meshi.geometry
Class Distance

java.lang.Object
  meshi.geometry.Distance

All Implemented Interfaces:

Attributable

Direct Known Subclasses:

BondedDistance, DistanceMirror, FreeDistance, FrozenDistance

public class Distance
extends java.lang.Object
implements Attributable

The distance between two meshi.molecularElements.atoms
. Almost any measurable feature of a molecule is related to distances between pairs of meshi.molecularElements.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

   AtomCore	atom1 This object represent the distance between atom1 and atom2.
   int	atom1Number
   AtomCore	atom2 This object represent the distance between atom1 and atom2.
   protected int	atom2Number
   private AttributesRack	attributes
   double	distance The distance between atom1 & atom2 Not that the public accessability of of this variable improves computational efficiency but opens a wide door for bugs.
   double	dx atom1.x - atom2.x Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
   double	dy atom1.y - atom2.y Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
   double	dz atom1.z - atom2.z Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.
   static double	INFINITE_DISTANCE
   double	invDistance The inverse of the distance between atom1 & atom2.
   AtomType	largeType
   protected DistanceMode	mode
   AtomType	smallType

   Constructor Summary

   Distance(AtomCore atom1, AtomCore atom2, double dx, double dy, double dz, double distance)
   

   Method Summary

   void	addAttribute(MeshiAttribute attribute)
   Atom	atom1() Get atom1.
   Atom	atom2() Get atom2.
   int	atom2Number()
   double	dDistanceDx() The derivative of the distance between atom1 & atom2 by the X coordinate of atom1.
   double	dDistanceDy() The derivative of the distance between atom1 & atom2 by the Y coordinate of atom1.
   double	dDistanceDz() The derivative of the distance between atom1 & atom2 by the Z coordinate of atom1.
   boolean	dead()
   double	distance() Get the distance between atom1 and atom2.
   double	dx()
   double	dy()
   double	dz()
   MeshiAttribute	getAttribute(int key)
   double	invDistance() Get the inverse of the distance between atom1 and atom2.
   DistanceMode	mode()
   void	setMode(DistanceMode mode)
   java.lang.String	toString()
   protected void	update(double rMax2)

   Methods inherited from class java.lang.Object

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

   Field Detail

   INFINITE_DISTANCE

   public static final double INFINITE_DISTANCE

   See Also:

   Constant Field Values

   atom1

   public final AtomCore atom1

   This object represent the distance between atom1 and atom2.

   atom2

   public final AtomCore atom2

   This object represent the distance between atom1 and atom2.

   atom1Number

   public final int atom1Number

   atom2Number

   protected int atom2Number

   mode

   protected DistanceMode mode

   invDistance

   public double invDistance

   The inverse of the distance between atom1 & atom2.
   Not that the public accessability of of this variable improves computational efficiency but opens a wide door for bugs.

   distance

   public double distance

   The distance between atom1 & atom2
   Not that the public accessability of of this variable improves computational efficiency but opens a wide door for bugs.

   dx

   public double dx

   atom1.x - atom2.x Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.

   dy

   public double dy

   atom1.y - atom2.y Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.

   dz

   public double dz

   atom1.z - atom2.z Not that the protected accessability of of this variable improves computational efficiency but opens a wide door for bugs.

   largeType

   public final AtomType largeType

   smallType

   public final AtomType smallType

   attributes

   private AttributesRack attributes

   Constructor Detail

   Distance

   public Distance(AtomCore atom1,
                   AtomCore atom2,
                   double dx,
                   double dy,
                   double dz,
                   double distance)

   Method Detail

   addAttribute

   public final void addAttribute(MeshiAttribute attribute)

   Specified by:

   addAttribute in interface Attributable

   getAttribute

   public final MeshiAttribute getAttribute(int key)

   Specified by:

   getAttribute in interface Attributable

   update

   protected void update(double rMax2)

   distance

   public double distance()

   Get the distance between atom1 and atom2.

   invDistance

   public double invDistance()

   Get the inverse of the distance between atom1 and atom2.

   dDistanceDx

   public double dDistanceDx()

   The derivative of the distance between atom1 & atom2 by the X coordinate of atom1. The derivative by the X coordinate of atom2 is this value multiplied by -1.

   dDistanceDy

   public double dDistanceDy()

   The derivative of the distance between atom1 & atom2 by the Y coordinate of atom1. The derivative by the Y coordinate of atom2 is this value multiplied by -1.

   dDistanceDz

   public double dDistanceDz()

   The derivative of the distance between atom1 & atom2 by the Z coordinate of atom1. The derivative by the Z coordinate of atom2 is this value multiplied by -1.

   atom1

   public Atom atom1()

   Get atom1.

   atom2

   public Atom atom2()

   Get atom2.

   atom2Number

   public int atom2Number()

   dx

   public double dx()

   dy

   public double dy()

   dz

   public double dz()

   toString

   public java.lang.String toString()

   Overrides:

   toString in class java.lang.Object

   mode

   public final DistanceMode mode()

   setMode

   public void setMode(DistanceMode mode)

   dead

   public boolean dead()