Drawing 3d molecule on a 2d screen has some difficulties. For example, a point on the screen will correspond to a line or ray in 3d space:
So, some preliminary assumptions have to be made.
1) In the case of drawing from scratch the first atom is placed at the center of the coordinate system.
2) If a main window already contains atom(s) the procedure for adding a new atom/molecule should be following:
Send all questions, suggestions and comments to Vlad (email@example.com)
Dr. Vladislav Vasilyev
National Computational Infrastructure (NCI)
The Australian National University,
Canberra, ACT, 0200, Australia