meshi.symmetryComplex.utils
Class LoopUtils

java.lang.Object
  meshi.symmetryComplex.utils.LoopUtils

public class LoopUtils
extends java.lang.Object

Created by IntelliJ IDEA. User: TM Date: Mar 3, 2008 Time: 10:36:02 AM To change this template use File | Settings | File Templates.

Nested Class Summary

private static class	LoopUtils.Line
private static class	LoopUtils.Point

Constructor Summary

LoopUtils()

Method Summary

static AtomList	atomsCAOfLoopNumber(AtomList atoms, int i)
static AtomList	atomsCAOfLoops(AtomList atoms)
static AtomList	atomsOfLoopNumber(AtomList atoms, int i)
static AtomList	atomsOfLoops(AtomList atoms)
static double	getAngle(Coordinates coord1, Coordinates coord2)
static double	getAverageAngleForLoop(AtomList allAtoms, int loopNumber)
static double[]	getAverageAngleForLoopParts(AtomList allAtoms, int loopNumber, int numOfParts)
static double	getAverageDistanceBetweenCysCBconnexin(java.lang.String atomType, AtomList atoms) Returns the average distance between C-Beta atoms of cysteines which are thought to be bonded by disulfide links.
static double	getDistancesBetweenCysCBofConnexin(java.lang.String atomType, AtomList atoms) Returns distances between C-Beta atoms of some special cysteines pattern for connexin
static double	getDistancesBetweenCysCBofConnexons(java.lang.String atomType, AtomList atoms1, AtomList atoms2, AtomList atoms3, AtomList atoms4) Returns distances between C-Beta atoms of some special cysteines pattern
private static boolean	ifCrossing(Atom atom1, Atom atom2, Atom atom3, Atom atom4, boolean full_checking)
static int	numberOfChainCrosses(AtomList allAtoms, java.lang.String chain1, java.lang.String chain2)
static int	numberOfTwists(AtomList allAtoms, int loopNumber)
private static int	numOfClosestPairOfAtoms(Atom atom1, Atom atom2, Atom[] atomArray, int step, boolean sameArray)
static LoopUtils.Point	pointOfCrossing(double c1x, double c1y, double c2x, double c2y, double c3x, double c3y, double c4x, double c4y)
static ResidueList	residuesOfLoopNumber(ResidueList residues, int i)
static ResidueList	residuesOfLoops(ResidueList residues)

Methods inherited from class java.lang.Object

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

Constructor Detail

LoopUtils

public LoopUtils()

Method Detail

residuesOfLoops

public static ResidueList residuesOfLoops(ResidueList residues)

residuesOfLoopNumber

public static ResidueList residuesOfLoopNumber(ResidueList residues,
                                               int i)

atomsOfLoops

public static AtomList atomsOfLoops(AtomList atoms)

atomsOfLoopNumber

public static AtomList atomsOfLoopNumber(AtomList atoms,
                                         int i)

atomsCAOfLoops

public static AtomList atomsCAOfLoops(AtomList atoms)

atomsCAOfLoopNumber

public static AtomList atomsCAOfLoopNumber(AtomList atoms,
                                           int i)

pointOfCrossing

public static LoopUtils.Point pointOfCrossing(double c1x,
                                              double c1y,
                                              double c2x,
                                              double c2y,
                                              double c3x,
                                              double c3y,
                                              double c4x,
                                              double c4y)

numberOfTwists

public static int numberOfTwists(AtomList allAtoms,
                                 int loopNumber)

ifCrossing

private static boolean ifCrossing(Atom atom1,
                                  Atom atom2,
                                  Atom atom3,
                                  Atom atom4,
                                  boolean full_checking)

numberOfChainCrosses

public static int numberOfChainCrosses(AtomList allAtoms,
                                       java.lang.String chain1,
                                       java.lang.String chain2)

numOfClosestPairOfAtoms

private static int numOfClosestPairOfAtoms(Atom atom1,
                                           Atom atom2,
                                           Atom[] atomArray,
                                           int step,
                                           boolean sameArray)

getAverageAngleForLoop

public static double getAverageAngleForLoop(AtomList allAtoms,
                                            int loopNumber)

getAngle

public static double getAngle(Coordinates coord1,
                              Coordinates coord2)

getAverageAngleForLoopParts

public static double[] getAverageAngleForLoopParts(AtomList allAtoms,
                                                   int loopNumber,
                                                   int numOfParts)

getAverageDistanceBetweenCysCBconnexin

public static double getAverageDistanceBetweenCysCBconnexin(java.lang.String atomType,
                                                            AtomList atoms)

Returns the average distance between C-Beta atoms of cysteines which are thought to be bonded by disulfide links.

getDistancesBetweenCysCBofConnexin

public static double getDistancesBetweenCysCBofConnexin(java.lang.String atomType,
                                                        AtomList atoms)

Returns distances between C-Beta atoms of some special cysteines pattern for connexin

getDistancesBetweenCysCBofConnexons

public static double getDistancesBetweenCysCBofConnexons(java.lang.String atomType,
                                                         AtomList atoms1,
                                                         AtomList atoms2,
                                                         AtomList atoms3,
                                                         AtomList atoms4)

Returns distances between C-Beta atoms of some special cysteines pattern