Sample scripts

The hello.pdb example was created by the hello.py script, which creates a 78 by 20 by 2 carbon slab by attaching copies of an 8-carbon diamond(111) fragment to each other, then adding hydroxyl groups to create letters.

The lego blocks were created from:

These use groups diamondoid_fragment and cyanide.

Buckytubes can be created via buckytube.py, which uses groups buckball1 and buckytube.

With an argument of 0, buckytube.py produces a buckyball. Arguments greater than 0 will add 30 atoms of tube section for each increment.

The crambin_diamond.pdb was created with the fillshape.py script, with 1crn.pdb (a protein named Crambin) as input. The result is a diamondoid molecule in roughly the same shape as Crambin.

The Kaehler brackets are created by scripts

  1. kaehlera.py
  2. kaehlerb.py
  3. kaehlerc.py
  4. kaehlerd.py
  5. kaehlere.py
which put together the kaehler_a_layer and (in the case of kaehlerb.py) kaehler_si_layer groups.