ffe.lang
Class XYZUtils

java.lang.Object
  ffe.lang.XYZUtils

public final class XYZUtils

extends java.lang.Object

The XYZUtils class provides methods to locate functional units of a system.

Field Summary

static int[]	AAPATTERN
static int	AMINOACID
static java.util.ArrayList	arraylistpool
(package private) static int	count
static int[]	NAPATTERN
static int	NUCLEICACID

Constructor Summary

XYZUtils()

Method Summary

static void	addArraytoPool(java.util.ArrayList a)
static void	addCap(Atom end, Atom seed, Residue r)
static void	addPhosphate(Atom p, Residue r)
static boolean	bondsX(Atom a, int x)
static int	bondsXnum(Atom a, int x)
static int	countCO(Atom adjacent)
static boolean	divideBackbone(java.util.ArrayList backbone, Polymer c)
static Atom	findAlphaCarbon(Atom adjacent)
static Atom	findC5(Atom adjacent)
static Atom	findCarbonyl(Atom adjacent)
static Atom	findCCO(Atom adjacent)
static Atom	findCO(Atom adjacent)
static Atom	findOtherOxygen(Atom p, Atom o)
static java.util.ArrayList	findPolymer(java.util.ArrayList atoms, Atom currentAtom, java.util.ArrayList path)
static Atom	findSeed(Atom end, Atom other)
static Atom	findX(Atom a, int x)
static java.util.ArrayList	getArrayfromPool()
static void	groupXYZ(FSystem m, java.util.ArrayList atoms, MainPanel main)
static boolean	isWater(Atom a)
static java.lang.String	PolymerLookup(int i)

Methods inherited from class java.lang.Object

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

Field Detail

arraylistpool

public static java.util.ArrayList arraylistpool

count

static int count

AMINOACID

public static final int AMINOACID

See Also:

Constant Field Values

NUCLEICACID

public static final int NUCLEICACID

See Also:

Constant Field Values

AAPATTERN

public static final int[] AAPATTERN

NAPATTERN

public static final int[] NAPATTERN

Constructor Detail

XYZUtils

public XYZUtils()

Method Detail

addArraytoPool

public static void addArraytoPool(java.util.ArrayList a)

getArrayfromPool

public static java.util.ArrayList getArrayfromPool()

groupXYZ

public static void groupXYZ(FSystem m,
                            java.util.ArrayList atoms,
                            MainPanel main)

findPolymer

public static java.util.ArrayList findPolymer(java.util.ArrayList atoms,
                                              Atom currentAtom,
                                              java.util.ArrayList path)

divideBackbone

public static boolean divideBackbone(java.util.ArrayList backbone,
                                     Polymer c)

findOtherOxygen

public static Atom findOtherOxygen(Atom p,
                                   Atom o)

countCO

public static int countCO(Atom adjacent)

findCO

public static Atom findCO(Atom adjacent)

findCCO

public static Atom findCCO(Atom adjacent)

findC5

public static Atom findC5(Atom adjacent)

findCarbonyl

public static Atom findCarbonyl(Atom adjacent)

findAlphaCarbon

public static Atom findAlphaCarbon(Atom adjacent)

findX

public static Atom findX(Atom a,
                         int x)

bondsX

public static boolean bondsX(Atom a,
                             int x)

addPhosphate

public static void addPhosphate(Atom p,
                                Residue r)

findSeed

public static Atom findSeed(Atom end,
                            Atom other)

addCap

public static void addCap(Atom end,
                          Atom seed,
                          Residue r)

bondsXnum

public static int bondsXnum(Atom a,
                            int x)

isWater

public static boolean isWater(Atom a)

PolymerLookup

public static java.lang.String PolymerLookup(int i)