meshi.symmetryComplex.utils
Class GJUtils

java.lang.Object
  meshi.symmetryComplex.utils.GJUtils

public class GJUtils
extends java.lang.Object

This class contains utils for work on gap junctions. So far all of them are static -- use static import.

Field Summary

static HydrogenBondsCreator	hBondsCreator Residue number ranges of the gap junction's parts.
static double	RELATIVE_ORIENTATION

Constructor Summary

GJUtils()

Method Summary

static Transformation[]	getPartialTransformations(double relativeOrientation, int numberOfChains, boolean[] whichTrans)
static Transformation[]	getTransformations(double relativeOrientation, int numberOfChains)
static void	positionAndFreezeCas(Protein partialCas, Protein monomer) Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh.
static void	positionTMCas(Protein tmCasProtein, Protein monomer) Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh.
static double	quickDistanceFrom(Coordinates fromCoors, Coordinates toCoors)
static double	quickDistanceFrom(double x1, double y1, double z1, double x2, double y2, double z2)
static java.lang.String	whichChainsInZone(ChainList chainList, double zone)
static boolean[]	whichChainsInZone(double zone, AtomList atoms) Calculates the average distance between atoms from loops E1 and E2.

Methods inherited from class java.lang.Object

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

Field Detail

RELATIVE_ORIENTATION

public static final double RELATIVE_ORIENTATION

See Also:

Constant Field Values

hBondsCreator

public static HydrogenBondsCreator hBondsCreator

Residue number ranges of the gap junction's parts.

Constructor Detail

GJUtils

public GJUtils()

Method Detail

positionAndFreezeCas

public static void positionAndFreezeCas(Protein partialCas,
                                        Protein monomer)

Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh. This function takes a protein built from those Cas and a whole monomer, and positions and freezes the transmembranal Cas according to 1txh.

getTransformations

public static Transformation[] getTransformations(double relativeOrientation,
                                                  int numberOfChains)

positionTMCas

public static void positionTMCas(Protein tmCasProtein,
                                 Protein monomer)

Coordinates of transmembranal C-Alphas from Sar-el's work were deposited in the PDB under the entry 1txh. This function takes a protein built from those Cas and a whole monomer, and positions the transmembranal Cas according to 1txh.

whichChainsInZone

public static boolean[] whichChainsInZone(double zone,
                                          AtomList atoms)

Calculates the average distance between atoms from loops E1 and E2. If the given atom list contains more than one chain, only atoms from the first chain will be taken into account.

whichChainsInZone

public static java.lang.String whichChainsInZone(ChainList chainList,
                                                 double zone)

getPartialTransformations

public static Transformation[] getPartialTransformations(double relativeOrientation,
                                                         int numberOfChains,
                                                         boolean[] whichTrans)

quickDistanceFrom

public static double quickDistanceFrom(double x1,
                                       double y1,
                                       double z1,
                                       double x2,
                                       double y2,
                                       double z2)

quickDistanceFrom

public static double quickDistanceFrom(Coordinates fromCoors,
                                       Coordinates toCoors)