[cctbxbb] cctbx geometry modules?

[Ralf W. Grosse-Kunstleve]

Hi Artem,

> Quesiton 1 – is there a web site or some other form of a source for a
> complete cctbx documentation, most importantly with simple working
> examples?

There are a bunch of working examples in scitbx/examples,
cctbx/examples, iotbx/examples, mmtbx/examples. A few of these go with
newsletter articles or tutorials. -- I'm aware that this doesn't qualify
as complete documentation, sorry, that would just take an enormous
amount of time to write.
The examples are meant to be starting points if you have a specific
problem. Then ask questions via email. I'll help as much as I can. Also,
use the many resources available for learning Python; this is essential.

> Question 2 – is there anything inside cctbx that can compute elements of
> protein geometry – such as dihedral angles, planes, etc. (given
> selections of atoms)?

Assuming PDB input works for you,
mmtbx/monomer_library/pdb_interpretation.py is probably the best entry
point. To quickly see what it does, run the command:

  mmtbx.pdb_interpretation your.pdb

This builds the geometry restraint objects as used in phenix.refine (and
some other phenix tools).

If you let me know what you want to do with these restraints, I'll try
to work out specific examples showing how you could proceed. You are
welcome to email me directly.

Ralf