improves overall runtime of analysis pass

[richardjgowers]

• makes the step through the trajectory for analysis by default gather 500 frames of data
• for standard settings openmm rfe runs, this is a step of 10
• improve performance by loading PDB topology once, not 11 (=nlambda) times
• add progress bar to cli call for sanity

[richardjgowers]

@mikemhenry this reduces the total runtime for the dataset you put up from ~40 minutes to 45 seconds for me. If you can check that this patch gives a similar perf bump to acceptable levels then we should be good to go.

The stdout produced is 27MB, would you still want this bouncing off a file instead or is piping that much data OK?

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[mikemhenry]

I think that is fine, but with tdqm, will the output be something that we can easily read in with a logging tool? or is tdqm smart and doesn't output if its not going to stdout

[mikemhenry]

I will test it on the cluster to see how long it takes

[mikemhenry]

Very fast now and it looks like the TDQM bar doesn't end up in the output so calling the command like this $ openfe_analysis . | tee output.log lets you view the progress bar and save the output.

$ head -c 500 output.log 
{"protein_RMSD": [[0.0, 1.2808896885129466, 1.3386231474354495, 1.3704502925096826, 1.340629459943356, 1.2933647321006816, 1.0575695876290574, 1.1609251163130452, 1.1765957326639387, 1.325367601887441, 1.284754975758849, 1.2320423906041964, 1.217751234670653, 1.4551268444519825, 1.3134513541802377, 1.1945956838969465, 1.2136881911195208, 1.0910438893996461, 1.4721771533412353, 1.2923550390274625, 1.1123489761886183, 1.2387564476170243, 1.0531361145744993, 1.2627956618008394, 1.487708349464851, 1

[richardjgowers]

Tqdm goes to stderr, probably for this reason?