Add python script directories: commands, scripts, misc

[charlestonchas]

[Updated 28 july 2017]

Need to create missing directories in ptools/ptools

commands: scripts invoked from command line using the cli syntax. They must have

• unit/integration tests [Where are we on this?]
• a "help" mode of operation, invoked by ptools somescript -h

scripts: other scripts including those that may aspire to be included in tools but are not yet ready for it. They are invoked using the standard python command python somescript.py args ...

misc: working scripts or compilations of usage examples that are judged potentially useful for users

[benboyer]

list of script that should be in tools for ptools 2.0.0 :
Pyattract.py
reduce.py
heligeom.py
translate.py
extract.py
energy_map.py
cluster.py

top priority for transfer from script to tools:
irmsd
fnat
fpib

[benboyer]

putative list of script going to example:

demi-virus.py
sampling_MC_metrop_prot_heligeom.py
axgen.py (?)
miniMC.py
mini_MC_DNA.py

need confirmation from @chantalprevost

[charlestonchas]

Update: we've now decided to use commands instead of tools. The rest are still under discussion.