Description of applied algorithms.

The code is based on the Graph.java applet distributed in JDK1.1 by java.sun.com .

Relaxation.

Relaxation is a standard numerical procedure which finds a local minimum of
a predefined energy landscape by iteration.
Two measurements contribute to the relaxation process.

a) the distance of interacting pairs, this contributes when the value is smaller or larger than a predefined value.
b) the distances of all displayed proteins to each other, these contribute if the distances are lower than a predefined value.
 

Finding neighbors.

A) Clicking a protein will define the selected protein to have the neighboring level of zero (n=0).
B) The level is inceremented by 1.
C) Then all other proteins will be scanned, and if they interact with the protein(s) of the previous level (n-1), they will be assigned to the level (n), if they do not have already a lower level.

B and C will be repeated until the the chosen level of neighboring distance is reached.