naccess does not like dots in path names. Some temporary directories
contain dots, which causes naccess to fail. We now provide a scratch_dir
option, which allows to specify a temporary directory.

Also, allow to set the maximal number of atoms supported by naccess.

Fixes BZDNG-385

installation docu: mentioning fortran as requirement for TMTOOLS; fixing typos; fixing link to compoundlib docu

forgotten, before)

Fixes BZDNG-391

The ClashScore functions were not properly exported.
This is BZDNG-387

Fixes BZDNG-386

The examples don't really make a lof of sense without
shaders enabled

On many systems, there are several parallel python
installations. There is usually a "python" symlink that
points to the currently active python version. That might
not be the one we need. Instead of picking up that one, we
now search for python$VERSION and as a last resort use
python.

Also, make sure found python lib/binaries match. This
fixes BZDNG-388.

On a special note: I have removed the special code taking
care of CASP models from the lDDT executable. This code
should not be part of lDDT but rather be part of a
preprocessing script for CASP models.