Note that 'cluster' is not optional

[sonyahanson]

Useful to note that ensembler cluster is not optional, even if you know you want to use all your templates.

[jchodera]

I think you noted that all ensembler steps are obligate? This might be good to document in the manual, and we may want to add pass-through options that allow us to essentially just carry things through to the next stage.

[rafwiewiora]

Got caught by this!

It seems the issue is ensembler refine_implicit only will refine those models for which unique_by_clustering file exists?

I will update docs ASAP, but also would like to suggest securing this with some exceptions, currently what happened:

• didn't do ensembler cluster
• ensembler refine_improper seems to be working ok, before you realize that it should take much longer and print out a a progress message for every model
• ensembler solvate then doesn't cause an exception, but says No nwaters (...) - and you're not sure what's happening

How about adding something to every command that checks that previous command was called and has completed successfully - I guess by checking for presence for files that were produced by the previous command? So in this case the exception would be thrown when at ensembler refine_implicit no unique_by_clustering files are found. What do you think? @danielparton