TransitionCountModel properties

[hassanuiuc]

Hello!

I had some confusion in understanding the following properties of the Transition Count Model object:

property selected_state_fraction: The fraction of states represented in this count model.
property state_symbols_with_blank: Symbols for states that are represented in this count model plus a state -1 for states which are not represented in this count model.

I assumed that represented here meant visited. But it seems it is not the case? Can you clarify what it means?
For my case the dtraj data only has 23 unique states, whereas the original clustering object used 100 states. I was expecting selected_state_fraction to give 23/100, but it still gives me 1.0.
I found however that the visited_set property gives 23.

Best,
Hassan

[clonker]

Hi Hassan,
this means that from your 100 states, only 23 have counts (check state_histogram_full). The fraction reflects how many of these states you end up using; typically you would only use states which are connected via a transition. Otherwise quantities like stationary distribution are not meaningful. Once you have made that subselection (see, e.g., submodel_largest), the selected_state_fraction should change. :)

Hope this helps and best,
Moritz