Algorithms

Drawing molecules requires a transformation between molecular coordinates (usually, but not always, in Angstrom units) and the screen. Because many molecules are chiral it is essential that the handedness of the system (almost always right-handed) is preserved. In molecular graphics the origin (0, 0) is usually at the lower left, while in many computer systems the origin is at top left. If the z-coordinate is out of the screen (towards the viewer) the molecule will be referred to right-handed axes, while the screen display will be left-handed. Molecular transformations normally require: Conformational changes (e.g. rotations about bonds) require rotation of one part of the molecule relative to another. The programmer must decide whether a transformation on the screen reflects a change of view or a change in the molecule or its reference frame.
 * scaling of the display (but not the molecule).
 * translations of the molecule and objects on the screen.
 * rotations about points and lines.