kinalysis

 python inputs.py
 python make_summary_pdf.py
 --or--
 python inputs.py
 python make_summary_pdf.py --project 11401

If your trajectories are in trajectories/*.h5, you're golden, but if you want you can change the default path in line 52 of make_summary_pdf.py.

If you're analyzing another protein besides Src kinas and not using the --project flag, change protein = 'SRC' (line 51 of make_summary_pdf.py) to your protein of choice, and make sure all the appropriate inputs are in inputs.py.

If you want to analyze a whole project in the choderalab munged3 FAH projects folders, you can just use the --project flag as above using the project name, and make sure the appropriate inputs are in inputs.py.

Results, including png's, npy's, and the final pdf summary will show up in the results folder sorted by the protein name by default or the project number if you used the --project flag.