meshi.geometry
Class FreeDistance

java.lang.Object
  meshi.geometry.Distance
      meshi.geometry.FreeDistance

All Implemented Interfaces:

Attributable

public class FreeDistance
extends Distance

The distance between two Atoms
. Almost any measurable feature of a molecule is related to distances between pairs of Atoms. Thus, The calculation of distances (and their inverse and derivatives) are typically a computational bottleneck in computational structural biology applications. In all applications that we are aware of (Please, enlighten us if you know better) distance calculation is done as part of the procedures that use it (say, as part of the van-der-Waals energy calculation). As a result the distance between two atoms may be calculated more then once. For example the distance between two atoms may be calculated both during angle and torsion angle energies calculations. In Meshi We tried to consentrate all distance related issues in a few classes: this one, its subclasses and the closely connected class DistanceMatrix.

Possible pitfalls

1. The object variables dx, dy, dz, distance, distance2, invDistance, dDistanceDx, dDistanceDy and dDistanceDz should have been private and accessed through "get methods". Energy functions though, use the values of these variables intensively and a considerable computational gain is achieved granting them public accessability (protected for dx, dy and dz) and removing the function call overhead. Thus, changing the values of these variables by other classes is possible (from the compiler point of view) but not very much recommended.
2. The distance object "is not aware" of changes in the atoms coordinates. The values stored in this object are correct only after the update method is explicitly called.

   Field Summary

   private static double

   d2

   Fields inherited from class meshi.geometry.Distance

   atom1, atom1Number, atom2, atom2Number, distance, dx, dy, dz, INFINITE_DISTANCE, invDistance, largeType, mode, smallType

   Constructor Summary

   FreeDistance(Atom atom1, Atom atom2)
   

   Method Summary

   static double	getDistance(Atom atom1, Atom atom2)
   static double	getDx(Atom atom1, Atom atom2)
   static double	getDy(Atom atom1, Atom atom2)
   static double	getDz(Atom atom1, Atom atom2)
   void	update()

   Methods inherited from class meshi.geometry.Distance

   addAttribute, atom1, atom2, atom2Number, dDistanceDx, dDistanceDy, dDistanceDz, dead, distance, dx, dy, dz, getAttribute, invDistance, mode, setMode, toString, update

   Methods inherited from class java.lang.Object

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

   Field Detail

   d2

   private static double d2

   Constructor Detail

   FreeDistance

   public FreeDistance(Atom atom1,
                       Atom atom2)

   Method Detail

   getDx

   public static double getDx(Atom atom1,
                              Atom atom2)

   getDy

   public static double getDy(Atom atom1,
                              Atom atom2)

   getDz

   public static double getDz(Atom atom1,
                              Atom atom2)

   getDistance

   public static double getDistance(Atom atom1,
                                    Atom atom2)

   update

   public void update()