adding ability to create new trajectory based on own frame index file

[gwirn]

This adds the ability to create a new trajectory based on provided frame indices.
It can be useful if a certain property per frame was calculated and frames were clustered based on that property.
Now one only needs to supply the frame indices that index the representative frame(s) of each cluster in an index.txt file and a new trajectory will be saved and everything is formatted like with any other clustering method or by striding.

Additionally, it adds a boolean flag whether to calculate the distance matrix needed for agglomerative clustering or not (so the calculation can be omitted for striding, clustering with PCA or when providing your own indices)

[degiacom]

Useful update, approved