

MAX_SEQ_PAIRS_DISTANCE

public final int MAX_SEQ_PAIRS_DISTANCE

See Also:

Constant Field Values

lookAtThisPair

protected boolean lookAtThisPair

atoms

private AtomList atoms

HB_PAIR_CAPACITY

private static final int HB_PAIR_CAPACITY

See Also:

Constant Field Values

pairValue

private double pairValue

pairFactor

private double pairFactor

oAtom1

protected Atom oAtom1

hAtom1

protected Atom hAtom1

oAtom2

protected Atom oAtom2

hAtom2

protected Atom hAtom2

helixPair

private boolean helixPair

betaPair

private boolean betaPair

oneHelix

private boolean oneHelix

oneBetta

private boolean oneBetta

Constructor Detail

PairOfHydrogenBondsElements

PairOfHydrogenBondsElements()

PairOfHydrogenBondsElements

PairOfHydrogenBondsElements(PairOfHydrogenBondsElements pair)

PairOfHydrogenBondsElements

PairOfHydrogenBondsElements(Distance _HOelement1,
                            Distance _HOelement2)

Method Detail

getPairValue

public double getPairValue()

setPairValue

public void setPairValue(double pairValue)

setPairFactor

public void setPairFactor(double pairFactor)

seqDistance1

public final int seqDistance1()

seqDistance2

public final int seqDistance2()

hoSeqDistance

public final int hoSeqDistance()

hhSeqDistance

public final int hhSeqDistance()

ooSeqDistance

public final int ooSeqDistance()

ohSeqDistance

public final int ohSeqDistance()

HOelement1

public final Distance HOelement1()

HOelement2

public final Distance HOelement2()

atoms

public final AtomList atoms()

isHelixPair

public boolean isHelixPair()

isBetaPair

public boolean isBetaPair()

isOneHelix

public boolean isOneHelix()

isOneBetta

public boolean isOneBetta()

set

public void set(Distance _HOelement1,
                Distance _HOelement2)

hAtom

public Atom hAtom(Distance atomPair)

oAtom

public Atom oAtom(Distance atomPair)

helixPair

public boolean helixPair(Distance atomPair)

sheetPair

public boolean sheetPair(Distance atomPair)

helixSheetPair

public boolean helixSheetPair(Distance atomPair)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object