Figure 2
From: Rule-based spatial modeling with diffusing, geometrically constrained molecules
Exemplary SRSim geometry: On the left, a molecule m
i
with two components c
ij
and c
ik
, given in polar coordinates, is depicted. The angle θ can be imagined as descending from an imaginary polar component 
, while φ rotates the component in the equatorial plane from the imaginary zero-meridian φ0. The lengths from the center are given with d
ij
and d
ik
. The angle α that is not specified but calculated from the polar coordinates is the effective angle between the components j and k. Three molecules and two bonds are shown on the right side. Because the middle molecule is connected with two other molecules (thick red arrows), the angle α would be realized under ideal conditions.