meshi.util
Class GDTcalculator

java.lang.Object
  meshi.util.GDTcalculator

public class GDTcalculator
extends java.lang.Object

Field Summary

static double[][]	C1
static double[][]	C2
static int	len
static double	maximal_distance
static int	num_of_loops
static HubbardPosition[]	Popo
static int	SUB

Constructor Summary

GDTcalculator()

Method Summary

static void	build_best_distance(double[] best_distance, HubbardPosition[] Popo)
static double	fracBelowRMS(double[] best_distance, double rms, int referLength)
static double[]	gdt(AtomList reference, AtomList protein1, int refLength)
static double[]	gdt(ResidueAlignment residueAlignment, int refLength)
static double[]	gdt(ResidueAlignment residueAlignment, int refLength, MeshiWriter output)
static void	init(AtomList al1, AtomList al2)
static void	initialize(HubbardPosition[] Popo)
static void	loop_over_Popo(HubbardPosition[] Popo)

Methods inherited from class java.lang.Object

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

Field Detail

C1

public static double[][] C1

C2

public static double[][] C2

Popo

public static HubbardPosition[] Popo

len

public static int len

SUB

public static final int SUB

See Also:

Constant Field Values

maximal_distance

public static final double maximal_distance

See Also:

Constant Field Values

num_of_loops

public static final int num_of_loops

See Also:

Constant Field Values

Constructor Detail

GDTcalculator

public GDTcalculator()

Method Detail

gdt

public static double[] gdt(ResidueAlignment residueAlignment,
                           int refLength)

gdt

public static double[] gdt(ResidueAlignment residueAlignment,
                           int refLength,
                           MeshiWriter output)

gdt

public static double[] gdt(AtomList reference,
                           AtomList protein1,
                           int refLength)

initialize

public static void initialize(HubbardPosition[] Popo)

loop_over_Popo

public static void loop_over_Popo(HubbardPosition[] Popo)

build_best_distance

public static void build_best_distance(double[] best_distance,
                                       HubbardPosition[] Popo)

fracBelowRMS

public static double fracBelowRMS(double[] best_distance,
                                  double rms,
                                  int referLength)

init

public static void init(AtomList al1,
                        AtomList al2)