Ttclust

Bug fixed in logfile RMSD table.

v4.6.2_old
[OLD release, but same as new v4.6.2 which was published for zenodo DOI
- TTclust GUI is now in 1.0
- Improvments in MAC os compatibility
- Adding time in barplot graph
- Adding transparency in barplot & distance matrix graphs.
- minor bugs fixed.

[version for zenodo DOI]
- TTclust GUI is now in 1.0
- Improvments in MAC os compatibility
- Adding time in barplot graph
- Adding transparency in barplot & distance matrix graphs.
- minor bugs fixed.

A new automatic clustering method was implemented based on
kmeans clustering method and the Elbow method to find the
optimal number of clusters. Use with Caution : to my point of
view, it does not cluster enough. I will improve this automatic
methode laters. To use it, just specify **auto** to the **-ng** argument.

- DNA and RNA selection keywords added!
You can use now theses keywords : dna; rna; backbone_na; base; base_rna; base_dna. See README for precision.

- A new graph is created (distance matrix graph, based on the RMSD matrix)

Improve DNA/RNA trajectory compatibility
Sometimes, with some trajectory (eg. traj with RNA/DNA) if you want to clusterize the DNA/RNA and align to the protein backbone, it fails because MDTRAJ didn't recognize DNA/RNA backbone.

Now the alignement is made before the extraction of the trajectory.If you don't want protein alignement, use "-sr none"

README.md :
- Replace USAGE examples with examples file from example folder
- Replace examples graphics output.

ttclust.py:
- Now if you specify the `-st` argument, the subtrajectory will be saved.
- Argcomplete will be loaded only on linux (useless on MAC & Windows)
- Cleaning of ArgParse() function