meshi.applications.prediction
Class AbitSmarterLoopBuilder

java.lang.Object
  meshi.applications.prediction.AbitSmarterLoopBuilder

public class AbitSmarterLoopBuilder
extends java.lang.Object

Nested Class Summary

private static class	AbitSmarterLoopBuilder.Loop
private static class	AbitSmarterLoopBuilder.LoopComperator

Field Summary

static double	CA_CA_DISTANCE
static double	CA_CA_DISTANCE2
private static AbitSmarterLoopBuilder.Loop	cTerm
static int	MAX_CLASHES
private int	maxNumberOfClashes
private static AbitSmarterLoopBuilder.Loop	nTerm
private static java.util.Random	random

Constructor Summary

AbitSmarterLoopBuilder()

Method Summary

static void	addLoops(Protein protein, double clashDistance, int optimalNumberOfClashes, int nTrys)
private static java.util.ArrayList<AbitSmarterLoopBuilder.Loop>	getLoops(Protein model, double clashDistance, int optimalNumberOfClashes, int nTrys)
private static java.util.ArrayList<Atom>	getNeighbors(Atom atom, Protein protein, double clashDistance)
private static boolean	hasNowhereAtoms(Chain chain)

Methods inherited from class java.lang.Object

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

Field Detail

maxNumberOfClashes

private int maxNumberOfClashes

CA_CA_DISTANCE

public static final double CA_CA_DISTANCE

See Also:

Constant Field Values

CA_CA_DISTANCE2

public static final double CA_CA_DISTANCE2

See Also:

Constant Field Values

MAX_CLASHES

public static final int MAX_CLASHES

See Also:

Constant Field Values

nTerm

private static AbitSmarterLoopBuilder.Loop nTerm

cTerm

private static AbitSmarterLoopBuilder.Loop cTerm

random

private static final java.util.Random random

Constructor Detail

AbitSmarterLoopBuilder

public AbitSmarterLoopBuilder()

Method Detail

addLoops

public static void addLoops(Protein protein,
                            double clashDistance,
                            int optimalNumberOfClashes,
                            int nTrys)

getNeighbors

private static java.util.ArrayList<Atom> getNeighbors(Atom atom,
                                                      Protein protein,
                                                      double clashDistance)

getLoops

private static java.util.ArrayList<AbitSmarterLoopBuilder.Loop> getLoops(Protein model,
                                                                         double clashDistance,
                                                                         int optimalNumberOfClashes,
                                                                         int nTrys)

hasNowhereAtoms

private static boolean hasNowhereAtoms(Chain chain)